Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 13 of 182
Found at i:5215254 original size:14 final size:14
Alignment explanation
Indices: 5215235--5215263 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5215225 CTATTTTCCC
5215235 TTTTTTTTT-CTTT
1 TTTTTTTTTACTTT
5215248 TTTTTTTTTACTTT
1 TTTTTTTTTACTTT
5215262 TT
1 TT
5215264 CATATACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.03, C:0.07, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTTTTTTACTTT
Found at i:5223382 original size:6 final size:6
Alignment explanation
Indices: 5223373--5223397 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5223363 CAATCTCAAT
5223373 AAAGAG AAAGAG AAAGAG AAAGAG A
1 AAAGAG AAAGAG AAAGAG AAAGAG A
5223398 GGCCGGCCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
AAAGAG
Found at i:5232224 original size:25 final size:25
Alignment explanation
Indices: 5232190--5232261 Score: 144
Period size: 25 Copynumber: 2.9 Consensus size: 25
5232180 ATAGGAAAAA
5232190 AGTTAGAAGATGTTGAACTTATCCT
1 AGTTAGAAGATGTTGAACTTATCCT
5232215 AGTTAGAAGATGTTGAACTTATCCT
1 AGTTAGAAGATGTTGAACTTATCCT
5232240 AGTTAGAAGATGTTGAACTTAT
1 AGTTAGAAGATGTTGAACTTAT
5232262 TCGTGTAGGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (25 bp):
AGTTAGAAGATGTTGAACTTATCCT
Found at i:5234709 original size:23 final size:25
Alignment explanation
Indices: 5234655--5234709 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
5234645 TTGTTAAATT
*
5234655 TATATTTATAGTAATAATAAATAAAT
1 TATATTTATAGT-ATAATAAATAAAG
* *
5234681 TGTATTTATA-T-TAATCAATAAAG
1 TATATTTATAGTATAATAAATAAAG
5234704 TATATT
1 TATATT
5234710 AAATTTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 15 0.60
25 1 0.04
26 9 0.36
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.45
Consensus pattern (25 bp):
TATATTTATAGTATAATAAATAAAG
Found at i:5235131 original size:20 final size:20
Alignment explanation
Indices: 5235106--5235155 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
5235096 AGTTCGTCCG
* * *
5235106 AAAAATAAAAGAGTTTGAAT
1 AAAAATAAAAGAGATGGAAA
5235126 AAAAATAATAAGAGATGGAAA
1 AAAAATAA-AAGAGATGGAAA
5235147 AAAAATAAA
1 AAAAATAAA
5235156 GAATGAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.18
Consensus pattern (20 bp):
AAAAATAAAAGAGATGGAAA
Found at i:5246416 original size:16 final size:17
Alignment explanation
Indices: 5246375--5246416 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
5246365 TTTACAATCC
5246375 CACCTTTTGCTTTATTTT
1 CACCTTTT-CTTTATTTT
* *
5246393 C-CATTTTTTTTATTTT
1 CACCTTTTCTTTATTTT
5246409 CACCTTTT
1 CACCTTTT
5246417 AAGAAAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
16 9 0.45
17 10 0.50
18 1 0.05
ACGTcount: A:0.12, C:0.21, G:0.02, T:0.64
Consensus pattern (17 bp):
CACCTTTTCTTTATTTT
Found at i:5247663 original size:32 final size:32
Alignment explanation
Indices: 5247593--5247663 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
5247583 TATAAAAATT
* *
5247593 TAATTTCATCATTTGAATAACTTATATTTTTA
1 TAATTTTACCATTTGAATAACTTATATTTTTA
5247625 TAATTTTACCATTTGAATAACTTATATTTTTA
1 TAATTTTACCATTTGAATAACTTATATTTTTA
5247657 TAATTTT
1 TAATTTT
5247664 TAAATAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.55
Consensus pattern (32 bp):
TAATTTTACCATTTGAATAACTTATATTTTTA
Found at i:5248029 original size:17 final size:17
Alignment explanation
Indices: 5248003--5248035 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5247993 GAATTAATCG
*
5248003 AATTATCCGAATTAAAA
1 AATTAACCGAATTAAAA
5248020 AATTAACCGAATTAAA
1 AATTAACCGAATTAAA
5248036 GTATTGAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.12, G:0.06, T:0.27
Consensus pattern (17 bp):
AATTAACCGAATTAAAA
Found at i:5248365 original size:15 final size:16
Alignment explanation
Indices: 5248339--5248369 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
5248329 GATAGCGAGT
5248339 TAATATTTATTTATTA
1 TAATATTTATTTATTA
5248355 TAATA-TTATTTATTA
1 TAATATTTATTTATTA
5248370 ATTCGATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TAATATTTATTTATTA
Found at i:5249628 original size:31 final size:31
Alignment explanation
Indices: 5249565--5249634 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
5249555 GGAACTTCAT
* ** *
5249565 TTTAATGATTTAAATAAAAACTTTTGAGTAA
1 TTTAATGACTTAAATAAAAACTTTCAAATAA
*
5249596 TTTAATGACTTAAATGAAAACTTTCAAATAA
1 TTTAATGACTTAAATAAAAACTTTCAAATAA
*
5249627 TTCAATGA
1 TTTAATGA
5249635 TCAAATTGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.39
Consensus pattern (31 bp):
TTTAATGACTTAAATAAAAACTTTCAAATAA
Found at i:5250030 original size:14 final size:15
Alignment explanation
Indices: 5250011--5250043 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
5250001 ACATTTTTTA
5250011 TTTTTTAAA-AAGTTT
1 TTTTTTAAATAA-TTT
5250026 TTTTTTAAATAATTT
1 TTTTTTAAATAATTT
5250041 TTT
1 TTT
5250044 GGTGAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.88
16 2 0.12
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTTTTAAATAATTT
Found at i:5250030 original size:16 final size:16
Alignment explanation
Indices: 5250006--5250043 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5249996 TTTTAACATT
5250006 TTTTATTTTTTAAA-AA
1 TTTT-TTTTTTAAATAA
*
5250022 GTTTTTTTTTAAATAA
1 TTTTTTTTTTAAATAA
5250038 TTTTTT
1 TTTTTT
5250044 GGTGAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTTTTTTTTAAATAA
Found at i:5254820 original size:28 final size:30
Alignment explanation
Indices: 5254757--5254823 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 30
5254747 AATACTTAAA
*
5254757 TTATACATGAACTATGGTTTAATGTGCAATT
1 TTATACATGAACTATGATTT-ATGTGCAATT
* *
5254788 ATATACATGAACT-TGATTT-TGTGTAATT
1 TTATACATGAACTATGATTTATGTGCAATT
5254816 TTATACAT
1 TTATACAT
5254824 AAAATTTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 15 0.47
30 5 0.16
31 12 0.38
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (30 bp):
TTATACATGAACTATGATTTATGTGCAATT
Found at i:5264744 original size:14 final size:14
Alignment explanation
Indices: 5264725--5264751 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5264715 ACTTCTCGAA
5264725 AATTTAATTTTTTT
1 AATTTAATTTTTTT
5264739 AATTTAATTTTTT
1 AATTTAATTTTTT
5264752 ATAAATTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
AATTTAATTTTTTT
Found at i:5268661 original size:19 final size:20
Alignment explanation
Indices: 5268634--5268698 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
5268624 AAAAAAGAAA
* *
5268634 ATTTAGAATTTTTATAAA-C
1 ATTTTGAATTTTTAAAAATC
*
5268653 ATTTTGAA-TTTTAAAAATT
1 ATTTTGAATTTTTAAAAATC
* *
5268672 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTTAAAAATC
5268692 ATTTTGA
1 ATTTTGA
5268699 TTATTTTGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
18 8 0.20
19 15 0.38
20 17 0.43
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (20 bp):
ATTTTGAATTTTTAAAAATC
Found at i:5268711 original size:20 final size:20
Alignment explanation
Indices: 5268653--5268698 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
5268643 TTTTATAAAC
*
5268653 ATTTTGAA-TTTTAAAAATT
1 ATTTTGAATTTTTGAAAATT
5268672 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTTGAAAATT
5268692 ATTTTGA
1 ATTTTGA
5268699 TTATTTTGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (20 bp):
ATTTTGAATTTTTGAAAATT
Found at i:5275090 original size:30 final size:28
Alignment explanation
Indices: 5275054--5275113 Score: 75
Period size: 30 Copynumber: 2.1 Consensus size: 28
5275044 CAAATAAATG
* *
5275054 ATTAATTTATTTTTTATTTAATATATAAAA
1 ATTAATTAATTTATT-TTTAA-ATATAAAA
*
5275084 ATTAATTAATTTATTTTTCAATATAAAA
1 ATTAATTAATTTATTTTTAAATATAAAA
5275112 AT
1 AT
5275114 CGAATCGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 10 0.37
29 4 0.15
30 13 0.48
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
ATTAATTAATTTATTTTTAAATATAAAA
Found at i:5275651 original size:18 final size:18
Alignment explanation
Indices: 5275615--5275652 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5275605 TTATTATATT
*
5275615 AATTTAAAAATCATTAAA
1 AATTTAAAAATCATAAAA
5275633 AATTCTAAAAAT-ATAAAA
1 AATT-TAAAAATCATAAAA
5275651 AA
1 AA
5275653 AAACAGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (18 bp):
AATTTAAAAATCATAAAA
Found at i:5275710 original size:19 final size:19
Alignment explanation
Indices: 5275615--5275712 Score: 56
Period size: 20 Copynumber: 5.0 Consensus size: 19
5275605 TTATTATATT
5275615 AATT-TAAAAATCATT-AAA
1 AATTATAAAAAT-ATTAAAA
* *
5275633 AATTCTAAAAATATAAAAAA
1 AATTATAAAAATAT-TAAAA
** * *
5275653 AAACAGAAAAATCATTTAAA
1 AATTATAAAAAT-ATTAAAA
* * *
5275673 AATAAAAATAGAATTTTAAAA
1 AATTATAA-A-AATATTAAAA
5275694 AATTATAAAAATATTAAAA
1 AATTATAAAAATATTAAAA
5275713 TTTATTACAA
Statistics
Matches: 59, Mismatches: 15, Indels: 11
0.69 0.18 0.13
Matches are distributed among these distances:
18 6 0.10
19 16 0.27
20 20 0.34
21 14 0.24
22 3 0.05
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (19 bp):
AATTATAAAAATATTAAAA
Found at i:5286366 original size:15 final size:17
Alignment explanation
Indices: 5286346--5286379 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
5286336 TACTCACTCA
5286346 CCTCCCC-CCCC-CCCC
1 CCTCCCCACCCCACCCC
5286361 CCTCCCCACCCCACCCC
1 CCTCCCCACCCCACCCC
5286378 CC
1 CC
5286380 AGAAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 4 0.24
17 6 0.35
ACGTcount: A:0.06, C:0.88, G:0.00, T:0.06
Consensus pattern (17 bp):
CCTCCCCACCCCACCCC
Found at i:5293258 original size:3 final size:3
Alignment explanation
Indices: 5293252--5293301 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
5293242 ATGATGGGTG
* * *
5293252 ATA ATA ATA ATA ATA ATA ATA ATA AT- GTA ATC ATA AAA ATA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5293298 ATA A
1 ATA A
5293302 AAATGAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 3 0.08
3 36 0.92
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:5293287 original size:20 final size:20
Alignment explanation
Indices: 5293259--5293296 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5293249 GTGATAATAA
*
5293259 TAATAATAATAATAATAATG
1 TAATAATAAAAATAATAATG
*
5293279 TAATCATAAAAATAATAA
1 TAATAATAAAAATAATAA
5293297 AATAAAAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (20 bp):
TAATAATAAAAATAATAATG
Found at i:5297461 original size:24 final size:24
Alignment explanation
Indices: 5297425--5297470 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
5297415 ATATTTATAT
*
5297425 ATTTTTTACATAATCTATTAAAATA
1 ATTTTTTACATAAT-TATAAAAATA
*
5297450 ATTTTTT-TATAATTATAAAAA
1 ATTTTTTACATAATTATAAAAA
5297471 ATATACTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.37
24 5 0.26
25 7 0.37
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (24 bp):
ATTTTTTACATAATTATAAAAATA
Found at i:5312417 original size:24 final size:26
Alignment explanation
Indices: 5312371--5312421 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
