Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008689.1 Hibiscus syriacus cultivar Beakdansim tig00111715_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 959342
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 1 of 4
Found at i:1582 original size:29 final size:29
Alignment explanation
Indices: 1548--1606 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1538 CCTAAATTAA
1548 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1577 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1606 T
1 T
1607 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:7614 original size:3 final size:3
Alignment explanation
Indices: 7606--7634 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
7596 GGTTAGCTTT
7606 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
7635 TTAAATCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:12643 original size:2 final size:2
Alignment explanation
Indices: 12636--12667 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12626 TTTTATTAGA
12636 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12668 TAACAATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15562 original size:46 final size:46
Alignment explanation
Indices: 15484--15678 Score: 277
Period size: 46 Copynumber: 4.3 Consensus size: 46
15474 GCATATCCAA
* *
15484 TATTTTACC-ATATACTTACCA-TTCATTCCATAAGCTCGTAAACT
1 TATTTTACCAATATACTTACCATTTAATACCATAAGCTCGTAAACT
* * * * * *
15528 TATTTAACCAATTTACTTATCGTTTAATCCCATAAGCTCGTAAGCT
1 TATTTTACCAATATACTTACCATTTAATACCATAAGCTCGTAAACT
*
15574 TATTTTACCAATATACTTACCATTTAATACCATAAGCTCGTAAGCT
1 TATTTTACCAATATACTTACCATTTAATACCATAAGCTCGTAAACT
* *
15620 TATTTTATCAATATACTTACCATTAAATACCATAAGCTCGTAAACT
1 TATTTTACCAATATACTTACCATTTAATACCATAAGCTCGTAAACT
15666 TATTTTACCAATA
1 TATTTTACCAATA
15679 AACCATAAAC
Statistics
Matches: 133, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
44 8 0.06
45 9 0.07
46 116 0.87
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.38
Consensus pattern (46 bp):
TATTTTACCAATATACTTACCATTTAATACCATAAGCTCGTAAACT
Found at i:15882 original size:59 final size:59
Alignment explanation
Indices: 15788--15908 Score: 170
Period size: 59 Copynumber: 2.1 Consensus size: 59
15778 CAATCCTGAG
* * **
15788 TATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAGTCCCGAA
1 TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAGTCCCGAA
* ** *
15847 TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTATTCCCGAA
1 TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAGTCCCGAA
15906 TAT
1 TAT
15909 ACAGCCTGCT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (59 bp):
TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAGTCCCGAA
Found at i:16901 original size:30 final size:31
Alignment explanation
Indices: 16843--16901 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
16833 ACAACCATTA
** *
16843 TCAACTTTTTCCAAAATTATGAATTGGTCCC
1 TCAACTTTTTCCAAAATTACAAAATGGTCCC
*
16874 TCAACTTTTT-GAAAATTACAAAATGGTC
1 TCAACTTTTTCCAAAATTACAAAATGGTC
16902 TCCAAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (31 bp):
TCAACTTTTTCCAAAATTACAAAATGGTCCC
Found at i:21372 original size:13 final size:13
Alignment explanation
Indices: 21339--21365 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
21329 GCGGTGCGGC
21339 TAGCAGAGCCGTT
1 TAGCAGAGCCGTT
21352 TAGCAGAGCCGTT
1 TAGCAGAGCCGTT
21365 T
1 T
21366 CTCAGAGGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.26
Consensus pattern (13 bp):
TAGCAGAGCCGTT
Found at i:28226 original size:21 final size:20
Alignment explanation
Indices: 28202--28300 Score: 85
Period size: 21 Copynumber: 4.8 Consensus size: 20
28192 CATATTCGCA
28202 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTT-GCG
** *
28223 TTGCGATTTTCCAAATT-CG
1 TTGCGATAGTCCAAGTTGCG
* *
28242 TTGCGATAATCCAAGTTTGCT
1 TTGCGATAGTCCAAG-TTGCG
* *
28263 TTGCGATTTATTCCAAATT-CG
1 TTGCGA--TAGTCCAAGTTGCG
28284 TTGCGATAGTCCAAGTT
1 TTGCGATAGTCCAAGTT
28301 TACAAATTCG
Statistics
Matches: 62, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
19 23 0.37
20 2 0.03
21 28 0.45
22 2 0.03
23 7 0.11
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCCAAGTTGCG
Found at i:28245 original size:19 final size:19
Alignment explanation
Indices: 28221--28290 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
28211 TCCAAGTTCG
28221 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
** *
28240 CGTTGCGATAATCCAAGTTT
1 CGTTGCGATTTTCCAA-ATT
*
28260 GCTTTGCGATTTATTCCAAATT
1 -CGTTGCGA-TT-TTCCAAATT
28282 CGTTGCGAT
1 CGTTGCGAT
28291 AGTCCAAGTT
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
19 14 0.36
20 3 0.08
21 14 0.36
22 3 0.08
23 5 0.13
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (19 bp):
CGTTGCGATTTTCCAAATT
Found at i:28255 original size:40 final size:42
Alignment explanation
Indices: 28202--28300 Score: 157
Period size: 42 Copynumber: 2.4 Consensus size: 42
28192 CATATTCGCA
28202 TTGCGATAGTCCAAGTTCGCGTTGCGA-TT-TTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* * *
28242 TTGCGATAATCCAAGTTTGCTTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
28284 TTGCGATAGTCCAAGTT
1 TTGCGATAGTCCAAGTT
28301 TACAAATTCG
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
40 24 0.45
41 2 0.04
42 27 0.51
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.37
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:28445 original size:6 final size:6
Alignment explanation
Indices: 28434--28472 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
28424 AGACATGTAT
*
28434 GACCAC GACCAC GACCAC GACCAC GATCAC GACC-C GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC
28473 CGAGACGGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.31, C:0.49, G:0.18, T:0.03
Consensus pattern (6 bp):
GACCAC
Found at i:29522 original size:21 final size:21
Alignment explanation
Indices: 29496--29540 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
29486 AATTTGGAAT
*
29496 ACGCAAACTTGGACTATCGCA
1 ACGCAAACTTAGACTATCGCA