5312361 ATTTTGATAC
5312371 ATGCAATCTAAAATTTAAATATTTGT
1 ATGCAATCTAAAATTTAAATATTTGT
* *
5312397 ATGCAAT-TAATA-TTAATTATTTGT
1 ATGCAATCTAAAATTTAAATATTTGT
5312421 A
1 A
5312422 AAATTTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 12 0.52
25 4 0.17
26 7 0.30
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (26 bp):
ATGCAATCTAAAATTTAAATATTTGT
Found at i:5317533 original size:516 final size:518
Alignment explanation
Indices: 5316560--5317603 Score: 2038
Period size: 516 Copynumber: 2.0 Consensus size: 518
5316550 TTCATTCGAG
5316560 AATTAATTGAGAATAATCTATAGAATTGAAATATGTGTTTACTCAAAGTTAGCTAGTTGATTTGT
1 AATTAATTGAGAATAATCTATAGAATTGAAATATGTGTTTACTCAAAGTTAGCTAGTTGATTTGT
*
5316625 TCACCAAAACCTTAGACTGAAACATATTTGAGAGCTCGAGAAGCTTATAAATTACATTAACATAT
66 TCACCAAAACCTTAGACTGAAACATATTTGAGAGCTCGAGAAGCTTATAAACTACATTAACATAT
5316690 AAATATTAAGGGTTAATTTTTTTAAAAATAAAATTTAAATTGAAATAATGTGGAATTGTCGTTAA
131 AAATATTAAGGGTTAATTTTTTTAAAAATAAAATTTAAATTGAAATAATGTGGAATTGTCGTTAA
*
5316755 TCATTTAATGACTGGTGGTAAAAAAATTAAATAACTATTTTGTAATTTACCCACTAAAAAAAGGG
196 CCATTTAATGACTGGTGGTAAAAAAATTAAATAACTATTTTGTAATTTACCCACTAAAAAAAGGG
*
5316820 CATGACATGTGGGAGGGTCCATGGGTTTTATATTCTAGGAATGCGTCCAAAATGTTCATTAATTT
261 CATGACATGTGGGAGGGTCCATGGGTTTTATATTCTAGGAATGCGTCCAAAATGCTCATTAATTT
5316885 CCTCTGCAGGACGTTGTTCCTTGGTGCCCAAACTAGCTCTCTATTATTTTTGAAACTTATAAATA
326 CCTCTGCAGGACGTTGTTCCTTGGTGCCCAAACTAGCTCTCTATTATTTTTGAAACTTATAAATA
5316950 TTTAAATGTAGGTACCTACGTAAAATTTGGATAAAAGTATTAGAATCTAATTTATTAGAAATTGA
391 TTTAAATGTAGGTACCTACGTAAAATTTGGATAAAAGTATTAGAATCTAATTTATTAGAAATTGA
5317015 ATTGTATTAACTGAATTAATTAAGTTTTTTTAATAGTTAATTGAATTGAATTTTTTTC-AAAA
456 ATTGTATTAACTGAATTAATTAAGTTTTTTTAATAGTTAATTGAATTGAATTTTTTTCAAAAA
5317077 AATTAATTGAGAATAATCTATAGAATTGAAATATGTGTTTACTCAAAGTTAGCTAGTTGATTTGT
1 AATTAATTGAGAATAATCTATAGAATTGAAATATGTGTTTACTCAAAGTTAGCTAGTTGATTTGT
*
5317142 TCACCAAAACTTTAGACTGAAACATATTTGAGAGCTCGAGAAGCTTATAAACTACA-TAACATAT
66 TCACCAAAACCTTAGACTGAAACATATTTGAGAGCTCGAGAAGCTTATAAACTACATTAACATAT
5317206 AAATATTAAGGGTTAATTTTTTTAAAAATAAAATTTAAATTGAAATAATGTGGAATTGTCGTTAA
131 AAATATTAAGGGTTAATTTTTTTAAAAATAAAATTTAAATTGAAATAATGTGGAATTGTCGTTAA
5317271 CCATTTAATGACTGGTGGTAAAAAAATTAAATAACTATTTTGTAATTTACCCACTAAAAAAAGGG
196 CCATTTAATGACTGGTGGTAAAAAAATTAAATAACTATTTTGTAATTTACCCACTAAAAAAAGGG
5317336 CATGACATGTGGGAGGGTCCATGGGTTTTATATTCTAGGAATGCGTCCAAAATGCTCATTAATTT
261 CATGACATGTGGGAGGGTCCATGGGTTTTATATTCTAGGAATGCGTCCAAAATGCTCATTAATTT
5317401 CCTCTGCAGGACGTTGTTCCTTGGTGCCCAAACTAGCTCTCTATTATTTTTGAAACTTATAAATA
326 CCTCTGCAGGACGTTGTTCCTTGGTGCCCAAACTAGCTCTCTATTATTTTTGAAACTTATAAATA
5317466 TTTAAATGTAGGTACCTACGTAAAATTTGGATAAAAGTATTAGAATCTAATTTATTAGAAATTGA
391 TTTAAATGTAGGTACCTACGTAAAATTTGGATAAAAGTATTAGAATCTAATTTATTAGAAATTGA
5317531 ATTGTATTAACTGAATTAATTAAGTTTTTTTAATAGTTAATTGAATTGAATTTTTTTCAAAAA
456 ATTGTATTAACTGAATTAATTAAGTTTTTTTAATAGTTAATTGAATTGAATTTTTTTCAAAAA
5317594 AATTAATTGA
1 AATTAATTGA
5317604 TTCGAAATAT
Statistics
Matches: 522, Mismatches: 4, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
516 389 0.75
517 133 0.25
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (518 bp):
AATTAATTGAGAATAATCTATAGAATTGAAATATGTGTTTACTCAAAGTTAGCTAGTTGATTTGT
TCACCAAAACCTTAGACTGAAACATATTTGAGAGCTCGAGAAGCTTATAAACTACATTAACATAT
AAATATTAAGGGTTAATTTTTTTAAAAATAAAATTTAAATTGAAATAATGTGGAATTGTCGTTAA
CCATTTAATGACTGGTGGTAAAAAAATTAAATAACTATTTTGTAATTTACCCACTAAAAAAAGGG
CATGACATGTGGGAGGGTCCATGGGTTTTATATTCTAGGAATGCGTCCAAAATGCTCATTAATTT
CCTCTGCAGGACGTTGTTCCTTGGTGCCCAAACTAGCTCTCTATTATTTTTGAAACTTATAAATA
TTTAAATGTAGGTACCTACGTAAAATTTGGATAAAAGTATTAGAATCTAATTTATTAGAAATTGA
ATTGTATTAACTGAATTAATTAAGTTTTTTTAATAGTTAATTGAATTGAATTTTTTTCAAAAA
Found at i:5320367 original size:24 final size:26
Alignment explanation
Indices: 5320316--5320367 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 26
5320306 TATTTTGATA
* *
5320316 TATGCAATGTAAATTTTAAATATTTG
1 TATGCAATGTAAATATTAAATATGTG
*
5320342 TATGCAAT-T-AATATTAATTATGTG
1 TATGCAATGTAAATATTAAATATGTG
5320366 TA
1 TA
5320368 AAATTTAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 14 0.61
25 1 0.04
26 8 0.35
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (26 bp):
TATGCAATGTAAATATTAAATATGTG
Found at i:5321804 original size:23 final size:21
Alignment explanation
Indices: 5321778--5321820 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5321768 GTTTATTTTT
*
5321778 AATTCATTAAATATTATATTTAC
1 AATTCA-TAAA-AATATATTTAC
*
5321801 AATTTATAAAAATATATTTA
1 AATTCATAAAAATATATTTA
5321821 TTAATTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 4 0.22
23 5 0.28
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (21 bp):
AATTCATAAAAATATATTTAC
Found at i:5322516 original size:19 final size:20
Alignment explanation
Indices: 5322492--5322534 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
5322482 AATTCATTTA
* *
5322492 ATTTTATATTGTT-TTTAAT
1 ATTTTATACTCTTGTTTAAT
5322511 ATTTTATACTCTTGTTTAAT
1 ATTTTATACTCTTGTTTAAT
5322531 ATTT
1 ATTT
5322535 AAATTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.65
Consensus pattern (20 bp):
ATTTTATACTCTTGTTTAAT
Found at i:5322535 original size:19 final size:18
Alignment explanation
Indices: 5322488--5322535 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
5322478 CTTAAATTCA
* *
5322488 TTTAAT-TTTATATTGTT
1 TTTAATATTTATACTCTT
5322505 TTTAATATTTTATACTCTT
1 TTTAATA-TTTATACTCTT
5322524 GTTTAATATTTA
1 -TTTAATATTTA
5322536 AATTTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 6 0.23
19 13 0.50
20 7 0.27
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (18 bp):
TTTAATATTTATACTCTT
Found at i:5323119 original size:29 final size:30
Alignment explanation
Indices: 5323086--5323145 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
5323076 TTCACGTGTG
*
5323086 TAATTATAC-TAAAATAAAATTCATGTATA
1 TAATTACACATAAAATAAAATTCATGTATA
*
5323115 TAATTACACATTAAATTAAAATTCATGTATA
1 TAATTACACA-TAAAATAAAATTCATGTATA
5323146 ATTTTGAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 8 0.30
31 19 0.70
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.38
Consensus pattern (30 bp):
TAATTACACATAAAATAAAATTCATGTATA
Found at i:5323689 original size:20 final size:20
Alignment explanation
Indices: 5323664--5323730 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
5323654 TTTTTTTTTT
5323664 TTACTTTTCAAAATAATATA
1 TTACTTTTCAAAATAATATA
*
5323684 TTACTTTTC---A-ACTAT-
1 TTACTTTTCAAAATAATATA
*
5323699 TTACTTTTTAAAATAATATTA
1 TTACTTTTCAAAATAATA-TA
5323720 TTACTTTTCAA
1 TTACTTTTCAA
5323731 TTTTTTACAT
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
15 8 0.22
16 4 0.11
17 1 0.03
18 1 0.03
19 3 0.08
20 10 0.27
21 10 0.27
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (20 bp):
TTACTTTTCAAAATAATATA
Found at i:5323738 original size:36 final size:35
Alignment explanation
Indices: 5323660--5323738 Score: 122
Period size: 35 Copynumber: 2.2 Consensus size: 35
5323650 CCAATTTTTT
5323660 TTTTTTACTTTTCAAAATAATATATTACTTTTCAA
1 TTTTTTACTTTTCAAAATAATATATTACTTTTCAA
* * *
5323695 CTATTTACTTTTTAAAATAATATTATTACTTTTCAA
1 TTTTTTACTTTTCAAAATAATA-TATTACTTTTCAA
5323731 TTTTTTAC
1 TTTTTTAC
5323739 ATTATTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
35 19 0.50
36 19 0.50
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (35 bp):
TTTTTTACTTTTCAAAATAATATATTACTTTTCAA
Found at i:5323952 original size:12 final size:12
Alignment explanation
Indices: 5323935--5323959 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5323925 ATTTGTATAT
5323935 TAGTTATATTAG
1 TAGTTATATTAG
5323947 TAGTTATATTAG
1 TAGTTATATTAG
5323959 T
1 T
5323960 TATAATATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TAGTTATATTAG
Found at i:5324253 original size:17 final size:17
Alignment explanation
Indices: 5324231--5324263 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5324221 TCCCCTTTTA
5324231 TAATTAAAAAAAAAAGC
1 TAATTAAAAAAAAAAGC
*
5324248 TAATTAAAAAACAAAG
1 TAATTAAAAAAAAAAG
5324264 TAAGAGGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.70, C:0.06, G:0.06, T:0.18
Consensus pattern (17 bp):
TAATTAAAAAAAAAAGC
Found at i:5324855 original size:14 final size:16
Alignment explanation
Indices: 5324825--5324857 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
5324815 TCTGTTATCC
5324825 TATTTTCATATTTATT
1 TATTTTCATATTTATT
5324841 TATTTT-ATA-TTATT
1 TATTTTCATATTTATT
5324855 TAT
1 TAT
5324858 GTAAAAAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 3 0.18
16 6 0.35
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTTTCATATTTATT
Found at i:5338038 original size:119 final size:120
Alignment explanation
Indices: 5337798--5338030 Score: 301
Period size: 119 Copynumber: 1.9 Consensus size: 120
5337788 TGAATTTAAC
* * *
5337798 AATTAAGTAACATGGGGAAATTAGGGTTTAAGAACTGAAATTTAGGAGAAAAAAAAAAGAAATTC
1 AATTAAGTAACATGGGGAAATTAGGGTTCAAGAACTGAAATTTACGACAAAAAAAAAAGAAATTC
* * *
5337863 GATAACTTCGTCGAGGCTGTGAATCACTGTTGGTTATAGTGCGGACATCCAAAGA
66 GATAACTTCGTCGAGGCTGTGAAGCACTGTTGCTTACAGTGCGGACATCCAAAGA
* * *
5337918 AATTAAGTAA-ATGGGGAAATTAGGGTTCAAGGATTGAAATTTACGACAAAACAAAAAGAAATTC
1 AATTAAGTAACATGGGGAAATTAGGGTTCAAGAACTGAAATTTACGACAAAAAAAAAAGAAATTC
* * * * *
5337982 GGTACCTTTGTCTAGTCTGTGAAGCA-TCGTTGCTTACAGT-CGGATCATC
66 GATAACTTCGTCGAGGCTGTGAAGCACT-GTTGCTTACAGTGCGGA-CATC
5338031 GGAAGAAACC
Statistics
Matches: 97, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
118 5 0.05
119 82 0.85
120 10 0.10
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (120 bp):
AATTAAGTAACATGGGGAAATTAGGGTTCAAGAACTGAAATTTACGACAAAAAAAAAAGAAATTC
GATAACTTCGTCGAGGCTGTGAAGCACTGTTGCTTACAGTGCGGACATCCAAAGA
Found at i:5357492 original size:8 final size:8
Alignment explanation
Indices: 5357479--5357503 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5357469 TTGTCTTAAT
5357479 CTTCTGGG
1 CTTCTGGG
5357487 CTTCTGGG
1 CTTCTGGG
5357495 CTTCTGGG
1 CTTCTGGG
5357503 C
1 C
5357504 CCTTTGGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.28, G:0.36, T:0.36
Consensus pattern (8 bp):
CTTCTGGG
Found at i:5360907 original size:15 final size:15
Alignment explanation
Indices: 5360887--5360916 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5360877 AATTTTTAAA
*
5360887 TAATTTTAATATTTT
1 TAATTTTAAAATTTT
5360902 TAATTTTAAAATTTT
1 TAATTTTAAAATTTT
5360917 AATAACAAAT
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TAATTTTAAAATTTT
Found at i:5360908 original size:26 final size:24
Alignment explanation
Indices: 5360871--5360920 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 24
5360861 AACGTGTAAG
5360871 TTTTATAATTTTTAAATAATTTTAATA
1 TTTTATAA-TTTT-AA-AATTTTAATA
5360898 TTTT-TAATTTTAAAATTTTAATA
1 TTTTATAATTTTAAAATTTTAATA
5360921 ACAAATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 10 0.43
24 2 0.09
25 4 0.17
26 3 0.13
27 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTTATAATTTTAAAATTTTAATA
Found at i:5364115 original size:18 final size:18
Alignment explanation
Indices: 5364092--5364127 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5364082 AGTGACTGTT
*
5364092 TTATAATTGAGATCAAAA
1 TTATAATTAAGATCAAAA
5364110 TTATAATTAAGATCAAAA
1 TTATAATTAAGATCAAAA
5364128 GTAAGTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.33
Consensus pattern (18 bp):
TTATAATTAAGATCAAAA
Found at i:5366209 original size:22 final size:25
Alignment explanation
Indices: 5366169--5366227 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 25
5366159 TCACATGTTA
*
5366169 TATATTTTGTATTGATTTAAT-T-T
1 TATATTTTGAATTGATTTAATATAT
*
5366192 TATATTTT-AATTGTTTTAATATAT
1 TATATTTTGAATTGATTTAATATAT
5366216 TATATTTATGAA
1 TATATTT-TGAA
5366228 GGTATTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 10 0.33
23 9 0.30
24 8 0.27
25 1 0.03
26 2 0.07
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (25 bp):
TATATTTTGAATTGATTTAATATAT
Found at i:5368482 original size:21 final size:21
Alignment explanation
Indices: 5368430--5368482 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
5368420 AAAAATATAT
* *
5368430 AATATATCAAATACACTTAAA
1 AATATAACAAATAAACTTAAA
*
5368451 AATATTA-AAATAAACATTAAA
1 AATATAACAAATAAAC-TTAAA
5368472 AATA-AACAAAT
1 AATATAACAAAT
5368483 TTAAAATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.26
Consensus pattern (21 bp):
AATATAACAAATAAACTTAAA
Found at i:5368631 original size:23 final size:23
Alignment explanation
Indices: 5368605--5368673 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
5368595 ATAGCATCTA
* *
5368605 AACAATCAAAATAACAGCAAAAT
1 AACAATAAAAATAACAACAAAAT
*
5368628 AACAATAAAAATAGCAACAAAAAT
1 AACAATAAAAATAACAAC-AAAAT
*
5368652 AA-AAGTAAAAATAGCAACAAAA
1 AACAA-TAAAAATAACAACAAAA
5368674 AATAATAGCA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
23 21 0.51
24 20 0.49
ACGTcount: A:0.70, C:0.13, G:0.06, T:0.12
Consensus pattern (23 bp):
AACAATAAAAATAACAACAAAAT
Found at i:5368638 original size:12 final size:12
Alignment explanation
Indices: 5368605--5368674 Score: 54
Period size: 12 Copynumber: 5.9 Consensus size: 12
5368595 ATAGCATCTA
*
5368605 AACAATCAAAAT
1 AACAATAAAAAT
**
5368617 AAC-AGCAAAAT
1 AACAATAAAAAT
5368628 AACAATAAAAAT
1 AACAATAAAAAT
* *
5368640 AGCAACAAAAAT
1 AACAATAAAAAT
5368652 AA-AAGTAAAAAT
1 AACAA-TAAAAAT
* *
5368664 AGCAACAAAAA
1 AACAATAAAAA
5368675 ATAATAGCAC
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
11 12 0.26
12 32 0.70
13 2 0.04
ACGTcount: A:0.70, C:0.13, G:0.06, T:0.11
Consensus pattern (12 bp):
AACAATAAAAAT
Found at i:5368660 original size:24 final size:24
Alignment explanation
Indices: 5368605--5368674 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
5368595 ATAGCATCTA
* * *
5368605 AACAATCAAAATAACAGC-AAAAT
1 AACAATAAAAATAGCAACAAAAAT
5368628 AACAATAAAAATAGCAACAAAAAT
1 AACAATAAAAATAGCAACAAAAAT
5368652 AA-AAGTAAAAATAGCAACAAAAA
1 AACAA-TAAAAATAGCAACAAAAA
5368675 ATAATAGCAC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
23 17 0.40
24 25 0.60
ACGTcount: A:0.70, C:0.13, G:0.06, T:0.11
Consensus pattern (24 bp):
AACAATAAAAATAGCAACAAAAAT
Found at i:5368682 original size:16 final size:17
Alignment explanation
Indices: 5368661--5368695 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
5368651 TAAAAGTAAA
5368661 AATAGCAACAAAA-AAT
1 AATAGCAACAAAACAAT
*
5368677 AATAGCACCAAAACAAT
1 AATAGCAACAAAACAAT
5368694 AA
1 AA
5368696 AAAAAAGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.66, C:0.17, G:0.06, T:0.11
Consensus pattern (17 bp):
AATAGCAACAAAACAAT
Found at i:5368704 original size:21 final size:21
Alignment explanation
Indices: 5368667--5368709 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5368657 TAAAAATAGC
*
5368667 AACAAAAAATAATAGCACCAA
1 AACAAAAAATAAAAGCACCAA
*
5368688 AACAATAAAA-AAAAGCATCAA
1 AACAA-AAAATAAAAGCACCAA
5368709 A
1 A
5368710 GCAGCAACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.70, C:0.16, G:0.05, T:0.09
Consensus pattern (21 bp):
AACAAAAAATAAAAGCACCAA
Found at i:5368721 original size:33 final size:34
Alignment explanation
Indices: 5368683--5368746 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
5368673 AAATAATAGC
5368683 ACCAAAACAAT-AAAAAAAAGCATCAAAGCAGCA
1 ACCAAAACAATAAAAAAAAAGCATCAAAGCAGCA
5368716 ACCAAAACAATAAAAAAAAAGCATCAAAGCA
1 ACCAAAACAATAAAAAAAAAGCATCAAAGCA
5368747 ACAAAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 11 0.37
34 19 0.63
ACGTcount: A:0.66, C:0.20, G:0.08, T:0.06
Consensus pattern (34 bp):
ACCAAAACAATAAAAAAAAAGCATCAAAGCAGCA
Found at i:5369611 original size:29 final size:30
Alignment explanation
Indices: 5369579--5369642 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
5369569 TAATACAAAT
*
5369579 AAAATTATACTTTAA-CCCTTAAAA-ATATA
1 AAAATT-TAATTTAATCCCTTAAAATATATA
* *
5369608 AAAATTTAATTTAATCCTTTAAAATTTATA
1 AAAATTTAATTTAATCCCTTAAAATATATA
5369638 AAAAT
1 AAAAT
5369643 ATAAACTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 7 0.23
29 14 0.47
30 9 0.30
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (30 bp):
AAAATTTAATTTAATCCCTTAAAATATATA
Found at i:5369853 original size:2 final size:2
Alignment explanation
Indices: 5369846--5369882 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5369836 TTATCAAACT
5369846 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 T
5369883 TAATTTTTTG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5370619 original size:22 final size:24
Alignment explanation
Indices: 5370568--5370619 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 24
5370558 AGGAAGAGGA
5370568 AGAAGAAATAAAGAAAATATAAAGT
1 AGAA-AAATAAAGAAAATATAAAGT
* *
5370593 A-AAAAATAAA-AATATATATAG-
1 AGAAAAATAAAGAAAATATAAAGT
5370614 AGAAAA
1 AGAAAA
5370620 TAATATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
21 1 0.04
22 13 0.54
23 7 0.29
24 2 0.08
25 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (24 bp):
AGAAAAATAAAGAAAATATAAAGT
Found at i:5385005 original size:442 final size:443
Alignment explanation
Indices: 5384180--5385065 Score: 1747
Period size: 442 Copynumber: 2.0 Consensus size: 443
5384170 CCCTTCAAAA
5384180 ATAATAAAAATTTGATTGAATCATTTAAAAATATAAATATATAAACTATTAAAATGATGAAATTG
1 ATAATAAAAATTTGATTGAATCATTTAAAAATATAAATATATAAACTATTAAAATGATGAAATTG
5384245 TATCTTTATGATCATAAAAATATATAATTTAATTCTACCCTTAAAATTTTGTTCTGATTCAATAG
66 TATCTTTATGATCATAAAAATATATAATTTAATTCTACCCTTAAAATTTTGTTCTGATTCAATAG
5384310 AAACTTATATATGAATGATTTATTCTCAAATAATATGGTCGGTTGGAGAGTCAATTCAAAAATGG
131 AAACTTATATATGAATGATTTATTCTCAAATAATATGGTCGGTTGGAGAGTCAATTCAAAAATGG
5384375 TAGTTGGAGAATCAATTCAAAACATGTGATTTTTTCTTTTCGGGGCATGTGAAATTTTATTTATC
196 TAGTTGGAGAATCAATTCAAAACATGTGATTTTTTCTTTTCGGGGCATGTGAAATTTTATTTATC
5384440 GTGAATTTAAAAAATTTGAATTCATTTTTAATATTTTCGTATTAATAAAATTCTTTTTTAATTTA
261 GTGAATTTAAAAAATTTGAATTCATTTTTAATATTTTCGTATTAATAAAATTCTTTTTTAATTTA
*
5384505 TTCATATCCTAACGTCAATTTTATAGTTTCAATTTTTGTTAAATAAATTCGATTTGGATGAAAAA
326 TTCATATCATAACGTCAATTTTATAGTTTCAATTTTTGTTAAATAAATTCGATTTGGATGAAAAA
5384570 TGTATCACAACTATTAATTAACTAACGACGAACAATGTCTATTGATGCGACAT
391 TGTATCACAACTATTAATTAACTAACGACGAACAATGTCTATTGATGCGACAT
5384623 ATAATAAAAATTTGATTGAATCATTTAAAAATATAAATATATAAACTATTAAAATGATGAAATTG
1 ATAATAAAAATTTGATTGAATCATTTAAAAATATAAATATATAAACTATTAAAATGATGAAATTG
*
5384688 TATCTTTATGATCATAAAAATATATAATTTAATTCTACCCTT-AAATTTTTTTCTGATTCAATAG
66 TATCTTTATGATCATAAAAATATATAATTTAATTCTACCCTTAAAATTTTGTTCTGATTCAATAG
5384752 AAACTTATATATGAATGATTTATTCTCAAATAATATGGTCGGTTGGAGAGTCAATTCAAAAATGG
131 AAACTTATATATGAATGATTTATTCTCAAATAATATGGTCGGTTGGAGAGTCAATTCAAAAATGG
5384817 TAGTTGGAGAATCAATTCAAAACATGTGATTTTTTCTTTTCGGGGCATGTGAAATTTTATTTATC
196 TAGTTGGAGAATCAATTCAAAACATGTGATTTTTTCTTTTCGGGGCATGTGAAATTTTATTTATC
5384882 GTGAATTTAAAAAATTTGAATTCATTTTTAATATTTTCGTATTAATAAAATTCTTTTTTAATTTA
261 GTGAATTTAAAAAATTTGAATTCATTTTTAATATTTTCGTATTAATAAAATTCTTTTTTAATTTA
5384947 TTCATATCATAACGTCAATTTTATAGTTTCAATTTTTGTTAAATAAATTCGATTTGGATGAAAAA
326 TTCATATCATAACGTCAATTTTATAGTTTCAATTTTTGTTAAATAAATTCGATTTGGATGAAAAA
5385012 TGTATCACAACTATTAATTAACTAACGACGAACAATGTCTATTGATGCGACAT
391 TGTATCACAACTATTAATTAACTAACGACGAACAATGTCTATTGATGCGACAT
5385065 A
1 A
5385066 ATTTTTTTTG
Statistics
Matches: 441, Mismatches: 2, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
442 334 0.76
443 107 0.24
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (443 bp):
ATAATAAAAATTTGATTGAATCATTTAAAAATATAAATATATAAACTATTAAAATGATGAAATTG
TATCTTTATGATCATAAAAATATATAATTTAATTCTACCCTTAAAATTTTGTTCTGATTCAATAG
AAACTTATATATGAATGATTTATTCTCAAATAATATGGTCGGTTGGAGAGTCAATTCAAAAATGG
TAGTTGGAGAATCAATTCAAAACATGTGATTTTTTCTTTTCGGGGCATGTGAAATTTTATTTATC
GTGAATTTAAAAAATTTGAATTCATTTTTAATATTTTCGTATTAATAAAATTCTTTTTTAATTTA
TTCATATCATAACGTCAATTTTATAGTTTCAATTTTTGTTAAATAAATTCGATTTGGATGAAAAA
TGTATCACAACTATTAATTAACTAACGACGAACAATGTCTATTGATGCGACAT
Found at i:5391405 original size:23 final size:22
Alignment explanation
Indices: 5391377--5391664 Score: 129
Period size: 23 Copynumber: 12.6 Consensus size: 22
5391367 CTAGCGCGCA
5391377 CTCTGTTTAGCACGTCTCGTGCT
1 CTCTGTTTAGCACGTCT-GTGCT
* *
5391400 CTCTGTTTAGCACTTTGTGTGCT
1 CTCTGTTTAGCAC-GTCTGTGCT
* * *
5391423 CTCTGATTAGTAC-TTTGTGTACT
1 CTCTGTTTAGCACGTCTGTG--CT
*
5391446 CTCTGTTTAGCACTGTGTGTGCT
1 CTCTGTTTAGCAC-GTCTGTGCT
*
5391469 CTCTGTTATTAGCACTGTGTGTGCT
1 CTCTG-T-TTAGCAC-GTCTGTGCT
* * *
5391494 CTCCGATTAGCACTTCGTGTGCT
1 CTCTGTTTAGCACGTC-TGTGCT
* * *
5391517 CTCTGATTAGCAC-TTTGTGCG
1 CTCTGTTTAGCACGTCTGTGCT
* ** * *
5391538 CTCAG--TA-C-TTTGTGTACT
1 CTCTGTTTAGCACGTCTGTGCT
* *
5391556 CTCTGTTTAGCACTTTGTGTGCT
1 CTCTGTTTAGCAC-GTCTGTGCT
* * *
5391579 CTCTGTTGCCCAGCACTTATGTGCT
1 CTCTGTT---TAGCACGTCTGTGCT
*
5391604 CTCTGTTATTAGCACTGTGTGTGCT
1 CTCTG-T-TTAGCAC-GTCTGTGCT
* * *
5391629 CTCCGATTAGCACTTCGTGTGCT
1 CTCTGTTTAGCACGTC-TGTGCT
*
5391652 CTCTGATTAGCAC
1 CTCTGTTTAGCAC
5391665 TTTGTGCGCT
Statistics
Matches: 211, Mismatches: 33, Indels: 42
0.74 0.12 0.15
Matches are distributed among these distances:
18 10 0.05
19 2 0.01
20 2 0.01
21 15 0.07
22 3 0.01
23 114 0.54
24 8 0.04
25 50 0.24
26 6 0.03
27 1 0.00
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.41
Consensus pattern (22 bp):
CTCTGTTTAGCACGTCTGTGCT
Found at i:5391504 original size:48 final size:44
Alignment explanation
Indices: 5391395--5391716 Score: 259
Period size: 48 Copynumber: 7.2 Consensus size: 44
5391385 AGCACGTCTC
* *
5391395 GTGCTCTCTGTTTAGCACTTTGTGTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCCG-TTAGCAC-TTGTGTGCTCTCTGATTAGCACTTTGT
* * *
5391441 GTACTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTATTAGCACTGTGT
1 GTGCTCTCCG-TTAGCACT-TGTGTGCTCTCTG--ATTAGCACTTTGT
5391489 GTGCTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCAC-TT-T