29517 ACGCAAACTTAGACTATCGCA
1 ACGCAAACTTAGACTATCGCA
29538 ACG
1 ACG
29541 AATTTGGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.29, G:0.18, T:0.18
Consensus pattern (21 bp):
ACGCAAACTTAGACTATCGCA
Found at i:30490 original size:19 final size:18
Alignment explanation
Indices: 30463--30529 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 18
30453 TATTATTTTT
30463 TATTAATATATTTATGTAAA
1 TATT-ATATATTTAT-TAAA
*
30483 TATTATATTTTTATTAAA
1 TATTATATATTTATTAAA
*
30501 -A-TA-ATATTTATATAAT
1 TATTATATATTTAT-TAAA
*
30517 TATTATTTATTTA
1 TATTATATATTTA
30530 GAATTATTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
15 7 0.18
16 5 0.13
17 2 0.05
18 6 0.15
19 15 0.38
20 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (18 bp):
TATTATATATTTATTAAA
Found at i:30497 original size:31 final size:32
Alignment explanation
Indices: 30453--30529 Score: 95
Period size: 34 Copynumber: 2.4 Consensus size: 32
30443 TTTAAATAGT
*
30453 TATTATTTTTTATT-AAT-ATATTTATGTAAA
1 TATTATTTTTTATTAAATAATATTTATATAAA
*
30483 TATTATATTTTTATTAAAATAATATTTATATAAT
1 TATTAT-TTTTTATT-AAATAATATTTATATAAA
30517 TATTATTTATTTA
1 TATTATTT-TTTA
30530 GAATTATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
30 6 0.15
31 8 0.20
33 5 0.12
34 21 0.52
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (32 bp):
TATTATTTTTTATTAAATAATATTTATATAAA
Found at i:30691 original size:17 final size:17
Alignment explanation
Indices: 30669--30722 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
30659 AATGTTAATA
30669 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
30686 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
30703 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
30720 TTT
1 TTT
30723 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:32277 original size:21 final size:21
Alignment explanation
Indices: 32247--32294 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
32237 GCAGGGGTAC
* *
32247 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
32268 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
32289 ATGCCA
1 ATGCCA
32295 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:32324 original size:21 final size:21
Alignment explanation
Indices: 32298--32370 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
32288 TATGCCATCT
*
32298 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
32319 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
32340 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
32361 CCGCAGGGTT
1 CCGCAGGGTT
32371 TTATACCATA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:32952 original size:33 final size:33
Alignment explanation
Indices: 32900--32989 Score: 108
Period size: 33 Copynumber: 2.7 Consensus size: 33
32890 TTTAAAATGC
*
32900 AAATTATATTATTAGAAATTTAAAATAAAAATAA
1 AAATTATATTATT-CAAATTTAAAATAAAAATAA
* * * *
32934 AAATAATATTATTCAAATTTAAATTTAAAATAT
1 AAATTATATTATTCAAATTTAAAATAAAAATAA
*
32967 AAATTATAGTATTCGAAATTTAA
1 AAATTATATTATTC-AAATTTAA
32990 CATTAAATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
33 28 0.58
34 20 0.42
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (33 bp):
AAATTATATTATTCAAATTTAAAATAAAAATAA
Found at i:32996 original size:34 final size:33
Alignment explanation
Indices: 32891--32996 Score: 115
Period size: 34 Copynumber: 3.2 Consensus size: 33
32881 ATAAATGTTT
** *
32891 TTAAAATGCAAATTATATTATTAGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
32925 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
32957 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
32992 TTAAA
1 TTAAA
32997 TTTCAACTTA
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.42
34 31 0.52
35 1 0.02
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:36620 original size:2 final size:2
Alignment explanation
Indices: 36613--36653 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
36603 CAACAAGAAT
36613 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36654 CTCAACTCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45504 original size:21 final size:21
Alignment explanation
Indices: 45480--45525 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
45470 ATTTATTATA
45480 ATTACAAATATAATAAATATT
1 ATTACAAATATAATAAATATT
** * *
45501 ATTATGATTATTATAAATATT
1 ATTACAAATATAATAAATATT
45522 ATTA
1 ATTA
45526 TTGTATAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
ATTACAAATATAATAAATATT
Found at i:46965 original size:25 final size:25
Alignment explanation
Indices: 46936--46990 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
46926 TCTATATTTT
46936 TCTTTCCATTAACAATTTTGTATTC
1 TCTTTCCATTAACAATTTTGTATTC
*
46961 TCTTTCCATTTACAATTTTGTATTC
1 TCTTTCCATTAACAATTTTGTATTC
46986 TCTTT
1 TCTTT
46991 TGTGAAATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.20, C:0.20, G:0.04, T:0.56
Consensus pattern (25 bp):
TCTTTCCATTAACAATTTTGTATTC
Found at i:58290 original size:23 final size:24
Alignment explanation
Indices: 58264--58315 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
58254 TTTATTACTA
58264 TTATTATTATATATATTT-CAT-TT
1 TTATTATTATATAT-TTTACATGTT
58287 TTATTATTATATATTTTACATGTT
1 TTATTATTATATATTTTACATGTT
58311 TTATT
1 TTATT
58316 TTGTTTTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 3 0.11
23 17 0.63
24 7 0.26
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (24 bp):
TTATTATTATATATTTTACATGTT
Found at i:58450 original size:13 final size:13
Alignment explanation
Indices: 58411--58537 Score: 52
Period size: 13 Copynumber: 9.1 Consensus size: 13
58401 TTTTATCTAG
58411 TTATTTACTT-TTT
1 TTATTTA-TTATTT
58424 TTATTTCA-T-TTT
1 TTATTT-ATTATTT
58436 TTATTTATTATTT
1 TTATTTATTATTT
58449 TTATCTTGCATCTATATAT
1 TTAT-TT--AT-TAT-T-T
58468 TGTCA-TTATTATTT
1 T-T-ATTTATTATTT
58482 TTAATTT-TTATTCT
1 TT-ATTTATTATT-T
58496 TT-TTTATTA-TT
1 TTATTTATTATTT
*
58507 TTATTTGTCTATTTT
1 TTATTTAT-TA-TTT
58522 TTACTTTATGTATTT
1 TTA-TTTAT-TATTT
58537 T
1 T
58538 ATTCACTCTT
Statistics
Matches: 91, Mismatches: 4, Indels: 36
0.69 0.03 0.27
Matches are distributed among these distances:
11 4 0.04
12 19 0.21
13 25 0.27
14 10 0.11
15 10 0.11
16 11 0.12
17 5 0.05
18 1 0.01
19 4 0.04
20 1 0.01
21 1 0.01
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (13 bp):
TTATTTATTATTT
Found at i:60038 original size:17 final size:17
Alignment explanation
Indices: 59999--60075 Score: 57
Period size: 17 Copynumber: 4.3 Consensus size: 17
59989 ACTTACAAAC
59999 AAAATAATAA-AAAATA
1 AAAATAATAATAAAATA
**
60015 CTTAATAATAATAAAATA
1 -AAAATAATAATAAAATA
*
60033 AAAATATTACTATAATAATA
1 AAAATAATA--ATAA-AATA
**
60053 TTAATAATAAATAAAATA
1 AAAATAAT-AATAAAATA
60071 AAAAT
1 AAAAT
60076 GTATTATACT
Statistics
Matches: 45, Mismatches: 10, Indels: 9
0.70 0.16 0.14
Matches are distributed among these distances:
17 14 0.31
18 13 0.29
19 8 0.18
20 9 0.20
21 1 0.02
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAATAATAATAAAATA
Found at i:60923 original size:20 final size:21
Alignment explanation
Indices: 60877--60932 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
60867 TTGGGCCAAC
*
60877 AGTATCGATACTCTATGAGTG
1 AGTATCGATACTTTATGAGTG
*
60898 AGTATCGATACTTTGTGAGT-
1 AGTATCGATACTTTATGAGTG
60918 AGTATCGATACTTTA
1 AGTATCGATACTTTA
60933 CTCTCAAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (21 bp):
AGTATCGATACTTTATGAGTG
Found at i:76034 original size:2 final size:2
Alignment explanation
Indices: 76027--76051 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
76017 TTAAATGTTG
76027 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
76052 CTGTACGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:82402 original size:20 final size:20
Alignment explanation
Indices: 82374--82413 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
82364 TTTTATTTTT
*
82374 ATTTTATAATAATTTAATAA
1 ATTTAATAATAATTTAATAA
* *
82394 ATTTAATAATTATTTTATAA
1 ATTTAATAATAATTTAATAA
82414 TATAAACTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTAATAATAATTTAATAA
Found at i:82427 original size:30 final size:31
Alignment explanation
Indices: 82372--82434 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
82362 ATTTTTATTT
*
82372 TTATTTTATAATAATTTAATAAATTTAATAA
1 TTATTTTATAATAATTAAATAAATTTAATAA
82403 TTATTTTATAAT-A-TAAACTAAATTTAATAA
1 TTATTTTATAATAATTAAA-TAAATTTAATAA
82433 TT
1 TT
82435 TACTAAAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 3 0.10
30 15 0.50
31 12 0.40
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (31 bp):
TTATTTTATAATAATTAAATAAATTTAATAA
Found at i:82642 original size:16 final size:17
Alignment explanation
Indices: 82605--82645 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
82595 AAAAAAATTT
82605 GTTGCTCATTTAAGCTC
1 GTTGCTCATTTAAGCTC
* *
82622 ATTGCTCA-TTAAGTTC
1 GTTGCTCATTTAAGCTC
82638 GTTGCTCA
1 GTTGCTCA
82646 CCTAATTGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.41
Consensus pattern (17 bp):
GTTGCTCATTTAAGCTC
Found at i:92182 original size:13 final size:13
Alignment explanation
Indices: 92166--92190 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
92156 TTTCCGTTAA
92166 ATTTTTATTTTTT
1 ATTTTTATTTTTT
92179 ATTTTTATTTTT
1 ATTTTTATTTTT
92191 GTTCGACCAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
ATTTTTATTTTTT
Found at i:95107 original size:18 final size:16
Alignment explanation
Indices: 95084--95128 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 16
95074 AAAAAATGTT
95084 GAAAAAAAATAGCAGTTC
1 GAAAAAAAA-A-CAGTTC
*
95102 GAAAAAAAAACTGTTC
1 GAAAAAAAAACAGTTC
95118 GAAAGAAAAAA
1 GAAA-AAAAAA
95129 AAAAGACATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 9 0.36
17 7 0.28
18 9 0.36
ACGTcount: A:0.62, C:0.09, G:0.16, T:0.13
Consensus pattern (16 bp):
GAAAAAAAAACAGTTC
Found at i:95117 original size:16 final size:16
Alignment explanation
Indices: 95074--95128 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
95064 TCTCCATCAC
95074 AAAAAA-TGTT-GAAA
1 AAAAAACTGTTCGAAA
*
95088 AAAAATAGCAGTTCGAAA
1 AAAAA-A-CTGTTCGAAA
95106 AAAAAACTGTTCGAAA
1 AAAAAACTGTTCGAAA
95122 GAAAAAA
1 -AAAAAA
95129 AAAAGACATG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
14 5 0.15
15 1 0.03
16 9 0.26
17 10 0.29
18 9 0.26
ACGTcount: A:0.62, C:0.07, G:0.15, T:0.16
Consensus pattern (16 bp):
AAAAAACTGTTCGAAA
Found at i:101140 original size:12 final size:12
Alignment explanation
Indices: 101123--101154 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
101113 GGAGAAAGAA
101123 ATGATTTTTGGG
1 ATGATTTTTGGG
101135 ATGATTTTTGGG
1 ATGATTTTTGGG
101147 ATGATTTT
1 ATGATTTT
101155 GAAGCTAAAT
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:0.19, C:0.00, G:0.28, T:0.53
Consensus pattern (12 bp):
ATGATTTTTGGG
Found at i:104128 original size:26 final size:26
Alignment explanation
Indices: 104098--104188 Score: 83
Period size: 26 Copynumber: 3.3 Consensus size: 26
104088 CGTTAAGCTA
104098 ATTAAAATTTTGCTCGACTCGTGCTC
1 ATTAAAATTTTGCTCGACTCGTGCTC
* * * *
104124 GTTAAGAAAATTTATTGCTCGAGTTGTTACTC
1 ATT---AAAA-TT-TTGCTCGACTCG-TGCTC
*
104156 ATTAAAATTTTGCTCAACTCGTGCTC
1 ATTAAAATTTTGCTCGACTCGTGCTC
104182 ATTAAAA
1 ATTAAAA
104189 AAATTTGTTG
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
26 13 0.26
27 9 0.18
28 2 0.04
29 8 0.16
30 2 0.04
31 10 0.20
32 6 0.12
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (26 bp):
ATTAAAATTTTGCTCGACTCGTGCTC
Found at i:104162 original size:58 final size:58
Alignment explanation
Indices: 104098--104212 Score: 167
Period size: 58 Copynumber: 2.0 Consensus size: 58
104088 CGTTAAGCTA
* * * * *
104098 ATTAAAATTTTGCTCGACTCGTGCTCGTTAAGAAAATTTATTGCTCGAGTTGTTACTC
1 ATTAAAATTTTGCTCAACTCGTGCTCATTAAAAAAATTTATTGCTCGACTCGTTACTC
* *
104156 ATTAAAATTTTGCTCAACTCGTGCTCATTAAAAAAATTTGTTGTTCGACTCGTTACT
1 ATTAAAATTTTGCTCAACTCGTGCTCATTAAAAAAATTTATTGCTCGACTCGTTACT
104213 TAAAGCTCAT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (58 bp):
ATTAAAATTTTGCTCAACTCGTGCTCATTAAAAAAATTTATTGCTCGACTCGTTACTC
Found at i:104467 original size:14 final size:14
Alignment explanation