1 GTGCTCTCCG-TTAGCACTT-GTGTGCTCTCTGATTAGCACTTTGT
* * * * *
5391533 GTGCGCTCAG-TA-C-TTTGTGTACTCTCTGTTTAGCACTTTGT
1 GTGCTCTCCGTTAGCACTTGTGTGCTCTCTGATTAGCACTTTGT
* * *
5391574 GTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTGTTATTAGCACTGTGT
1 GTGCTCTCCGTT----AGCACTTGTGTGCTCTCTG--ATTAGCACTTTGT
5391624 GTGCTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCAC-TT-T
1 GTGCTCTCCG-TTAGCACTT-GTGTGCTCTCTGATTAGCACTTTGT
* ** * * *
5391668 GTGCGCTAAG-TA-C-TTTGTGTACTCTCTGTTTAGCACTTTGT
1 GTGCTCTCCGTTAGCACTTGTGTGCTCTCTGATTAGCACTTTGT
5391709 GTGCTCTC
1 GTGCTCTC
5391717 TGTTGCCCAG
Statistics
Matches: 227, Mismatches: 30, Indels: 43
0.76 0.10 0.14
Matches are distributed among these distances:
39 36 0.16
40 8 0.04
41 18 0.08
42 5 0.02
44 17 0.07
45 3 0.01
46 47 0.21
47 9 0.04
48 62 0.27
50 20 0.09
51 2 0.01
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.42
Consensus pattern (44 bp):
GTGCTCTCCGTTAGCACTTGTGTGCTCTCTGATTAGCACTTTGT
Found at i:5391569 original size:39 final size:39
Alignment explanation
Indices: 5391505--5391714 Score: 132
Period size: 39 Copynumber: 4.9 Consensus size: 39
5391495 TCCGATTAGC
* *
5391505 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGCGCTCAGT
1 ACTTTGTGTGCTCTCTGTTTAGCACTTTGTGCGCTCAGT
* * *
5391544 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTT
1 ACTTTGTGTGCTCTCTGTTTAGCAC-TT-TGTGCGCTCAG-T
* * * *
5391586 GCCCAGCACTTATGTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGC
1 ----A-C-TTTGTGTGCTCTCTG-T-TTAGCACT-T-TGTGCGCT-C----AGT
* * *
5391640 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGCGCTAAGT
1 ACTTTGTGTGCTCTCTGTTTAGCACTTTGTGCGCTCAGT
* *
5391679 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTTGTGTGCTCTCTGTTTAGCACTTTGTGCGCTC
5391715 TCTGTTGCCC
Statistics
Matches: 132, Mismatches: 22, Indels: 34
0.70 0.12 0.18
Matches are distributed among these distances:
39 55 0.42
40 2 0.02
41 9 0.07
42 1 0.01
44 7 0.05
45 1 0.01
46 9 0.07
47 1 0.01
48 24 0.18
49 3 0.02
50 18 0.14
51 1 0.01
55 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.41
Consensus pattern (39 bp):
ACTTTGTGTGCTCTCTGTTTAGCACTTTGTGCGCTCAGT
Found at i:5391583 original size:62 final size:62
Alignment explanation
Indices: 5391486--5391718 Score: 243
Period size: 62 Copynumber: 3.6 Consensus size: 62
5391476 ATTAGCACTG
*
5391486 TGTGTGCTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGCGCTCAGTACTT
1 TGTGTACTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGCGCTCAGTACTT
* * * *
5391548 TGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTG-TTGCCCAGCACTTATGTGCTCTCTGTTA
1 TGTGTACTCTCCGATTAGCACTTCGTGTGCTCTCTGATT----AGCACTT-TGTGCGCTC-----
* *
5391612 TTAGCACTG
56 --AGTACTT
* *
5391621 TGTGTGCTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGCGCTAAGTACTT
1 TGTGTACTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGCGCTCAGTACTT
* * *
5391683 TGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTG
1 TGTGTACTCTCCGATTAGCACTTCGTGTGCTCTCTG
5391719 TTGCCCAGCA
Statistics
Matches: 139, Mismatches: 19, Indels: 26
0.76 0.10 0.14
Matches are distributed among these distances:
61 2 0.01
62 69 0.50
65 7 0.05
66 8 0.06
69 7 0.05
70 7 0.05
73 37 0.27
74 2 0.01
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.41
Consensus pattern (62 bp):
TGTGTACTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGCGCTCAGTACTT
Found at i:5391651 original size:135 final size:135
Alignment explanation
Indices: 5391411--5391741 Score: 569
Period size: 135 Copynumber: 2.5 Consensus size: 135
5391401 TCTGTTTAGC
* * * * * *
5391411 ACTTTGTGTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTT---TAGCACTGTGTGTGCTCTCT
1 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTGCCCAGCACT-TATGTGCTCTCT
5391473 GTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGCG
65 GTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGCG
*
5391538 CTCAGT
130 CTAAGT
5391544 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTG
1 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTG
5391609 TTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGCGC
66 TTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGCGC
5391674 TAAGT
131 TAAGT
5391679 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTC
1 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTC
5391742 CGTTCAGTAC
Statistics
Matches: 188, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
133 38 0.20
135 144 0.77
136 6 0.03
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.42
Consensus pattern (135 bp):
ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTG
TTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGCGC
TAAGT
Found at i:5391665 original size:23 final size:23
Alignment explanation
Indices: 5391544--5391718 Score: 143
Period size: 23 Copynumber: 7.7 Consensus size: 23
5391534 TGCGCTCAGT
* *
5391544 ACTTTGTGTACTCTCTGTTTAGC
1 ACTTTGTGTGCTCTCTGATTAGC
5391567 ACTTTGTGTGCTCTCTG-TTGCCCAGC
1 ACTTTGTGTGCTCTCTGATT----AGC
*
5391593 AC-TTATGTGCTCTCTGTTATTAGC
1 ACTTTGTGTGCTCTCTG--ATTAGC
* *
5391617 ACTGTGTGTGCTCTCCGATTAGC
1 ACTTTGTGTGCTCTCTGATTAGC
*
5391640 ACTTCGTGTGCTCTCTGATTAGC
1 ACTTTGTGTGCTCTCTGATTAGC
* *
5391663 AC-TT-TGTG--CGCT-A--AGT
1 ACTTTGTGTGCTCTCTGATTAGC
* *
5391679 ACTTTGTGTACTCTCTGTTTAGC
1 ACTTTGTGTGCTCTCTGATTAGC
5391702 ACTTTGTGTGCTCTCTG
1 ACTTTGTGTGCTCTCTG
5391719 TTGCCCAGCA
Statistics
Matches: 121, Mismatches: 16, Indels: 30
0.72 0.10 0.18
Matches are distributed among these distances:
16 4 0.03
17 2 0.02
18 4 0.03
19 3 0.02
20 3 0.02
21 4 0.03
22 3 0.02
23 62 0.51
24 5 0.04
25 24 0.20
26 5 0.04
28 2 0.02
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.42
Consensus pattern (23 bp):
ACTTTGTGTGCTCTCTGATTAGC
Found at i:5392512 original size:23 final size:22
Alignment explanation
Indices: 5392484--5392771 Score: 129
Period size: 23 Copynumber: 12.6 Consensus size: 22
5392474 CTAGCGCGCA
5392484 CTCTGTTTAGCACGTCTCGTGCT
1 CTCTGTTTAGCACGTCT-GTGCT
* *
5392507 CTCTGTTTAGCACTTTGTGTGCT
1 CTCTGTTTAGCAC-GTCTGTGCT
* * *
5392530 CTCTGATTAGTAC-TTTGTGTACT
1 CTCTGTTTAGCACGTCTGTG--CT
*
5392553 CTCTGTTTAGCACTGTGTGTGCT
1 CTCTGTTTAGCAC-GTCTGTGCT
*
5392576 CTCTGTTATTAGCACTGTGTGTGCT
1 CTCTG-T-TTAGCAC-GTCTGTGCT
* * *
5392601 CTCCGATTAGCACTTCGTGTGCT
1 CTCTGTTTAGCACGTC-TGTGCT
* * *
5392624 CTCTGATTAGCAC-TTTGTGCG
1 CTCTGTTTAGCACGTCTGTGCT
* ** * *
5392645 CTCAG--TA-C-TTTGTGTACT
1 CTCTGTTTAGCACGTCTGTGCT
* *
5392663 CTCTGTTTAGCACTTTGTGTGCT
1 CTCTGTTTAGCAC-GTCTGTGCT
* * *
5392686 CTCTGTTGCCCAGCACTTATGTGCT
1 CTCTGTT---TAGCACGTCTGTGCT
*
5392711 CTCTGTTATTAGCACTGTGTGTGCT
1 CTCTG-T-TTAGCAC-GTCTGTGCT
* * *
5392736 CTCCGATTAGCACTTCGTGTGCT
1 CTCTGTTTAGCACGTC-TGTGCT
*
5392759 CTCTGATTAGCAC
1 CTCTGTTTAGCAC
5392772 TTTGTGCGCT
Statistics
Matches: 211, Mismatches: 33, Indels: 42
0.74 0.12 0.15
Matches are distributed among these distances:
18 10 0.05
19 2 0.01
20 2 0.01
21 15 0.07
22 3 0.01
23 114 0.54
24 8 0.04
25 50 0.24
26 6 0.03
27 1 0.00
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.41
Consensus pattern (22 bp):
CTCTGTTTAGCACGTCTGTGCT
Found at i:5392611 original size:48 final size:44
Alignment explanation
Indices: 5392502--5392823 Score: 259
Period size: 48 Copynumber: 7.2 Consensus size: 44
5392492 AGCACGTCTC
* *
5392502 GTGCTCTCTGTTTAGCACTTTGTGTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCCG-TTAGCAC-TTGTGTGCTCTCTGATTAGCACTTTGT
* * *
5392548 GTACTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTATTAGCACTGTGT
1 GTGCTCTCCG-TTAGCACT-TGTGTGCTCTCTG--ATTAGCACTTTGT
5392596 GTGCTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCAC-TT-T
1 GTGCTCTCCG-TTAGCACTT-GTGTGCTCTCTGATTAGCACTTTGT
* * * * *
5392640 GTGCGCTCAG-TA-C-TTTGTGTACTCTCTGTTTAGCACTTTGT
1 GTGCTCTCCGTTAGCACTTGTGTGCTCTCTGATTAGCACTTTGT
* * *
5392681 GTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTGTTATTAGCACTGTGT
1 GTGCTCTCCGTT----AGCACTTGTGTGCTCTCTG--ATTAGCACTTTGT
5392731 GTGCTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCAC-TT-T
1 GTGCTCTCCG-TTAGCACTT-GTGTGCTCTCTGATTAGCACTTTGT
* ** * * *
5392775 GTGCGCTAAG-TA-C-TTTGTGTACTCTCTGTTTAGCACTTTGT
1 GTGCTCTCCGTTAGCACTTGTGTGCTCTCTGATTAGCACTTTGT
5392816 GTGCTCTC
1 GTGCTCTC
5392824 TGTTGCCCAG
Statistics
Matches: 227, Mismatches: 30, Indels: 43
0.76 0.10 0.14
Matches are distributed among these distances:
39 36 0.16
40 8 0.04
41 18 0.08
42 5 0.02
44 17 0.07
45 3 0.01
46 47 0.21
47 9 0.04
48 62 0.27
50 20 0.09
51 2 0.01
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.42
Consensus pattern (44 bp):
GTGCTCTCCGTTAGCACTTGTGTGCTCTCTGATTAGCACTTTGT
Found at i:5392676 original size:39 final size:39
Alignment explanation
Indices: 5392612--5392821 Score: 132
Period size: 39 Copynumber: 4.9 Consensus size: 39
5392602 TCCGATTAGC
* *
5392612 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGCGCTCAGT
1 ACTTTGTGTGCTCTCTGTTTAGCACTTTGTGCGCTCAGT
* * *
5392651 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTT
1 ACTTTGTGTGCTCTCTGTTTAGCAC-TT-TGTGCGCTCAG-T
* * * *
5392693 GCCCAGCACTTATGTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGC
1 ----A-C-TTTGTGTGCTCTCTG-T-TTAGCACT-T-TGTGCGCT-C----AGT
* * *
5392747 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGCGCTAAGT
1 ACTTTGTGTGCTCTCTGTTTAGCACTTTGTGCGCTCAGT
* *
5392786 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTTGTGTGCTCTCTGTTTAGCACTTTGTGCGCTC
5392822 TCTGTTGCCC
Statistics
Matches: 132, Mismatches: 22, Indels: 34
0.70 0.12 0.18
Matches are distributed among these distances:
39 55 0.42
40 2 0.02
41 9 0.07
42 1 0.01
44 7 0.05
45 1 0.01
46 9 0.07
47 1 0.01
48 24 0.18
49 3 0.02
50 18 0.14
51 1 0.01
55 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.41
Consensus pattern (39 bp):
ACTTTGTGTGCTCTCTGTTTAGCACTTTGTGCGCTCAGT
Found at i:5392690 original size:62 final size:62
Alignment explanation
Indices: 5392593--5392825 Score: 243
Period size: 62 Copynumber: 3.6 Consensus size: 62
5392583 ATTAGCACTG
*
5392593 TGTGTGCTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGCGCTCAGTACTT
1 TGTGTACTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGCGCTCAGTACTT
* * * *
5392655 TGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTG-TTGCCCAGCACTTATGTGCTCTCTGTTA
1 TGTGTACTCTCCGATTAGCACTTCGTGTGCTCTCTGATT----AGCACTT-TGTGCGCTC-----
* *
5392719 TTAGCACTG
56 --AGTACTT
* *
5392728 TGTGTGCTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGCGCTAAGTACTT
1 TGTGTACTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGCGCTCAGTACTT
* * *
5392790 TGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTG
1 TGTGTACTCTCCGATTAGCACTTCGTGTGCTCTCTG
5392826 TTGCCCAGCA
Statistics
Matches: 139, Mismatches: 19, Indels: 26
0.76 0.10 0.14
Matches are distributed among these distances:
61 2 0.01
62 69 0.50
65 7 0.05
66 8 0.06
69 7 0.05
70 7 0.05
73 37 0.27