Indices: 104445--104501 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
104435 TTGAGTGTAG
*
104445 TTAAATAATAATTA
1 TTAATTAATAATTA
104459 TTAATTAATAATTTA
1 TTAATTAATAA-TTA
* *
104474 GTAATT-TTAATTA
1 TTAATTAATAATTA
* *
104487 TTTATTAAAAATTA
1 TTAATTAATAATTA
104501 T
1 T
104502 AGATTAAGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
13 7 0.21
14 19 0.56
15 8 0.24
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
TTAATTAATAATTA
Found at i:104562 original size:19 final size:21
Alignment explanation
Indices: 104512--104562 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 21
104502 AGATTAAGAA
* *
104512 TTTATCATATTTTTAATTATC
1 TTTATCAAATTATTAATTATC
*
104533 TATTATTAAATTATTAATT-T-
1 T-TTATCAAATTATTAATTATC
104553 TTTATCAAAT
1 TTTATCAAAT
104563 AATTTTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 8 0.32
20 1 0.04
21 2 0.08
22 14 0.56
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTATCAAATTATTAATTATC
Found at i:110142 original size:43 final size:43
Alignment explanation
Indices: 110094--110185 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
110084 CATTAGTGGT
* * * *
110094 GTTTGTATCCAAAACATCGCTAAATAACATGACTTTTTGCGGC
1 GTTTGTATCCAAAACATCACTAAATAACATAACTTTTTACGAC
* ** *
110137 GTTTGTCTCCAAAATGTCACTAAATAACCTAACTTTTTACGAC
1 GTTTGTATCCAAAACATCACTAAATAACATAACTTTTTACGAC
110180 GTTTGT
1 GTTTGT
110186 TAATGTAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (43 bp):
GTTTGTATCCAAAACATCACTAAATAACATAACTTTTTACGAC
Found at i:118055 original size:6 final size:6
Alignment explanation
Indices: 118044--118070 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
118034 AGGATGAGAT
118044 TTTTTG TTTTTG TTTTTG TTTTTG TTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTT
118071 CCGGAAAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTTTG
Found at i:118388 original size:17 final size:17
Alignment explanation
Indices: 118366--118399 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
118356 AAAGGAGTAA
118366 ACTTCGAAATTATTATT
1 ACTTCGAAATTATTATT
118383 ACTTCGAAATTATTATT
1 ACTTCGAAATTATTATT
118400 CTAAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (17 bp):
ACTTCGAAATTATTATT
Found at i:119400 original size:2 final size:2
Alignment explanation
Indices: 119393--119430 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
119383 TGTTAAAATA
119393 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
119431 GGTTAAAGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:120957 original size:16 final size:16
Alignment explanation
Indices: 120913--120965 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
120903 CTGGAATGTT
* *
120913 TCTGATGGAATTGAAA
1 TCTGAAGGAATTGGAA
120929 TCTGTGAAGGAATTGGAA
1 TC--TGAAGGAATTGGAA
*
120947 TCTGAATGAATTGGAA
1 TCTGAAGGAATTGGAA
120963 TCT
1 TCT
120966 AAATATGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 18 0.56
18 14 0.44
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.32
Consensus pattern (16 bp):
TCTGAAGGAATTGGAA
Found at i:124286 original size:22 final size:22
Alignment explanation
Indices: 124258--124303 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
124248 TGAGAGATTT
124258 ATATAAATTTTTGTCTTCGTTC
1 ATATAAATTTTTGTCTTCGTTC
*
124280 ATATAAATTTTTGTCTTTGTTC
1 ATATAAATTTTTGTCTTCGTTC
124302 AT
1 AT
124304 GGCTTCTATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.11, G:0.09, T:0.57
Consensus pattern (22 bp):
ATATAAATTTTTGTCTTCGTTC
Found at i:124536 original size:16 final size:16
Alignment explanation
Indices: 124515--124546 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
124505 ATACTTTTAA
124515 CCACTCAAATGCCAGC
1 CCACTCAAATGCCAGC
124531 CCACTCAAATGCCAGC
1 CCACTCAAATGCCAGC
124547 AGACAAGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.44, G:0.12, T:0.12
Consensus pattern (16 bp):
CCACTCAAATGCCAGC
Found at i:124958 original size:21 final size:22
Alignment explanation
Indices: 124932--124973 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
124922 TCGAATTGAG
124932 TTTTTAAATTTT-AATTTAAAA
1 TTTTTAAATTTTGAATTTAAAA
* *
124953 TTTTTAATTTTTGTATTTAAA
1 TTTTTAAATTTTGAATTTAAA
124974 GACAACCGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTTTAAATTTTGAATTTAAAA
Found at i:125173 original size:89 final size:89
Alignment explanation
Indices: 125022--125199 Score: 322
Period size: 89 Copynumber: 2.0 Consensus size: 89
125012 AAGGGTGTTA
125022 ATCCTTCATTGACCGTAACCGACTTCCGAGCCCGACATATTTCTGGTGAAACGTAAATCAGGTAA
1 ATCCTTCATTGACCGTAACCGACTTCCGAGCCCGACATATTTCTGGTGAAACGTAAATCAGGTAA
125087 GATGGTATCCGACCCACCTAAATT
66 GATGGTATCCGACCCACCTAAATT
* *
125111 ATCCTTCATTGATCGTAACCGAC-TCTCGAGCCCGACATATTTCTGGTGAAACGTAGATCAGGTA
1 ATCCTTCATTGACCGTAACCGACTTC-CGAGCCCGACATATTTCTGGTGAAACGTAAATCAGGTA
125175 AGATGGTATCCGACCCACCTAAATT
65 AGATGGTATCCGACCCACCTAAATT
125200 CGTTTTAAAA
Statistics
Matches: 86, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
88 2 0.02
89 84 0.98
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (89 bp):
ATCCTTCATTGACCGTAACCGACTTCCGAGCCCGACATATTTCTGGTGAAACGTAAATCAGGTAA
GATGGTATCCGACCCACCTAAATT
Found at i:126406 original size:3 final size:3
Alignment explanation
Indices: 126330--126387 Score: 64
Period size: 3 Copynumber: 19.0 Consensus size: 3
126320 TACTGTGTCC
* * *
126330 TCT TCTT TCT T-T TCC TCT TCGG TCT TCT CCT TCT TCT TCT TCT TCT
1 TCT TC-T TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT
126376 TCT TCT TCT TCT
1 TCT TCT TCT TCT
126388 CTCCTCCTCC
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
2 2 0.04
3 39 0.85
4 5 0.11
ACGTcount: A:0.00, C:0.34, G:0.03, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:127477 original size:21 final size:20
Alignment explanation
Indices: 127426--127477 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
127416 ATCAGTAGAG
*
127426 TATTATTTAAAATATTATTT
1 TATTATCTAAAATATTATTT
*
127446 T-TTATCAAAAATATTAATTT
1 TATTATCTAAAATATT-ATTT
127466 TATTATCTAAAA
1 TATTATCTAAAA
127478 CGAATATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 12 0.44
20 6 0.22
21 9 0.33
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTATCTAAAATATTATTT
Found at i:148035 original size:176 final size:177
Alignment explanation
Indices: 147710--148039 Score: 425
Period size: 176 Copynumber: 1.9 Consensus size: 177
147700 AGGCAAATAT
* * * * *
147710 ATAATTTTATTTTAAAATTGAAAGAGTCATAAAAAATAATAATATCTTGGAAGGGGACAAAAGAT
1 ATAATTTTATTTTAAAATTAAAAGAGTCATAAAAAATAATAATAACTTGAAAAGAGACAAAAGAT
* **
147775 AATTATAACAATTTAAAAAATATTAATGATCTAAAAATAATCAAACCATCAAAATTTAGGCAACA
66 AATTATAAAAATTTAAAAAATATTAATGATCTAAAAATAATCAAACCATCAAAATTTAAACAACA
*
147840 ATTACCTTTCAACTTTCATTGAAAGGAAAATAATTAAAGGTAAGTAC
131 ATTACCTTCCAACTTTCATTGAAAGGAAAATAATTAAAGGTAAGTAC
* * *
147887 ATAATTTTTATTTTGAAATTAAAA-AGATCATAGAAAATAATAA-AACTT-AAAAGAGACAAAGG
1 ATAA-TTTTATTTTAAAATTAAAAGAG-TCATAAAAAATAATAATAACTTGAAAAGAGACAAAAG
* * * * * *
147949 CTACTTATAAAAATTTCAAAAATATTAATGATCTAAAAGTAATTAAATCATCAAAATTTAAACAA
64 ATAATTATAAAAATTTAAAAAATATTAATGATCTAAAAATAATCAAACCATCAAAATTTAAACAA
* *
148014 CAACTT-TCTTCCAATTTTCATTGAAA
129 CAA-TTACCTTCCAACTTTCATTGAAA
148040 TAAAATGATT
Statistics
Matches: 130, Mismatches: 20, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
176 86 0.66
177 12 0.09
178 32 0.25
ACGTcount: A:0.50, C:0.10, G:0.09, T:0.31
Consensus pattern (177 bp):
ATAATTTTATTTTAAAATTAAAAGAGTCATAAAAAATAATAATAACTTGAAAAGAGACAAAAGAT
AATTATAAAAATTTAAAAAATATTAATGATCTAAAAATAATCAAACCATCAAAATTTAAACAACA
ATTACCTTCCAACTTTCATTGAAAGGAAAATAATTAAAGGTAAGTAC
Found at i:165886 original size:12 final size:12
Alignment explanation
Indices: 165871--165903 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
165861 GTACTATAGC
165871 TGTAACTAATGA
1 TGTAACTAATGA
165883 TGTAACTAATGA
1 TGTAACTAATGA
165895 TGTAACTAA
1 TGTAACTAA
165904 CTTCAACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.33
Consensus pattern (12 bp):
TGTAACTAATGA
Found at i:166267 original size:17 final size:17
Alignment explanation
Indices: 166245--166329 Score: 152
Period size: 17 Copynumber: 5.0 Consensus size: 17
166235 GTAGGCACAA
166245 CCATCATGCACAGCAGT
1 CCATCATGCACAGCAGT
166262 CCATCATGCACAGCAGT
1 CCATCATGCACAGCAGT
*
166279 CCATCATGCAAAGCAGT
1 CCATCATGCACAGCAGT
*
166296 CCATCATGCACAACAGT
1 CCATCATGCACAGCAGT
166313 CCATCATGCACAGCAGT
1 CCATCATGCACAGCAGT
166330 AGTACGTGTG
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 64 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (17 bp):
CCATCATGCACAGCAGT
Found at i:166498 original size:71 final size:70
Alignment explanation
Indices: 166370--166503 Score: 241
Period size: 71 Copynumber: 1.9 Consensus size: 70
166360 ACTTCATTCA
166370 TTCATTTACACTAACATTCCCCTTGCAACTTCAACTTCAAACCTCCTTCAAAACTCAAATTGAAC
1 TTCATTTACACTAACATTCCCCTTGCAACTTCAACTTCAAACCTCCTTCAAAACTCAAATTGAAC
166435 TAATG
66 TAATG
* *
166440 TTCATTTACACTAACATTCCCCTTGCAACCTTCAACTTCAAACCTCCTTGAAAACTCAAGTTGA
1 TTCATTTACACTAACATTCCCCTTGCAA-CTTCAACTTCAAACCTCCTTCAAAACTCAAATTGA
166504 TATATTTTAA
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
70 28 0.46
71 33 0.54
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (70 bp):
TTCATTTACACTAACATTCCCCTTGCAACTTCAACTTCAAACCTCCTTCAAAACTCAAATTGAAC
TAATG
Found at i:168116 original size:16 final size:16
Alignment explanation
Indices: 168095--168126 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
168085 GATGTACATC
168095 GGAGACAGCTCGTGGT
1 GGAGACAGCTCGTGGT
168111 GGAGACAGCTCGTGGT
1 GGAGACAGCTCGTGGT
168127 ACACCACTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.44, T:0.19
Consensus pattern (16 bp):
GGAGACAGCTCGTGGT
Found at i:174503 original size:31 final size:31
Alignment explanation
Indices: 174461--174521 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
174451 AGCCTTTATG
* *
174461 TGAAAAATATATTTAATTGAATT-TTTAAATT
1 TGAAAAATATA-TCAATTAAATTCTTTAAATT
*
174492 TGAAAAGTATATCAATTAAATTCTTTAAAT
1 TGAAAAATATATCAATTAAATTCTTTAAAT
174522 AATAAAAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (31 bp):
TGAAAAATATATCAATTAAATTCTTTAAATT
Found at i:181453 original size:175 final size:175
Alignment explanation
Indices: 181162--181516 Score: 701
Period size: 175 Copynumber: 2.0 Consensus size: 175
181152 ATCTCATAAA
*
181162 TTTATAGGTGTGTGCTTGAAATAGTCATAGTTAAAAGAAAGCTGAATACGATATGCAACTCCTAT
1 TTTATAGGTGTGTGCTTGAAATAGTCATAGTTAAAAGAAAGCTGAATAAGATATGCAACTCCTAT
181227 TTGTAGTACTGAATGAATAATCAACTCCAAGTTTCAAGGTTTGCTTATGCTATACTTGTAAACGA
66 TTGTAGTACTGAATGAATAATCAACTCCAAGTTTCAAGGTTTGCTTATGCTATACTTGTAAACGA
181292 GATTAAGGACTGGAAACCGAAACAAGAAACATAAAATCCACACCC
131 GATTAAGGACTGGAAACCGAAACAAGAAACATAAAATCCACACCC
181337 TTTATAGGTGTGTGCTTGAAATAGTCATAGTTAAAAGAAAGCTGAATAAGATATGCAACTCCTAT
1 TTTATAGGTGTGTGCTTGAAATAGTCATAGTTAAAAGAAAGCTGAATAAGATATGCAACTCCTAT
181402 TTGTAGTACTGAATGAATAATCAACTCCAAGTTTCAAGGTTTGCTTATGCTATACTTGTAAACGA
66 TTGTAGTACTGAATGAATAATCAACTCCAAGTTTCAAGGTTTGCTTATGCTATACTTGTAAACGA
181467 GATTAAGGACTGGAAACCGAAACAAGAAACATAAAATCCACACCC
131 GATTAAGGACTGGAAACCGAAACAAGAAACATAAAATCCACACCC
181512 TTTAT
1 TTTAT
181517 CCAGAAAGGA
Statistics
Matches: 179, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
175 179 1.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (175 bp):
TTTATAGGTGTGTGCTTGAAATAGTCATAGTTAAAAGAAAGCTGAATAAGATATGCAACTCCTAT
TTGTAGTACTGAATGAATAATCAACTCCAAGTTTCAAGGTTTGCTTATGCTATACTTGTAAACGA
GATTAAGGACTGGAAACCGAAACAAGAAACATAAAATCCACACCC
Found at i:195540 original size:371 final size:371
Alignment explanation
Indices: 194857--195598 Score: 1412
Period size: 371 Copynumber: 2.0 Consensus size: 371
194847 GCGGTGATTG
*
194857 TGGCTCAACGAATAGTCAAGTTTCAGCATCATATGCATATGGCTCACGAAGAGGTTCCTCTGGTA
1 TGGCTCAACGAATAGTCAAGTTTCAGCATCATATGCATATGGCTCACGAAGAGGTTCATCTGGTA
*
194922 AAGTTGAAGTTTCCTCTGTGATGCCTATATTTAGGTAGAACAAGTTGGTAGTTGAATTCCTTCCT
66 AAGTTGAAGGTTCCTCTGTGATGCCTATATTTAGGTAGAACAAGTTGGTAGTTGAATTCCTTCCT
* *
194987 TTTAAACTTAAAGGCATCGTATTATACGGGTTTTGAACTGAGTGTTGTGTCGTAGACATCTCGAC
131 TTTAAACTTAAAGGCATCATATTATACGGGTTTTGAACTGAGTGTTGTGTCGCAGACATCTCGAC