74 2 0.01
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.41
Consensus pattern (62 bp):
TGTGTACTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGCGCTCAGTACTT
Found at i:5392758 original size:135 final size:135
Alignment explanation
Indices: 5392518--5392848 Score: 569
Period size: 135 Copynumber: 2.5 Consensus size: 135
5392508 TCTGTTTAGC
* * * * * *
5392518 ACTTTGTGTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTT---TAGCACTGTGTGTGCTCTCT
1 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTGCCCAGCACT-TATGTGCTCTCT
5392580 GTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGCG
65 GTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGCG
*
5392645 CTCAGT
130 CTAAGT
5392651 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTG
1 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTG
5392716 TTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGCGC
66 TTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGCGC
5392781 TAAGT
131 TAAGT
5392786 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTC
1 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTC
5392849 CGTTCAGTAC
Statistics
Matches: 188, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
133 38 0.20
135 144 0.77
136 6 0.03
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.42
Consensus pattern (135 bp):
ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTG
TTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGCGC
TAAGT
Found at i:5392772 original size:23 final size:23
Alignment explanation
Indices: 5392651--5392825 Score: 143
Period size: 23 Copynumber: 7.7 Consensus size: 23
5392641 TGCGCTCAGT
* *
5392651 ACTTTGTGTACTCTCTGTTTAGC
1 ACTTTGTGTGCTCTCTGATTAGC
5392674 ACTTTGTGTGCTCTCTG-TTGCCCAGC
1 ACTTTGTGTGCTCTCTGATT----AGC
*
5392700 AC-TTATGTGCTCTCTGTTATTAGC
1 ACTTTGTGTGCTCTCTG--ATTAGC
* *
5392724 ACTGTGTGTGCTCTCCGATTAGC
1 ACTTTGTGTGCTCTCTGATTAGC
*
5392747 ACTTCGTGTGCTCTCTGATTAGC
1 ACTTTGTGTGCTCTCTGATTAGC
* *
5392770 AC-TT-TGTG--CGCT-A--AGT
1 ACTTTGTGTGCTCTCTGATTAGC
* *
5392786 ACTTTGTGTACTCTCTGTTTAGC
1 ACTTTGTGTGCTCTCTGATTAGC
5392809 ACTTTGTGTGCTCTCTG
1 ACTTTGTGTGCTCTCTG
5392826 TTGCCCAGCA
Statistics
Matches: 121, Mismatches: 16, Indels: 30
0.72 0.10 0.18
Matches are distributed among these distances:
16 4 0.03
17 2 0.02
18 4 0.03
19 3 0.02
20 3 0.02
21 4 0.03
22 3 0.02
23 62 0.51
24 5 0.04
25 24 0.20
26 5 0.04
28 2 0.02
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.42
Consensus pattern (23 bp):
ACTTTGTGTGCTCTCTGATTAGC
Found at i:5396935 original size:21 final size:22
Alignment explanation
Indices: 5396909--5397049 Score: 106
Period size: 23 Copynumber: 6.2 Consensus size: 22
5396899 ATACGGAATG
*
5396909 AACAGAGAGTAC-CAAAGTACT
1 AACAGAGAGCACACAAAGTACT
*
5396930 AACAGAGAGCACA-TAAGTACT
1 AACAGAGAGCACACAAAGTACT
* * * *
5396951 GGGCAATAAAGAGCACACACAGTGCT
1 ----AACAGAGAGCACACAAAGTACT
*
5396977 AAACAGAGAGTACACAAAGTACT
1 -AACAGAGAGCACACAAAGTACT
* *
5397000 AATCAGAGAGCACACAAAATGCT
1 AA-CAGAGAGCACACAAAGTACT
* *
5397023 AATCAGAGAGCACACACAGTGCT
1 AA-CAGAGAGCACACAAAGTACT
5397046 AACA
1 AACA
5397050 ATAGAGAGCA
Statistics
Matches: 95, Mismatches: 18, Indels: 13
0.75 0.14 0.10
Matches are distributed among these distances:
21 18 0.19
22 4 0.04
23 57 0.60
25 11 0.12
26 5 0.05
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.13
Consensus pattern (22 bp):
AACAGAGAGCACACAAAGTACT
Found at i:5397033 original size:69 final size:67
Alignment explanation
Indices: 5396909--5397047 Score: 183
Period size: 69 Copynumber: 2.0 Consensus size: 67
5396899 ATACGGAATG
* *
5396909 AACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTACTGGGCAATAAAGAGCACACACAGT
1 AACAGAGAGTACCAAAGTACTAACAGAGAGCACACAAG-AAT-GGCAATAAAGAGCACACACAGT
5396974 GCTA
64 GCTA
*
5396978 AACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAA-AAT-GCTAATCAGAGAGCACACACA
1 AACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACACAAGAATGGC-AAT-AAAGAGCACACACA
5397041 GTGCTA
62 GTGCTA
5397047 A
1 A
5397048 CAATAGAGAG
Statistics
Matches: 63, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
67 2 0.03
68 3 0.05
69 34 0.54
70 11 0.17
71 13 0.21
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.13
Consensus pattern (67 bp):
AACAGAGAGTACCAAAGTACTAACAGAGAGCACACAAGAATGGCAATAAAGAGCACACACAGTGC
TA
Found at i:5397055 original size:23 final size:23
Alignment explanation
Indices: 5396960--5397047 Score: 122
Period size: 23 Copynumber: 3.8 Consensus size: 23
5396950 TGGGCAATAA
* *
5396960 AGAGCACACACAGTGCTAAACAG
1 AGAGCACACAAAGTGCTAATCAG
* *
5396983 AGAGTACACAAAGTACTAATCAG
1 AGAGCACACAAAGTGCTAATCAG
*
5397006 AGAGCACACAAAATGCTAATCAG
1 AGAGCACACAAAGTGCTAATCAG
*
5397029 AGAGCACACACAGTGCTAA
1 AGAGCACACAAAGTGCTAA
5397048 CAATAGAGAG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.45, C:0.23, G:0.19, T:0.12
Consensus pattern (23 bp):
AGAGCACACAAAGTGCTAATCAG
Found at i:5399073 original size:23 final size:23
Alignment explanation
Indices: 5398974--5399098 Score: 114
Period size: 23 Copynumber: 5.5 Consensus size: 23
5398964 AAGTGCTGGG
* *
5398974 GAAACAGTAAGCACACACAGTGC
1 GAAATAGTAAGCACACAAAGTGC
* *
5398997 --AATCCAGTAGGCACACACAGTGC
1 GAAAT--AGTAAGCACACAAAGTGC
* * * *
5399020 -AATTAGCAAGCGCACAAGGTGC
1 GAAATAGTAAGCACACAAAGTGC
*
5399042 G-AATAGTAAGCATACAAAGTGC
1 GAAATAGTAAGCACACAAAGTGC
5399064 GAAATAGTAAGCACACAAAGTGC
1 GAAATAGTAAGCACACAAAGTGC
*
5399087 GAAACAGTAAGC
1 GAAATAGTAAGC
5399099 GCGCTAGCGT
Statistics
Matches: 82, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
21 2 0.02
22 30 0.37
23 48 0.59
24 2 0.02
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (23 bp):
GAAATAGTAAGCACACAAAGTGC
Found at i:5399081 original size:45 final size:44
Alignment explanation
Indices: 5398974--5399098 Score: 110
Period size: 45 Copynumber: 2.8 Consensus size: 44
5398964 AAGTGCTGGG
* * *
5398974 GAAACAGTAAGCACACACAGTGC-AATCCAGTAGGCACACACAGTGC
1 GAAATAGTAAGCACACA-AGTGCGAAT--AGTAAGCACACAAAGTGC
* * * *
5399020 -AATTAGCAAGCGCACAAGGTGCGAATAGTAAGCATACAAAGTGC
1 GAAATAGTAAGCACACAA-GTGCGAATAGTAAGCACACAAAGTGC
*
5399064 GAAATAGTAAGCACACAAAGTGCGAAACAGTAAGC
1 GAAATAGTAAGCACAC-AAGTGCG-AATAGTAAGC
5399099 GCGCTAGCGT
Statistics
Matches: 63, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
44 16 0.25
45 33 0.52
46 14 0.22
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (44 bp):
GAAATAGTAAGCACACAAGTGCGAATAGTAAGCACACAAAGTGC
Found at i:5410365 original size:29 final size:30
Alignment explanation
Indices: 5410315--5410371 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
5410305 TTAGTACCCT
* *
5410315 AACTTTATAAAAATTTATTTTAGTCCTTTC
1 AACTTTATAAAAAATCATTTTAGTCCTTTC
5410345 AACTTTATAAAAAATCA-TTTAGTCCTT
1 AACTTTATAAAAAATCATTTTAGTCCTT
5410372 AATTTAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.37, C:0.14, G:0.04, T:0.46
Consensus pattern (30 bp):
AACTTTATAAAAAATCATTTTAGTCCTTTC
Found at i:5421606 original size:21 final size:22
Alignment explanation
Indices: 5421582--5421623 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
5421572 ACCCCCAATA
*
5421582 TCTGGTTTTA-AACCCATCATT
1 TCTGATTTTACAACCCATCATT
*
5421603 TCTGATTTTACAACCCTTCAT
1 TCTGATTTTACAACCCATCAT
5421624 CCCTTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.24, C:0.26, G:0.07, T:0.43
Consensus pattern (22 bp):
TCTGATTTTACAACCCATCATT
Found at i:5424356 original size:2 final size:2
Alignment explanation
Indices: 5424349--5424374 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5424339 ATCATCAGAT
5424349 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
5424375 GCCCACCCAA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5427905 original size:3 final size:3
Alignment explanation
Indices: 5427890--5427922 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
5427880 AAATGAATGC
5427890 CCT CCT ACCT CCT CCT CCT CCT CCT CCT CCT CC
1 CCT CCT -CCT CCT CCT CCT CCT CCT CCT CCT CC
5427923 ACCCTGTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.03, C:0.67, G:0.00, T:0.30
Consensus pattern (3 bp):
CCT
Found at i:5443450 original size:26 final size:25
Alignment explanation
Indices: 5443405--5443458 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
5443395 TTGGTACAAT
*
5443405 AATATTACTTTTCATTTTTTAGTTAA
1 AATATTACTTTTCATATTTTAG-TAA
**
5443431 AATATTACTTTTGGTATTTTAGTAA
1 AATATTACTTTTCATATTTTAGTAA
5443456 AAT
1 AAT
5443459 TTGAGAGTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.33, C:0.06, G:0.07, T:0.54
Consensus pattern (25 bp):
AATATTACTTTTCATATTTTAGTAA
Found at i:5459913 original size:27 final size:26
Alignment explanation
Indices: 5459858--5459928 Score: 115
Period size: 27 Copynumber: 2.7 Consensus size: 26
5459848 GGTAAGAAAC
5459858 TAATAATATAATTTTGTTTTTTAAGG
1 TAATAATATAATTTTGTTTTTTAAGG
**
5459884 TAATAATATGGTTTTGTGTTTTTAAGG
1 TAATAATATAATTTTGT-TTTTTAAGG
5459911 TAATAATATAATTTTGTT
1 TAATAATATAATTTTGTT
5459929 CAACCTTGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 16 0.40
27 24 0.60
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (26 bp):
TAATAATATAATTTTGTTTTTTAAGG
Found at i:5461887 original size:93 final size:92
Alignment explanation
Indices: 5461716--5461900 Score: 361
Period size: 93 Copynumber: 2.0 Consensus size: 92
5461706 CATCTCATAA
5461716 CTTCATAATGTTTGTTCATCCGAGAAATTCCTTGAAACTTTAAGATTCTACAAAATCCTAGCGGT
1 CTTCATAATGTTTGTTCATCCGAGAAATTCCTTGAAACTTTAAGATTCTACAAAATCCTAGCGGT
5461781 TTCATAATTTTTGGGATGGAGCAGCGG
66 TTCATAATTTTTGGGATGGAGCAGCGG
5461808 CTTCATAATGTTTGTTCATCCGAGAAATTCCTTGAAACTTTTAAGATTCTACAAAATCCTAGCGG
1 CTTCATAATGTTTGTTCATCCGAGAAATTCCTTGAAAC-TTTAAGATTCTACAAAATCCTAGCGG
5461873 TTTCATAATTTTTGGGATGGAGCAGCGG
65 TTTCATAATTTTTGGGATGGAGCAGCGG
5461901 ATATATTCAC
Statistics
Matches: 92, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
92 38 0.41
93 54 0.59
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.35
Consensus pattern (92 bp):
CTTCATAATGTTTGTTCATCCGAGAAATTCCTTGAAACTTTAAGATTCTACAAAATCCTAGCGGT
TTCATAATTTTTGGGATGGAGCAGCGG
Found at i:5465813 original size:30 final size:31
Alignment explanation
Indices: 5465763--5465844 Score: 84
Period size: 31 Copynumber: 2.7 Consensus size: 31
5465753 CTTTACGTGA
5465763 TTATATAT-AAAT-TTAT-AAATATC-ATTATT
1 TTATATATAAAATATT-TCAAATATCAATT-TT
* *
5465792 TT-TATGTGAAATATTTCAAATATCAATTTT
1 TTATATATAAAATATTTCAAATATCAATTTT
*
5465822 TTATATATAAAATATTTTAAATA
1 TTATATATAAAATATTTCAAATA
5465845 ATTACTTCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
28 4 0.09
29 7 0.16
30 13 0.30
31 20 0.45
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (31 bp):
TTATATATAAAATATTTCAAATATCAATTTT
Found at i:5475489 original size:12 final size:12
Alignment explanation
Indices: 5475472--5475503 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
5475462 GATGGATCCT
5475472 GATGAAGTGGAA
1 GATGAAGTGGAA