195052 ATTAAGGTCGAAGAAGCTCGCAGTTGAATGCCTCCCACTGGAACTTGAAGGCATCGTGTTAAATG
196 ATTAAGGTCGAAGAAGCTCGCAGTTGAATGCCTCCCACTGGAACTTGAAGGCATCGTGTTAAATG
*
195117 TGTACTGAACATATTGTTTTGTCAAGGGCATCCCCATATTCAAGTCAAAGTATTTGGTAGATAAA
261 TGTACTGAACATATTGTTTTGTCAAGGGAATCCCCATATTCAAGTCAAAGTATTTGGTAGATAAA
195182 TGCATTCCCCTTGAACTAGAAGCGATGTTGACATACATTTGTTCGT
326 TGCATTCCCCTTGAACTAGAAGCGATGTTGACATACATTTGTTCGT
* *
195228 TGGCTCAACGAATAGTTAAGTTTCAGCATCATCTGCATATGGCTCACGAAGAGGTTCATCTGGTA
1 TGGCTCAACGAATAGTCAAGTTTCAGCATCATATGCATATGGCTCACGAAGAGGTTCATCTGGTA
195293 AAGTTGAAGGTTCCTCTGTGATGCCTATATTTAGGTAGAACAAGTTGGTAGTTGAATTCCTTCCT
66 AAGTTGAAGGTTCCTCTGTGATGCCTATATTTAGGTAGAACAAGTTGGTAGTTGAATTCCTTCCT
195358 TTTAAACTTAAAGGCATCATATTATACGGGTTTTGAACTGAGTGTTGTGTCGCAGACATCTCGAC
131 TTTAAACTTAAAGGCATCATATTATACGGGTTTTGAACTGAGTGTTGTGTCGCAGACATCTCGAC
195423 ATTAAGGTCGAAGAAGCTCGCAGTTGAATGCCTCCCACTGGAACTTGAAGGCATCGTGTTAAATG
196 ATTAAGGTCGAAGAAGCTCGCAGTTGAATGCCTCCCACTGGAACTTGAAGGCATCGTGTTAAATG
195488 TGTACTGAACATATTGTTTTGTCAAGGGAATCCCCATATTCAAGTCAAAGTATTTGGTAGATAAA
261 TGTACTGAACATATTGTTTTGTCAAGGGAATCCCCATATTCAAGTCAAAGTATTTGGTAGATAAA
*
195553 TGCATTCTCCTTGAACTAGAAGCGATGTTGACATACATTTGTTCGT
326 TGCATTCCCCTTGAACTAGAAGCGATGTTGACATACATTTGTTCGT
195599 GGAGCTACCT
Statistics
Matches: 363, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
371 363 1.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (371 bp):
TGGCTCAACGAATAGTCAAGTTTCAGCATCATATGCATATGGCTCACGAAGAGGTTCATCTGGTA
AAGTTGAAGGTTCCTCTGTGATGCCTATATTTAGGTAGAACAAGTTGGTAGTTGAATTCCTTCCT
TTTAAACTTAAAGGCATCATATTATACGGGTTTTGAACTGAGTGTTGTGTCGCAGACATCTCGAC
ATTAAGGTCGAAGAAGCTCGCAGTTGAATGCCTCCCACTGGAACTTGAAGGCATCGTGTTAAATG
TGTACTGAACATATTGTTTTGTCAAGGGAATCCCCATATTCAAGTCAAAGTATTTGGTAGATAAA
TGCATTCCCCTTGAACTAGAAGCGATGTTGACATACATTTGTTCGT
Found at i:199814 original size:20 final size:20
Alignment explanation
Indices: 199789--199849 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
199779 TAGGGAGATG
199789 ATTGAAAGGTTAAGACCTTT
1 ATTGAAAGGTTAAGACCTTT
199809 ATTGAAAGGTTAAGACCTTT
1 ATTGAAAGGTTAAGACCTTT
**
199829 ATTGAAATATTAAGACCTTT
1 ATTGAAAGGTTAAGACCTTT
199849 A
1 A
199850 AATGAAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (20 bp):
ATTGAAAGGTTAAGACCTTT
Found at i:201367 original size:13 final size:13
Alignment explanation
Indices: 201349--201377 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
201339 AGAATCTTTA
201349 TCTACATAGTGTG
1 TCTACATAGTGTG
201362 TCTACATAGTGTG
1 TCTACATAGTGTG
201375 TCT
1 TCT
201378 GAGTCAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (13 bp):
TCTACATAGTGTG
Found at i:205122 original size:20 final size:20
Alignment explanation
Indices: 205097--205137 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
205087 TAGGGAGATG
205097 ATTGAAAGGTTAAGACCTTT
1 ATTGAAAGGTTAAGACCTTT
*
205117 ATTGAAAGGTTAAGATCTTT
1 ATTGAAAGGTTAAGACCTTT
205137 A
1 A
205138 AATGAAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.37
Consensus pattern (20 bp):
ATTGAAAGGTTAAGACCTTT
Found at i:213507 original size:31 final size:31
Alignment explanation
Indices: 213472--213533 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
213462 TAAATAAAAC
213472 CCTGACGAAAGTGATACTGGAACGAGGGAAA
1 CCTGACGAAAGTGATACTGGAACGAGGGAAA
* *
213503 CCTGACGAATGTGATACTGGCACGAGGGAAA
1 CCTGACGAAAGTGATACTGGAACGAGGGAAA
213534 TAAAACCATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.35, C:0.18, G:0.32, T:0.15
Consensus pattern (31 bp):
CCTGACGAAAGTGATACTGGAACGAGGGAAA
Found at i:215129 original size:19 final size:19
Alignment explanation
Indices: 215105--215156 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
215095 GAATGCAACT
215105 AATGCATCGATGCATAAGG
1 AATGCATCGATGCATAAGG
*
215124 AATGCATCGATGCATAAGT
1 AATGCATCGATGCATAAGG
*
215143 AGTGCATCGATGCA
1 AATGCATCGATGCA
215157 CATGTTAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (19 bp):
AATGCATCGATGCATAAGG
Found at i:215192 original size:20 final size:19
Alignment explanation
Indices: 215167--215222 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 19
215157 CATGTTAAGG
215167 GATGCATCGATACACTGTAA
1 GATGCATCGATACACTGT-A
215187 GATGCATCGATACACTGTA
1 GATGCATCGATACACTGTA
*
215206 GAATGCATCGATGCACT
1 G-ATGCATCGATACACT
215223 TCAAGGGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 2 0.06
20 32 0.94
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.25
Consensus pattern (19 bp):
GATGCATCGATACACTGTA
Found at i:216022 original size:23 final size:23
Alignment explanation
Indices: 215996--216101 Score: 131
Period size: 23 Copynumber: 4.6 Consensus size: 23
215986 ATGGCACTTT
215996 GGTGCATTTCTACGCGGCACTAC
1 GGTGCATTTCTACGCGGCACTAC
* * *
216019 GGTGCAATTCTACGTGGCACTTC
1 GGTGCATTTCTACGCGGCACTAC
*
216042 GGTGCATTTCTACGCGGTACTAC
1 GGTGCATTTCTACGCGGCACTAC
* * *
216065 GGTGCAATTCTACGTGGCACTTC
1 GGTGCATTTCTACGCGGCACTAC
* *
216088 GGTACATTTATACG
1 GGTGCATTTCTACG
216102 AGCTGTGGTG
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 69 1.00
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.30
Consensus pattern (23 bp):
GGTGCATTTCTACGCGGCACTAC
Found at i:216054 original size:46 final size:46
Alignment explanation
Indices: 215987--216101 Score: 194
Period size: 46 Copynumber: 2.5 Consensus size: 46
215977 CAACCTTATA
*
215987 TGGCACTTTGGTGCATTTCTACGCGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACGCGGCACTACGGTGCAATTCTACG
*
216033 TGGCACTTCGGTGCATTTCTACGCGGTACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACGCGGCACTACGGTGCAATTCTACG
* *
216079 TGGCACTTCGGTACATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
216102 AGCTGTGGTG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 65 1.00
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.31
Consensus pattern (46 bp):
TGGCACTTCGGTGCATTTCTACGCGGCACTACGGTGCAATTCTACG
Found at i:220431 original size:23 final size:23
Alignment explanation
Indices: 220398--220465 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