5475484 GATGAAGTGGAA
1 GATGAAGTGGAA
5475496 GATGAAGT
1 GATGAAGT
5475504 AGAGGAAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.41, T:0.19
Consensus pattern (12 bp):
GATGAAGTGGAA
Found at i:5480881 original size:5 final size:5
Alignment explanation
Indices: 5480871--5480898 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
5480861 GGTTTAGAAA
5480871 TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TAT
5480899 TCTTAATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:5500209 original size:17 final size:17
Alignment explanation
Indices: 5500178--5500212 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5500168 ACTTGTGAGT
5500178 TCGATAATTTCGATTAA
1 TCGATAATTTCGATTAA
5500195 TCGAGTAATTT-GATTAA
1 TCGA-TAATTTCGATTAA
5500212 T
1 T
5500213 TATTTGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (17 bp):
TCGATAATTTCGATTAA
Found at i:5501127 original size:2 final size:2
Alignment explanation
Indices: 5501122--5501155 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5501112 GGAAAAAACC
5501122 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
5501156 AAAGAAAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5509979 original size:22 final size:24
Alignment explanation
Indices: 5509937--5509990 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
5509927 CATATTTTAT
5509937 TATAATTTTAACACAAATATAA-A
1 TATAATTTTAACACAAATATAATA
* *
5509960 TATAATTTT-ACATAAATATAATT
1 TATAATTTTAACACAAATATAATA
5509983 TATAATTT
1 TATAATTT
5509991 AATTTAGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 11 0.39
23 17 0.61
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (24 bp):
TATAATTTTAACACAAATATAATA
Found at i:5521461 original size:2 final size:2
Alignment explanation
Indices: 5521450--5521482 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5521440 TTAAATGTCC
5521450 AT AT -T 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
5521483 GTTTATTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:5525419 original size:25 final size:25
Alignment explanation
Indices: 5525368--5525444 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 25
5525358 CACTAGCGCG
* *
5525368 CTCTCTGATTAGCACTGTGTGTGCT
1 CTCTCTTATTAGCACTGTCTGTGCT
*
5525393 CTCT-GT-TTAGCAC-GTCTCGTGCT
1 CTCTCTTATTAGCACTGTCT-GTGCT
* *
5525416 CTCTGTTATTAGCACTGTGTGTGCT
1 CTCTCTTATTAGCACTGTCTGTGCT
5525441 CTCT
1 CTCT
5525445 GATCAGTACT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
22 3 0.07
23 16 0.37
24 1 0.02
25 20 0.47
26 3 0.07
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.42
Consensus pattern (25 bp):
CTCTCTTATTAGCACTGTCTGTGCT
Found at i:5525538 original size:23 final size:23
Alignment explanation
Indices: 5525367--5525587 Score: 214
Period size: 23 Copynumber: 9.5 Consensus size: 23
5525357 ACACTAGCGC
* *
5525367 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
* *
5525390 GCTCTCTGTTTAGCACGTCT-CGT
1 GCTCTCTGTTTAGCAC-TTTGTGT
*
5525413 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCACTTTGTGT
* * *
5525438 GCTCTCTGATCAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
5525461 GCTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
* * *
5525484 GCTCTCTGATCAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
*
5525507 ACTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
*
5525530 GCTCTCTGTTTCCCAGCAC-TTATGT
1 GCTCTCTGTTT---AGCACTTTGTGT
* * *
5525555 GCTCTCTGTTCAGTACTTCG-GT
1 GCTCTCTGTTTAGCACTTTGTGT
*
5525577 ACTCTCTGTTT
1 GCTCTCTGTTT
5525588 GTTCCGTTTA
Statistics
Matches: 163, Mismatches: 27, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
22 15 0.09
23 106 0.65
24 5 0.03
25 32 0.20
26 5 0.03
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.43
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTTTGTGT
Found at i:5525571 original size:71 final size:68
Alignment explanation
Indices: 5525368--5525584 Score: 247
Period size: 71 Copynumber: 3.1 Consensus size: 68
5525358 CACTAGCGCG
* * * * * *
5525368 CTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTATTAGCACTG
1 CTCTCTGATTAGCACTTTGTGTGCTCTCTGTTTAGCACTTAT-GTGCTCTCTG-T-TCAGTACTT
*
5525433 TGTGTG
63 TGTGTA
* * * *
5525439 CTCTCTGATCAGTACTTTGTGTGCTCTCTGTTTAGCACTTTGTGTGCTCTCTGATCAGTACTTTG
1 CTCTCTGATTAGCACTTTGTGTGCTCTCTGTTTAGCAC-TTATGTGCTCTCTGTTCAGTACTTTG
5525504 TGTA
65 TGTA
*
5525508 CTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTTCCCAGCACTTATGTGCTCTCTGTTCAGTACTT
1 CTCTCTGATTAGCACTTTGTGTGCTCTCTGTTT---AGCACTTATGTGCTCTCTGTTCAGTACTT
*
5525573 CG-GTA
63 TGTGTA
5525578 CTCTCTG
1 CTCTCTG
5525585 TTTGTTCCGT
Statistics
Matches: 126, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
69 41 0.33
70 10 0.08
71 68 0.54
72 7 0.06
ACGTcount: A:0.12, C:0.25, G:0.21, T:0.43
Consensus pattern (68 bp):
CTCTCTGATTAGCACTTTGTGTGCTCTCTGTTTAGCACTTATGTGCTCTCTGTTCAGTACTTTGT
GTA
Found at i:5527399 original size:43 final size:43
Alignment explanation
Indices: 5527340--5527713 Score: 269
Period size: 43 Copynumber: 8.9 Consensus size: 43
5527330 CCTTTATCCA
* * *
5527340 TGTGTGCCAATATAGATGCCTCGATTTACCCGATGATACATTG
1 TGTGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTG
* * * * *
5527383 TGCGTGTCAGTATAGATGCCTCAATATATCC-A--ATGCA-T-
1 TGTGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTG
* * * * * * *
5527421 TGTGGGCCAGTATATATGTCTCGGTTAATCTGATGATGCACTG
1 TGTGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTG
* * * **
5527464 TGTGTGCCAGTATTGTTGTCTCGATTTACTTGATGATGCACTG
1 TGTGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTG
** * * *
5527507 TGTGTGGTAGTATATATGCCTCGGTTTACCCGATAATGCAC--
1 TGTGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTG
* *** * * *
5527548 TGTGTGCCAGTATGGATGCCTATTTTTACCTGATAATGCACTA
1 TGTGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTG
* * *
5527591 TATGTGCCAGTATAGATACCTCGATTTACCCGATGATACACTG
1 TGTGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTG
* * * * * *
5527634 TGTGTACCAGCATAAATGCTTC-AGTTTATCCGATAATGCACTG
1 TGTGTGCCAGTATAGATGCCTCGA-TTTACCCGATGATGCACTG
* * * * *
5527677 TGTGTACCAGTATAGATGCTTCGGTTTATCAGATGAT
1 TGTGTGCCAGTATAGATGCCTCGATTTACCCGATGAT
5527714 CCCTCGGTTT
Statistics
Matches: 255, Mismatches: 67, Indels: 18
0.75 0.20 0.05
Matches are distributed among these distances:
38 21 0.08
39 2 0.01
40 4 0.02
41 38 0.15
42 3 0.01
43 187 0.73
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (43 bp):
TGTGTGCCAGTATAGATGCCTCGATTTACCCGATGATGCACTG
Found at i:5527597 original size:127 final size:128
Alignment explanation
Indices: 5527342--5527695 Score: 313
Period size: 127 Copynumber: 2.8 Consensus size: 128
5527332 TTTATCCATG
* * * * ** * * *
5527342 TGTGCCAATATAGATGCCTCGATTTACCCGATGATACATTGTGCGTGTCAGTATAGATGCCTCAA
1 TGTGCCAGTATAGATACCTCGATTTACCCGATGATACACTGTGTGTACCAGCATAAATGCCTCAG
* * * * * * *** * * * * *
5527407 TATATCC---AATGCATTGTG-GGCCAGTATATATGTCTCGGTTAATCTGATGATGCACTGTG
66 TTTACCCGATAATGCACTGTGTGACCAGTATAGATGCCTATTTTTACCTGATAATGCACTATA
* * ** ** * *** * * *
5527466 TGTGCCAGTATTGTTGTCTCGATTTACTTGATGATGCACTGTGTGTGGTAGTATATATGCCTCGG
1 TGTGCCAGTATAGATACCTCGATTTACCCGATGATACACTGTGTGTACCAGCATAAATGCCTCAG
*
5527531 TTTACCCGATAATGCACTGTGTG-CCAGTATGGATGCCTATTTTTACCTGATAATGCACTATA
66 TTTACCCGATAATGCACTGTGTGACCAGTATAGATGCCTATTTTTACCTGATAATGCACTATA
*
5527593 TGTGCCAGTATAGATACCTCGATTTACCCGATGATACACTGTGTGTACCAGCATAAATGCTTCAG
1 TGTGCCAGTATAGATACCTCGATTTACCCGATGATACACTGTGTGTACCAGCATAAATGCCTCAG
*
5527658 TTTATCCGATAATGCACTGTGTGTACCAGTATAGATGC
66 TTTACCCGATAATGCACTGTGTG-ACCAGTATAGATGC
5527696 TTCGGTTTAT
Statistics
Matches: 180, Mismatches: 44, Indels: 7
0.78 0.19 0.03
Matches are distributed among these distances:
124 56 0.31
127 111 0.62
128 1 0.01
129 12 0.07
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.34
Consensus pattern (128 bp):
TGTGCCAGTATAGATACCTCGATTTACCCGATGATACACTGTGTGTACCAGCATAAATGCCTCAG
TTTACCCGATAATGCACTGTGTGACCAGTATAGATGCCTATTTTTACCTGATAATGCACTATA
Found at i:5527768 original size:43 final size:43
Alignment explanation
Indices: 5527715--5527999 Score: 245
Period size: 43 Copynumber: 6.7 Consensus size: 43
5527705 TCAGATGATC
* * *
5527715 CCTCGGTTTACCTGATGATGCACTGTGTGTGCTAGTATAGATG
1 CCTCAGTTTACCTAATGATGCACTGTGTGTGCCAGTATAGATG
* * * *
5527758 CCTCAGTTTACCTGATGATTCACTGTGTGTTCCAGTATATATG
1 CCTCAGTTTACCTAATGATGCACTGTGTGTGCCAGTATAGATG
* * * *
5527801 CCTCGGTTAATCC-AATGATGCATTGTGTGCGCCAGTATAGATG
1 CCTCAGTTTA-CCTAATGATGCACTGTGTGTGCCAGTATAGATG
* * * *
5527844 TCTC-GATTTACCCAATGATGCACTGTGTGTGCCAGTATAAATA
1 CCTCAG-TTTACCTAATGATGCACTGTGTGTGCCAGTATAGATG
* * *
5527887 CCTC-GATTTACCCAATAATGCACTGTGTGTGCCAGTATAAATG
1 CCTCAG-TTTACCTAATGATGCACTGTGTGTGCCAGTATAGATG
** * * * * * * *
5527930 TGTCAATTTACTTGATGATACATTGTATGTG-TAGTATAGATG
1 CCTCAGTTTACCTAATGATGCACTGTGTGTGCCAGTATAGATG
* * *
5527972 CCTCAATTTACCTTATTATGCACTGTGT
1 CCTCAGTTTACCTAATGATGCACTGTGT
5528000 ACCAACATAA
Statistics
Matches: 196, Mismatches: 42, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
42 32 0.16
43 162 0.83
44 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (43 bp):
CCTCAGTTTACCTAATGATGCACTGTGTGTGCCAGTATAGATG
Found at i:5527794 original size:106 final size:106
Alignment explanation
Indices: 5527609--5527808 Score: 267
Period size: 106 Copynumber: 1.9 Consensus size: 106
5527599 AGTATAGATA
*
5527609 CCTCGATTTACCCGATGATACACTGTGTGTACCAGCATAAATGCTTCAGTTTATCCGATAATGCA
1 CCTCGATTTACCCGATGATACACTGTGTGTACCAGCATAAATGCCTCAGTTTATCCGATAATGCA
*
5527674 CTGTGTGTACCAGTATAGATGCTTCGGTTTATCAGATGATC
66 CTGTGTGTACCAGTATAGATGCCTCGGTTTATCAGATGATC
* * * * * * * * *
5527715 CCTCGGTTTACCTGATGATGCACTGTGTGTGCTAGTATAGATGCCTCAGTTTA-CCTGATGATTC
1 CCTCGATTTACCCGATGATACACTGTGTGTACCAGCATAAATGCCTCAGTTTATCC-GATAATGC
* *
5527779 ACTGTGTGTTCCAGTATATATGCCTCGGTT
65 ACTGTGTGTACCAGTATAGATGCCTCGGTT
5527809 AATCCAATGA
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
105 2 0.03
106 78 0.98
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.35
Consensus pattern (106 bp):
CCTCGATTTACCCGATGATACACTGTGTGTACCAGCATAAATGCCTCAGTTTATCCGATAATGCA
CTGTGTGTACCAGTATAGATGCCTCGGTTTATCAGATGATC
Found at i:5527842 original size:149 final size:149
Alignment explanation
Indices: 5527572--5527843 Score: 366
Period size: 149 Copynumber: 1.8 Consensus size: 149
5527562 GATGCCTATT
5527572 TTTACCTGATAATGCACTATATGTGCCAGTATAGATACCTCGATTTACCCGATGATACACTGTGT
1 TTTACCTGATAATGCACTATATGTGCCAGTATAGATACCTCGATTTACCCGATGATACACTGTGT
* * * *
5527637 GTACCAGCATAAATGCTTCAGTTTATCCGATAATGCACTGTGTGTACCAGTATAGATGCTTCGGT
66 GTACCAGCATAAATGCCTCAGTTAATCCAATAATGCACTGTGTGCACCAGTATAGATGCTTCGGT
5527702 TTATCAGATGATCCCTCGG
131 TTATCAGATGATCCCTCGG
* * * * * * *
5527721 TTTACCTGATGATGCACTGTGTGTGCTAGTATAGATGCCTC-AGTTTACCTGATGATTCACTGTG
1 TTTACCTGATAATGCACTATATGTGCCAGTATAGATACCTCGA-TTTACCCGATGATACACTGTG
* * * * * * *
5527785 TGTTCCAGTATATATGCCTCGGTTAATCCAATGATGCATTGTGTGCGCCAGTATAGATG