220388 AACCTTATAT
220398 GGCACTTCGGTGCATTTCTACAC
1 GGCACTTCGGTGCATTTCTACAC
* * **
220421 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACAC
* *
220444 GGCACTTTGGTGCATTTATACA
1 GGCACTTCGGTGCATTTCTACA
220466 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACAC
Found at i:222645 original size:16 final size:16
Alignment explanation
Indices: 222615--222663 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
222605 TCCGTATCCG
*
222615 ATCCGAAAAAATCGGAT
1 ATCCG-AAAATTCGGAT
222632 ATCCGAAAATTCGGAT
1 ATCCGAAAATTCGGAT
* * *
222648 ATTCGGAATTTCGGAT
1 ATCCGAAAATTCGGAT
222664 CGGATATCCG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 23 0.82
17 5 0.18
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (16 bp):
ATCCGAAAATTCGGAT
Found at i:228888 original size:157 final size:153
Alignment explanation
Indices: 228576--228918 Score: 479
Period size: 157 Copynumber: 2.2 Consensus size: 153
228566 TTCCTCCTTC
* *
228576 ATTTTAAGTCCATATTTTTACCAAATTTGAACCACATACTCTTAAATCATAGTAGAATACATGTG
1 ATTTTAAGTCTAT-TTTTTACCAAATTTGAACCACATACTCCTAAATCATAGTAGAATACATGTG
* * *
228641 TACTTTCAATTCCTCTTTTTTATATTTTTTATTTTTCAATTTAGTCTTTCAATTTTTCATAATCT
65 TACTTTCAATTCCTCTTTTTTAAAGTTTTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCT
** *
228706 CCTTATTTTTTCAATTTGTGGTTT
130 CCTTATTCCTTCAATTTGTGATTT
** * * *
228730 ATTTTAAGTCTATTTTTTACCAAATTTGAGTCATATGCTCCTAAATCATAGTAGAATACTTGTGT
1 ATTTTAAGTCTATTTTTTACCAAATTTGAACCACATACTCCTAAATCATAGTAGAATACATGTGT
*
228795 ACTTTCAATTCTTCTTTTTGATAACAAGTTTTTATTTTTCAATTTAGTCCTTCAATTTTTCATAA
66 ACTTTCAATTCCTCTTTTT--T-A-AAGTTTTTATTTTTCAATTTAGTCCTTCAATTTTTCATAA
*
228860 TCTCTTTATTCCTTCAATTTGTGATTT
127 TCTCCTTATTCCTTCAATTTGTGATTT
*
228887 ATTTTAAGTCACTTTTTTTTACCAAATTTGAA
1 ATTTTAAGT--CTATTTTTTACCAAATTTGAA
228919 ATACATGCTC
Statistics
Matches: 166, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
153 64 0.39
154 12 0.07
155 1 0.01
156 1 0.01
157 69 0.42
159 19 0.11
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.51
Consensus pattern (153 bp):
ATTTTAAGTCTATTTTTTACCAAATTTGAACCACATACTCCTAAATCATAGTAGAATACATGTGT
ACTTTCAATTCCTCTTTTTTAAAGTTTTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCTC
CTTATTCCTTCAATTTGTGATTT
Found at i:229170 original size:20 final size:21
Alignment explanation
Indices: 229135--229183 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
229125 TCTTTAAGAT
229135 ATAATATTATGATTATATTTC
1 ATAATATTATGATTATATTTC
* *
229156 ATAATTTTA-GATTATATTTA
1 ATAATATTATGATTATATTTC
229176 AT-ATATTA
1 ATAATATTA
229184 AATAATATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 5 0.20
20 12 0.48
21 8 0.32
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (21 bp):
ATAATATTATGATTATATTTC
Found at i:229208 original size:18 final size:19
Alignment explanation
Indices: 229169--229221 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
229159 ATTTTAGATT
*
229169 ATATT-TAATATATTAAATA
1 ATATTATAATATA-TAAAGA
229188 ATATTATAATATA-AAAGA
1 ATATTATAATATATAAAGA
*
229206 ATAATATATATATATA
1 ATATTATA-ATATATA
229222 TATAGGCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 11 0.38
19 10 0.34
20 8 0.28
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
ATATTATAATATATAAAGA
Found at i:229617 original size:21 final size:21
Alignment explanation
Indices: 229591--229631 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
229581 AAATTAGAAC
* *
229591 AAATAAATATCATAATATTAT
1 AAATAAATATAATAAAATTAT
*
229612 AAATAATTATAATAAAATTA
1 AAATAAATATAATAAAATTA
229632 AAACAAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
AAATAAATATAATAAAATTAT
Found at i:238446 original size:2 final size:2
Alignment explanation
Indices: 238439--238475 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
238429 GGATATTTTG
238439 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
238476 GGGGGGAGGG
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:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:238932 original size:14 final size:14
Alignment explanation
Indices: 238915--238942 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
238905 ATCATAACAA
238915 AATTATATAACTAT
1 AATTATATAACTAT
238929 AATTATATAACTAT
1 AATTATATAACTAT
238943 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:239557 original size:2 final size:2
Alignment explanation
Indices: 239550--239584 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
239540 GTTAGTTTAT
239550 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
239585 ATGAATTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:242357 original size:4 final size:4
Alignment explanation
Indices: 242348--242372 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
242338 ATCATCAGAA
242348 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
242373 TATATATATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:242771 original size:2 final size:2
Alignment explanation
Indices: 242764--242803 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
242754 CCAATGCAAA
242764 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
242804 TTAAAGCACG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:249774 original size:21 final size:21
Alignment explanation
Indices: 249738--249789 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
249728 ATAATTATTT
*
249738 AAAAATTAAATAAAAATACCAA
1 AAAAATTTAATAAAAA-ACCAA
* *
249760 AAACATTTAATAAAAAATCAA
1 AAAAATTTAATAAAAAACCAA
249781 AAAAATTTA
1 AAAAATTTA
249790 GGTTGAACCG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAATTTAATAAAAAACCAA
Found at i:268865 original size:15 final size:15
Alignment explanation
Indices: 268847--268875 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
268837 ATTCTAAATG
268847 TTTAAATAAAAATTA
1 TTTAAATAAAAATTA
268862 TTTAAATAAAAATT
1 TTTAAATAAAAATT
268876 CTATTTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TTTAAATAAAAATTA
Found at i:273534 original size:31 final size:31
Alignment explanation
Indices: 273498--273590 Score: 150