65 TGTACCAGCATAAATGCCTCAGTTAATCCAATAATGCACTGTGTGCACCAGTATAGATG
5527844 TCTCGATTTA
Statistics
Matches: 104, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
148 1 0.01
149 103 0.99
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.34
Consensus pattern (149 bp):
TTTACCTGATAATGCACTATATGTGCCAGTATAGATACCTCGATTTACCCGATGATACACTGTGT
GTACCAGCATAAATGCCTCAGTTAATCCAATAATGCACTGTGTGCACCAGTATAGATGCTTCGGT
TTATCAGATGATCCCTCGG
Found at i:5527948 original size:86 final size:86
Alignment explanation
Indices: 5527732--5527999 Score: 277
Period size: 86 Copynumber: 3.1 Consensus size: 86
5527722 TTACCTGATG
* * * * *
5527732 ATGCACTGTGTGTGCTAGTATAGATGCCTCAGTTTACCTGATGATTCACTGTGTGTTCCAGTATA
1 ATGCACTGTGTGTGCCAGTATAGATGTCTCAATTTACCTGATGATACACTGTGTGTGCCAGTATA
* * * * *
5527797 TATGCCTCGGTTAATCCAATG
66 AATGCCTCGATTTACCCAATA
* * * ** *
5527818 ATGCATTGTGTGCGCCAGTATAGATGTCTCGATTTACCCAATGATGCACTGTGTGTGCCAGTATA
1 ATGCACTGTGTGTGCCAGTATAGATGTCTCAATTTACCTGATGATACACTGTGTGTGCCAGTATA
*
5527883 AATACCTCGATTTACCCAATA
66 AATGCCTCGATTTACCCAATA
* * * * * *
5527904 ATGCACTGTGTGTGCCAGTATAAATGTGTCAATTTACTTGATGATACATTGTATGTG-TAGTATA
1 ATGCACTGTGTGTGCCAGTATAGATGTCTCAATTTACCTGATGATACACTGTGTGTGCCAGTATA
* * ** *
5527968 GATGCCTCAATTTACCTTATT
66 AATGCCTCGATTTACCCAATA
5527989 ATGCACTGTGT
1 ATGCACTGTGT
5528000 ACCAACATAA
Statistics
Matches: 148, Mismatches: 34, Indels: 1
0.81 0.19 0.01
Matches are distributed among these distances:
85 32 0.22
86 116 0.78
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.36
Consensus pattern (86 bp):
ATGCACTGTGTGTGCCAGTATAGATGTCTCAATTTACCTGATGATACACTGTGTGTGCCAGTATA
AATGCCTCGATTTACCCAATA
Found at i:5528251 original size:41 final size:41
Alignment explanation
Indices: 5528206--5528343 Score: 125
Period size: 41 Copynumber: 3.3 Consensus size: 41
5528196 AATATTTTGG
*
5528206 TTTACCCGATGATATATTGTATGCCAGTATAGATGCCTCGA
1 TTTACCCGATGATATATTGTGTGCCAGTATAGATGCCTCGA
* ** * * * * *
5528247 TTTACCCAAAAATACACTGTGTGTCAGTATAAATACCTCGA
1 TTTACCCGATGATATATTGTGTGCCAGTATAGATGCCTCGA
* * * *
5528288 TTTACCTGATGTTGTATTGTGGGTGCCAATATAGATGCCTC-A
1 TTTACCCGATGATATATTGT--GTGCCAGTATAGATGCCTCGA
5528330 GTTTACCCGATGAT
1 -TTTACCCGATGAT
5528344 GCATTATGTG
Statistics
Matches: 71, Mismatches: 23, Indels: 4
0.72 0.23 0.04
Matches are distributed among these distances:
41 44 0.62
42 1 0.01
43 26 0.37
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (41 bp):
TTTACCCGATGATATATTGTGTGCCAGTATAGATGCCTCGA
Found at i:5528315 original size:84 final size:84
Alignment explanation
Indices: 5528227--5528418 Score: 210
Period size: 84 Copynumber: 2.3 Consensus size: 84
5528217 ATATATTGTA
* * *
5528227 TGCCAGTATAGATGCCTC-GATTTACCCAAAAATACACTGTGTGTCAGTATAAATACCTCGATTT
1 TGCCAGTATAGATGCCTCAG-TTTACCCAAAAATACACTATGTGTCAGCATAAATACCTCGACTT
*
5528291 A-CCTGATGT-TGTATTGTGGG
65 ATCC-GAT-TATGCATTGTGGG
* * ** * * * *
5528311 TGCCAATATAGATGCCTCAGTTTACCCGATGATGCATTATGTGTCAGCATAAATACTTCGGCTTA
1 TGCCAGTATAGATGCCTCAGTTTACCCAAAAATACACTATGTGTCAGCATAAATACCTCGACTTA
*
5528376 TCCGATTATGCATTGTGTG
66 TCCGATTATGCATTGTGGG
*
5528395 TGCCAGTATAGATGCTTCAGTTTA
1 TGCCAGTATAGATGCCTCAGTTTA
5528419 TCAGATGATG
Statistics
Matches: 90, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
83 1 0.01
84 86 0.96
85 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.34
Consensus pattern (84 bp):
TGCCAGTATAGATGCCTCAGTTTACCCAAAAATACACTATGTGTCAGCATAAATACCTCGACTTA
TCCGATTATGCATTGTGGG
Found at i:5528473 original size:43 final size:43
Alignment explanation
Indices: 5528425--5528654 Score: 250
Period size: 43 Copynumber: 5.3 Consensus size: 43
5528415 TTTATCAGAT
* *
5528425 GATGCCTCGATTTACTCGATGATGCACTCTGTATGCCAGTATA
1 GATGCCTCGATTTACTCGATGATTCACTCTGTGTGCCAGTATA
* * * * * *
5528468 GATGCCTCAATTTACCCAATGATGCACTGTGTGTGCGAGTATA
1 GATGCCTCGATTTACTCGATGATTCACTCTGTGTGCCAGTATA
** *
5528511 GATGTTTC-ATTTTTCTCGATGATTCACTGC-GTGTGCCAGTATA
1 GATGCCTCGA-TTTACTCGATGATTCACT-CTGTGTGCCAGTATA
* * * * *
5528554 AATACCTCGATTTACCCGATGATTCAC-CGTGTGTGACAGTATG
1 GATGCCTCGATTTACTCGATGATTCACTC-TGTGTGCCAGTATA
* *
5528597 GATGCCTCGATTTACTCGATGATTCACTGTGTGTGCCAATATA
1 GATGCCTCGATTTACTCGATGATTCACTCTGTGTGCCAGTATA
5528640 GATGCCTCGATTTAC
1 GATGCCTCGATTTAC
5528655 CTGATATATG
Statistics
Matches: 152, Mismatches: 29, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 149 0.98
44 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (43 bp):
GATGCCTCGATTTACTCGATGATTCACTCTGTGTGCCAGTATA
Found at i:5528586 original size:86 final size:86
Alignment explanation
Indices: 5528425--5528655 Score: 288
Period size: 86 Copynumber: 2.7 Consensus size: 86
5528415 TTTATCAGAT
* * *
5528425 GATGCCTCGATTTACTCGATGATGCACT-CTGTATGCCAGTATAGATGCCTCAATTTACCCAATG
1 GATGCCTCGATTTACTCGATGATTCACTGC-GTGTGCCAGTATAGATGCCTCGATTTACCCAATG
*
5528489 ATGCACTGTGTGTG-CGAGTATA
65 ATGCACCGTGTGTGAC-AGTATA
** * * * *
5528511 GATGTTTC-ATTTTTCTCGATGATTCACTGCGTGTGCCAGTATAAATACCTCGATTTACCCGATG
1 GATGCCTCGA-TTTACTCGATGATTCACTGCGTGTGCCAGTATAGATGCCTCGATTTACCCAATG
* *
5528575 ATTCACCGTGTGTGACAGTATG
65 ATGCACCGTGTGTGACAGTATA
* *
5528597 GATGCCTCGATTTACTCGATGATTCACTGTGTGTGCCAATATAGATGCCTCGATTTACC
1 GATGCCTCGATTTACTCGATGATTCACTGCGTGTGCCAGTATAGATGCCTCGATTTACC
5528656 TGATATATGT
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
85 1 0.01
86 118 0.97
87 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (86 bp):
GATGCCTCGATTTACTCGATGATTCACTGCGTGTGCCAGTATAGATGCCTCGATTTACCCAATGA
TGCACCGTGTGTGACAGTATA
Found at i:5528815 original size:43 final size:43
Alignment explanation
Indices: 5528703--5529358 Score: 436
Period size: 43 Copynumber: 15.4 Consensus size: 43
5528693 TCCGATGATA
* ** *
5528703 CCTCGATTTACCCGATGATTCACTGTGTTTGTTAG-A-AAGATA
1 CCTCGATTTACCCGATGATTCACTGTGTGTGCCAGTATAA-ATG
* * *
5528745 CTTCGATTAACCCGATGATTCACTGTGTATGCCAGTATAAATG
1 CCTCGATTTACCCGATGATTCACTGTGTGTGCCAGTATAAATG
* * * * *
5528788 TCTCGGTTTACCCGATGATTAATTGTGTGTGCGAGTATAAATG
1 CCTCGATTTACCCGATGATTCACTGTGTGTGCCAGTATAAATG
* * * *
5528831 TCTCGATTTACCCGATAATTCACTGTGTGTGTCAGTATAAATA
1 CCTCGATTTACCCGATGATTCACTGTGTGTGCCAGTATAAATG
** * **
5528874 CCTTAATTTACCCGATGATTCACTGTGTGTTCCAGTATTGATG
1 CCTCGATTTACCCGATGATTCACTGTGTGTGCCAGTATAAATG
* * * *
5528917 CCTCGATTTACTCAATGATTCAC--TGTGTGCCAATATAAACG
1 CCTCGATTTACCCGATGATTCACTGTGTGTGCCAGTATAAATG
* * *
5528958 CCTCCG-TTTACCCGATGATTCGC--TGTGTGCCAATATTATTAT-
1 CCT-CGATTTACCCGATGATTCACTGTGTGTGCCAGTA-TA-AATG
* * ** * * * *
5529000 CTTAG-TTTACCTAATGATGCATTGTGTGTGCCAGTATAGATA
1 CCTCGATTTACCCGATGATTCACTGTGTGTGCCAGTATAAATG
* * * * *
5529042 CCTCGATTTACCTGATGATGCATTGTGTGTGCCAGTATAGATT
1 CCTCGATTTACCCGATGATTCACTGTGTGTGCCAGTATAAATG
* * * * *
5529085 CTTCGATTTACCCTATGATGCACTGTGTGTGCTAGTAT-AGTG
1 CCTCGATTTACCCGATGATTCACTGTGTGTGCCAGTATAAATG
* * * * * * *
5529127 CCTCGGTTTACCCAATAATGCAC--TGTGTGCTATTATAGATG
1 CCTCGATTTACCCGATGATTCACTGTGTGTGCCAGTATAAATG
* * * ** * *
5529168 TCTCAATTTACCCGATGATGCTTTGTGTGTGCTAGTATAGATG
1 CCTCGATTTACCCGATGATTCACTGTGTGTGCCAGTATAAATG
* * * * * *
5529211 CCTCGATTTACCCGATAATGCATTGTATGTGCCAATATAGATG
1 CCTCGATTTACCCGATGATTCACTGTGTGTGCCAGTATAAATG
* ** * ** * * *
5529254 CCACGATTTACTTGCTGATGAACTATGTGTGCTAGTATAAATC
1 CCTCGATTTACCCGATGATTCACTGTGTGTGCCAGTATAAATG
* * * * * *
5529297 CCTCGATTTACCCGATGATGCATTGTGTTTGCTAGCAAAAATG
1 CCTCGATTTACCCGATGATTCACTGTGTGTGCCAGTATAAATG
* **
5529340 CTTCGATTTATTCGATGAT
1 CCTCGATTTACCCGATGAT
5529359 GGAAGGTTAA
Statistics
Matches: 488, Mismatches: 114, Indels: 23
0.78 0.18 0.04
Matches are distributed among these distances:
40 12 0.02
41 75 0.15
42 61 0.12
43 338 0.69
44 2 0.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (43 bp):
CCTCGATTTACCCGATGATTCACTGTGTGTGCCAGTATAAATG
Found at i:5529187 original size:126 final size:128
Alignment explanation
Indices: 5529024--5529324 Score: 345
Period size: 126 Copynumber: 2.4 Consensus size: 128
5529014 TGATGCATTG
* * * *
5529024 TGTGTGCCAGTATAGATACCTCGATTTACCTGATGATGCATTGTGTGTGCCAGTATAGATTCTTC
1 TGTGTGCTAGTATAGATACCTCGATTTACCCGATGATGCATTGTGTGTGCCAGTATAGATGCCTC
* * * * * * * *
5529089 GATTTACCCTATGATGCACTGTGTGTGCTAGTATAG-TGCCTCGGTTTACCCAATAATGCAC-
66 GATTTACCCGATAATGCACTGTATGTGCCAATATAGATGCCACGATTTACCCAATAATGAACA
* ** * * *
5529150 TGTGTGCTATTATAGATGTCTCAATTTACCCGATGATGCTTTGTGTGTGCTAGTATAGATGCCTC
1 TGTGTGCTAGTATAGATACCTCGATTTACCCGATGATGCATTGTGTGTGCCAGTATAGATGCCTC
* **** *
5529215 GATTTACCCGATAATGCATTGTATGTGCCAATATAGATGCCACGATTTACTTGCTGATGAACTA
66 GATTTACCCGATAATGCACTGTATGTGCCAATATAGATGCCACGATTTACCCAATAATGAAC-A
* *
5529279 TGTGTGCTAGTATAAATCCCTCGATTTACCCGATGATGCATTGTGT
1 TGTGTGCTAGTATAGATACCTCGATTTACCCGATGATGCATTGTGT
5529325 TTGCTAGCAA
Statistics
Matches: 142, Mismatches: 30, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
126 85 0.60
127 17 0.12
129 40 0.28
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (128 bp):
TGTGTGCTAGTATAGATACCTCGATTTACCCGATGATGCATTGTGTGTGCCAGTATAGATGCCTC
GATTTACCCGATAATGCACTGTATGTGCCAATATAGATGCCACGATTTACCCAATAATGAACA
Found at i:5534230 original size:41 final size:41
Alignment explanation
Indices: 5534132--5534579 Score: 620
Period size: 41 Copynumber: 11.0 Consensus size: 41
5534122 CACAAAAACT
* *
5534132 AGAGCAATAGCGGCGCTTATAGAAAAGCGCCGCTAAAAGT-
1 AGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAGGTC
* *
5534172 GGAGCAATAGCGGCGCTTATGGTAAAGCGCCGCTAAAGGTC
1 AGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAGGTC
5534213 AGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAGGTC
1 AGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAGGTC
* * * * * *
5534254 AGATCAATAGCGGCTCTTGCT-CATAAGCACCGCT-AAGGTC
1 AGAGCAATAGCGGCGCTT-ATGGAAAAGCGCCGCTAAAGGTC
5534294 AGAGCAATAGCGGCGCTTAT-GAGAAAGCGCCGCTAAAGGTC
1 AGAGCAATAGCGGCGCTTATGGA-AAAGCGCCGCTAAAGGTC
**
5534335 AGAGCAATAGCGGCGCTTATGGTCAAGCGCCGCTAAAGGTC
1 AGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAGGTC
5534376 AGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAGGTC
1 AGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAGGTC
* * *
5534417 AGATCAATAGCGGCGCTTAT-GAGCAAGCGCCGCTAAAAGTC
1 AGAGCAATAGCGGCGCTTATGGA-AAAGCGCCGCTAAAGGTC
**
5534458 AGAGCAATAGCGGCGCTTATGGTCAAGCGCCGCTAAAGGTC
1 AGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAGGTC
* *
5534499 AGACCAATAGCGGCGCTTATGGAAAAGCGCCGCTAAATGTC
1 AGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAGGTC
* * *
5534540 ATAGCAATAGCGGCGCTTAT-GAGCAAGCTCCGCTAAAGGT
1 AGAGCAATAGCGGCGCTTATGGA-AAAGCGCCGCTAAAGGT
5534580 TAAAGCAGAA
Statistics
Matches: 363, Mismatches: 37, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
39 2 0.01
40 71 0.20
41 287 0.79
42 3 0.01
ACGTcount: A:0.30, C:0.23, G:0.29, T:0.17
Consensus pattern (41 bp):
AGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAGGTC
Found at i:5537143 original size:43 final size:43
Alignment explanation
Indices: 5537072--5537299 Score: 300
Period size: 43 Copynumber: 5.3 Consensus size: 43
5537062 TTTATTAATA
*
5537072 TTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* *
5537114 TTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAA-AGCAATGTTCT
1 TTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGA-CCATGTTCT
* * * * *
5537157 TTAGTGGCGTTTGTGTGAAAAGCGCCGCTGAAGATCATGTTCT
1 TTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* *
5537200 TTAGCGGCGTTTTT-TGAGAAAGCGCCGCTAAAGACCATATTCT
1 TTAGCGGCGTTTTTGGGA-AAAGCGCCGCTAAAGACCATGTTCT
* *
5537243 TTAGCGGCGTTTTTGTGAAAAGCGCCGCTAAAAACCATGTTCT
1 TTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGACCATGTTCT
*
5537286 ATAGCGGCGTTTTT
1 TTAGCGGCGTTTTT
5537300 TCTAATAAAC
Statistics
Matches: 163, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
42 17 0.10
43 142 0.87
44 4 0.02
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.30
Consensus pattern (43 bp):
TTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGACCATGTTCT
Found at i:5537300 original size:86 final size:86
Alignment explanation
Indices: 5537072--5537300 Score: 345
Period size: 86 Copynumber: 2.7 Consensus size: 86
5537062 TTTATTAATA
* *
5537072 TTAGCGGCGTTTGTG-GAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTTTGGGGAAAG
1 TTAGCGGCGTTTGTGTGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTTTTGAGAAAG
*
5537136 CGCCGCTAAAAGCAATGTTCT
66 CGCCGCTAAAAGCAATATTCT
* * *
5537157 TTAGTGGCGTTTGTGTGAAAAGCGCCGCTGAAGATCATGTTCTTTAGCGGCGTTTTTTGAGAAAG
1 TTAGCGGCGTTTGTGTGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTTTTGAGAAAG
*
5537222 CGCCGCT-AAAGACCATATTCT
66 CGCCGCTAAAAG-CAATATTCT
* * *
5537243 TTAGCGGCGTTTTTGTGAAAAGCGCCGCTAAAAACCATGTTCTATAGCGGCGTTTTTT
1 TTAGCGGCGTTTGTGTGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTTTT
5537301 CTAATAAACG
Statistics
Matches: 129, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
85 18 0.14
86 111 0.86
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (86 bp):
TTAGCGGCGTTTGTGTGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTTTTGAGAAAG
CGCCGCTAAAAGCAATATTCT
Found at i:5547314 original size:2 final size:2
Alignment explanation
Indices: 5547307--5547335 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5547297 TGTCTTACGT
5547307 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5547336 TCGTTTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5554345 original size:3 final size:3
Alignment explanation
Indices: 5554337--5554363 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5554327 ATGTATCATC
5554337 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
5554364 ATCATTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5556037 original size:17 final size:19
Alignment explanation
Indices: 5555992--5556037 Score: 62
Period size: 17 Copynumber: 2.5 Consensus size: 19
5555982 GTAATGGCAT
5555992 TAATAATTATGTTATTATA
1 TAATAATTATGTTATTATA
5556011 TAA-AATTTAT-TT-TTATA
1 TAATAA-TTATGTTATTATA
5556028 TAATAATTAT
1 TAATAATTAT
5556038 AAACTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 12 0.48
18 6 0.24
19 7 0.28
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
TAATAATTATGTTATTATA
Found at i:5556067 original size:20 final size:19
Alignment explanation
Indices: 5556003--5556072 Score: 52
Period size: 21 Copynumber: 3.4 Consensus size: 19
5555993 AATAATTATG
*
5556003 TTATTATATAAAATTTATTT
1 TTATTATAT-AAATATATTT
*
5556023 TTA-TATAATAATTATAAACTTT
1 TTATTAT-ATAA--ATATA-TTT
5556045 TTATTATGATAAATATATTT
1 TTATTAT-ATAAATATATTT
5556065 TTAATTAT
1 TT-ATTAT
5556073 TCAAAAGATA
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
19 5 0.12
20 10 0.25
21 12 0.30
22 6 0.15
23 7 0.17
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (19 bp):
TTATTATATAAATATATTT
Found at i:5562651 original size:27 final size:27
Alignment explanation
Indices: 5562607--5562675 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 27
5562597 ATTTCATGTA
*
5562607 TTATTATATTAATTA-TTTAAATATAAT
1 TTATTATATTAATAATTTTAAA-ATAAT
*
5562634 TTATTATATTTAA-AATTTTAAAATATT
1 TTATTATA-TTAATAATTTTAAAATAAT
5562661 TTATGTACTATTAAT
1 TTAT-TA-TATTAAT
5562676 TTTACAAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
27 17 0.49
28 16 0.46
29 2 0.06
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (27 bp):
TTATTATATTAATAATTTTAAAATAAT
Found at i:5564156 original size:19 final size:19
Alignment explanation
Indices: 5564127--5564187 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
5564117 TATTATGTAT
5564127 TATTATTAAATTTTAAATTA
1 TATT-TTAAATTTTAAATTA
*
5564147 TATTTTAAATTATT-TATTA
1 TATTTTAAATT-TTAAATTA
* *
5564166 TATGTT-ATTTTTAAATATA
1 TATTTTAAATTTTAAAT-TA
5564185 TAT
1 TAT
5564188 CTATATTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
17 2 0.06
18 5 0.15
19 21 0.62
20 6 0.18
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
TATTTTAAATTTTAAATTA
Found at i:5564192 original size:25 final size:26
Alignment explanation
Indices: 5564144--5564193 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
5564134 AAATTTTAAA
*
5564144 TTATATTTTAAATTATTTATTATATG
1 TTATATTTTAAATTATATATTATATG
5564170 TTAT-TTTTAAA-TATATATCTATAT
1 TTATATTTTAAATTATATAT-TATAT
5564194 TTAAAATTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 6 0.27
25 12 0.55
26 4 0.18
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (26 bp):
TTATATTTTAAATTATATATTATATG
Found at i:5565338 original size:35 final size:35
Alignment explanation
Indices: 5565299--5565367 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
5565289 ACACAAATTT
* * *
5565299 TAAAAGATTGCTTGCAAGT-AAAGTTAAACAAAATC
1 TAAAAGAATACTTACAAGTCAAA-TTAAACAAAATC
5565334 TAAAAGAATACTTACAAGTCAAATTAAACAAAAT
1 TAAAAGAATACTTACAAGTCAAATTAAACAAAAT
5565368 ATATTATCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 27 0.90
36 3 0.10
ACGTcount: A:0.54, C:0.12, G:0.10, T:0.25
Consensus pattern (35 bp):
TAAAAGAATACTTACAAGTCAAATTAAACAAAATC
Found at i:5580333 original size:31 final size:31
Alignment explanation
Indices: 5580293--5580363 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
5580283 ATTTTTAGAA
*
5580293 AATTAAATATAATAATAAAT-GTGATTTAAAT
1 AATTTAATATAATAATAAATGGT-ATTTAAAT
* * *
5580324 AGTTTAATATAATACTAAGTGGTATTTAAAT
1 AATTTAATATAATAATAAATGGTATTTAAAT
5580355 AATTTAATA
1 AATTTAATA
5580364 CATTGATCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 32 0.94
32 2 0.06
ACGTcount: A:0.49, C:0.01, G:0.08, T:0.41
Consensus pattern (31 bp):
AATTTAATATAATAATAAATGGTATTTAAAT
Found at i:5583716 original size:6 final size:6
Alignment explanation
Indices: 5583707--5583742 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
5583697 ATGAAAAGTA
5583707 AAAAAG AAAAAG AAAAAG AAAAAAG AAAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG -AAAAAG -AAAAAG AAAA
5583743 GCATAAACGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 16 0.55
7 13 0.45
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:5583716 original size:7 final size:7
Alignment explanation
Indices: 5583700--5583742 Score: 63
Period size: 7 Copynumber: 6.3 Consensus size: 7
5583690 ACGAGAAATG
5583700 AAAAGTAA
1 AAAAG-AA
5583708 AAAAG-A
1 AAAAGAA
5583714 AAAAG-A
1 AAAAGAA
5583720 AAAAGAA
1 AAAAGAA
5583727 AAAAGAA
1 AAAAGAA
5583734 AAAAGAA
1 AAAAGAA
5583741 AA
1 AA
5583743 GCATAAACGT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
6 12 0.35
7 17 0.50
8 5 0.15
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (7 bp):
AAAAGAA
Found at i:5583729 original size:20 final size:20
Alignment explanation
Indices: 5583700--5583742 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
5583690 ACGAGAAATG
5583700 AAAAGTAAAAAAG-AAAAAGA
1 AAAAG-AAAAAAGAAAAAAGA
5583720 AAAAGAAAAAAGAAAAAAGA
1 AAAAGAAAAAAGAAAAAAGA
5583740 AAA
1 AAA
5583743 GCATAAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (20 bp):
AAAAGAAAAAAGAAAAAAGA
Found at i:5583743 original size:19 final size:19
Alignment explanation
Indices: 5583699--5583743 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 19
5583689 CACGAGAAAT
5583699 GAAAAGTAAAAAAGAAAAA
1 GAAAAGTAAAAAAGAAAAA
5583718 GAAAAAG-AAAAAAGAAAAAA
1 G-AAAAGTAAAAAAG-AAAAA
5583738 GAAAAG
1 GAAAAG
5583744 CATAAACGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (19 bp):
GAAAAGTAAAAAAGAAAAA
Found at i:5585748 original size:2 final size:2
Alignment explanation
Indices: 5585741--5585775 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5585731 AGCACTGATG
5585741 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5585776 AACAGTGAAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5590895 original size:17 final size:18
Alignment explanation
Indices: 5590870--5590913 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
5590860 TTTATTTAAT
5590870 AATAC-TTTTATCTCAAA
1 AATACTTTTTATCTCAAA
*
5590887 AATATTTTTTATCTCAAA
1 AATACTTTTTATCTCAAA
5590905 AATACTTTT
1 AATACTTTT
5590914 GAAAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.48
Consensus pattern (18 bp):
AATACTTTTTATCTCAAA
Found at i:5602000 original size:17 final size:17
Alignment explanation
Indices: 5601978--5602037 Score: 111
Period size: 17 Copynumber: 3.5 Consensus size: 17
5601968 TTCCCATCTT
5601978 TGCGCAGAAAATTGTAG
1 TGCGCAGAAAATTGTAG
5601995 TGCGCAGAAAATTGTAG
1 TGCGCAGAAAATTGTAG
5602012 TGCGCAGAAAATTGTAG
1 TGCGCAGAAAATTGTAG
*
5602029 TGCACAGAA
1 TGCGCAGAA
5602038 GGATCATTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.37, C:0.13, G:0.28, T:0.22
Consensus pattern (17 bp):
TGCGCAGAAAATTGTAG
Found at i:5607887 original size:3 final size:3
Alignment explanation
Indices: 5607879--5607903 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5607869 ATTTTGACAG
5607879 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
5607904 GTCTAAGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5609741 original size:29 final size:30
Alignment explanation
Indices: 5609707--5609764 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
5609697 TCTTTGTAAA
* *
5609707 TATAAATTTAAATTTTAAAA-ATTATTATT
1 TATAAATTTAAATTCTAAAATACTATTATT
5609736 TATAAATTTAAATTCTAAAATACTATTAT
1 TATAAATTTAAATTCTAAAATACTATTAT
5609765 GCATTATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (30 bp):
TATAAATTTAAATTCTAAAATACTATTATT
Found at i:5614248 original size:34 final size:35
Alignment explanation
Indices: 5614209--5614279 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 35
5614199 ATTTTACATT
5614209 GATGATGTGCTTGAGCGG-AAAAAAAGGAAGGATA
1 GATGATGTGCTTGAGCGGAAAAAAAAGGAAGGATA
5614243 GATGATGTGCTTGAGCGGAAAAAAAAGGAAGGATA
1 GATGATGTGCTTGAGCGGAAAAAAAAGGAAGGATA
5614278 GA
1 GA
5614280 ATGAGAGAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 18 0.50
35 18 0.50
ACGTcount: A:0.42, C:0.06, G:0.35, T:0.17
Consensus pattern (35 bp):
GATGATGTGCTTGAGCGGAAAAAAAAGGAAGGATA
Done.