Period size: 31 Copynumber: 3.0 Consensus size: 31
273488 CCTCGACAAT
* **
273498 TGTCCATAAGTCCCGGCGAACCTAGGTAAAC
1 TGTCCATAGGTCCCGAAGAACCTAGGTAAAC
*
273529 TGTCCATAGGTCCCGAAGAACCTAGGTAAAT
1 TGTCCATAGGTCCCGAAGAACCTAGGTAAAC
273560 TGTCCATAGGTCCCGAAGAACCTAGGTAAAC
1 TGTCCATAGGTCCCGAAGAACCTAGGTAAAC
273591 CCTCGACTCT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.20
Consensus pattern (31 bp):
TGTCCATAGGTCCCGAAGAACCTAGGTAAAC
Found at i:274565 original size:20 final size:22
Alignment explanation
Indices: 274540--274597 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
274530 TTCCCCTTGA
274540 AGTGCATCGATGCATGC-T-AC
1 AGTGCATCGATGCATGCTTAAC
*
274560 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATGC-TTAAC
274583 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
274598 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (22 bp):
AGTGCATCGATGCATGCTTAAC
Found at i:276109 original size:13 final size:13
Alignment explanation
Indices: 276093--276121 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
276083 TTTAAAAAAA
276093 TTCATTTAATTAT
1 TTCATTTAATTAT
276106 TTCATTTAATTAT
1 TTCATTTAATTAT
276119 TTC
1 TTC
276122 CTTTTTCAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (13 bp):
TTCATTTAATTAT
Found at i:277186 original size:105 final size:105
Alignment explanation
Indices: 276978--277200 Score: 286
Period size: 105 Copynumber: 2.1 Consensus size: 105
276968 GATTGTCCAT
* * * *
276978 AAGGACCACATA-TAAATTCCTTAAGAACCATATACATATACCAAGGATCAAGTAAGTGTCTCAA
1 AAGGACCACGTAGAAAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCTCAA
277042 AAGACCTCATACATGCTCCAAAGAATACATATACATCCCG
66 AAGACCTCATACATGCTCCAAAGAATACATATACATCCCG
* * * *
277082 AAGGACCACGTAGAAAATTCCTTAAGAATCATATACATATGCTAAGGACCAAATACGTGTCTCAA
1 AAGGACCACGTAGAAAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCTCAA
* * * * * * **
277147 ATGACCTCATAGATGTTCCATAGGATACCTATATGTCCCG
66 AAGACCTCATACATGCTCCAAAGAATACATATACATCCCG
*
277187 AAGGACCGCGTAGA
1 AAGGACCACGTAGA
277201 CCCTCGACTC
Statistics
Matches: 101, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
104 11 0.11
105 90 0.89
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.23
Consensus pattern (105 bp):
AAGGACCACGTAGAAAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCTCAA
AAGACCTCATACATGCTCCAAAGAATACATATACATCCCG
Found at i:277397 original size:53 final size:53
Alignment explanation
Indices: 277340--277503 Score: 138
Period size: 53 Copynumber: 3.1 Consensus size: 53
277330 ACACATACAT
277340 GTAATCACGTAGTTCATATCAATTCTCATATGATTTCATATTCATATAATCAC
1 GTAATCACGTAGTTCATATCAATTCTCATATGATTTCATATTCATATAATCAC
* ** * * * * * * ** *
277393 GTAATTCACTTA-CACATAGCACATTTTCATGT-AATTCACA--GATATCCCTTAGC
1 GTAA-TCACGTAGTTCATATCA-ATTCTCATATGATTTCATATTCATAT-AATCA-C
* *
277446 TTAATCACGTAGTTCATGTCAATTCTCATATGATTTCATATTCATATAATCAC
1 GTAATCACGTAGTTCATATCAATTCTCATATGATTTCATATTCATATAATCAC
277499 GTAAT
1 GTAAT
277504 TCACTTACAC
Statistics
Matches: 76, Mismatches: 27, Indels: 16
0.64 0.23 0.13
Matches are distributed among these distances:
51 4 0.05
52 16 0.21
53 36 0.47
54 16 0.21
55 4 0.05
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (53 bp):
GTAATCACGTAGTTCATATCAATTCTCATATGATTTCATATTCATATAATCAC
Found at i:277475 original size:106 final size:106
Alignment explanation
Indices: 277341--277554 Score: 410
Period size: 106 Copynumber: 2.0 Consensus size: 106
277331 CACATACATG
277341 TAATCACGTAGTTCATATCAATTCTCATATGATTTCATATTCATATAATCACGTAATTCACTTAC
1 TAATCACGTAGTTCATATCAATTCTCATATGATTTCATATTCATATAATCACGTAATTCACTTAC
277406 ACATAGCACATTTTCATGTAATTCACAGATATCCCTTAGCT
66 ACATAGCACATTTTCATGTAATTCACAGATATCCCTTAGCT
*
277447 TAATCACGTAGTTCATGTCAATTCTCATATGATTTCATATTCATATAATCACGTAATTCACTTAC
1 TAATCACGTAGTTCATATCAATTCTCATATGATTTCATATTCATATAATCACGTAATTCACTTAC
*
277512 ACATAGCACATTTTCATGTAATTCACATATATCCCTTAGCT
66 ACATAGCACATTTTCATGTAATTCACAGATATCCCTTAGCT
277553 TA
1 TA
277555 TATCTCTTGA
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 106 1.00
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.38
Consensus pattern (106 bp):
TAATCACGTAGTTCATATCAATTCTCATATGATTTCATATTCATATAATCACGTAATTCACTTAC
ACATAGCACATTTTCATGTAATTCACAGATATCCCTTAGCT
Found at i:278803 original size:22 final size:22
Alignment explanation
Indices: 278775--278847 Score: 112
Period size: 22 Copynumber: 3.4 Consensus size: 22
278765 GAGGGGATAT
278775 CGATTCCCCCTTAAATGGGTAC
1 CGATTCCCCCTTAAATGGGTAC
278797 CGATTCCCCCTTAAATGGGTAC
1 CGATTCCCCCTTAAATGGGTAC
* *
278819 CGATT-CCCATTGAATGGGTAC
1 CGATTCCCCCTTAAATGGGTAC
*
278840 AGATTCCC
1 CGATTCCC
278848 TTAGCCCAGA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
21 18 0.38
22 29 0.62
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.27
Consensus pattern (22 bp):
CGATTCCCCCTTAAATGGGTAC
Found at i:279637 original size:26 final size:27
Alignment explanation
Indices: 279589--279639 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
279579 GATTGAAAAC
* *
279589 CATTTATAATATAAAATTTATATTACT
1 CATTCATAATATAAAATTAATATTACT
*
279616 CATTCATAA-ATACAATTAATATTA
1 CATTCATAATATAAAATTAATATTA
279640 AAATTAGGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (27 bp):
CATTCATAATATAAAATTAATATTACT
Found at i:280496 original size:18 final size:18
Alignment explanation
Indices: 280473--280530 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
280463 TCTACTTCTG
**
280473 ATAACTGTAAAACATCTT
1 ATAACTGTAAAATGTCTT
* *
280491 ATAACTGAAAAATGTCTA
1 ATAACTGTAAAATGTCTT
*
280509 ATAACTATAAAATGTCTT
1 ATAACTGTAAAATGTCTT
280527 ATAA
1 ATAA
280531 TTATAAACAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (18 bp):
ATAACTGTAAAATGTCTT
Found at i:280535 original size:18 final size:18
Alignment explanation
Indices: 280499--280537 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
280489 TTATAACTGA
280499 AAAATGTCTAATAACTAT
1 AAAATGTCTAATAACTAT
* *
280517 AAAATGTCTTATAATTAT
1 AAAATGTCTAATAACTAT
280535 AAA
1 AAA
280538 CATTTAGGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (18 bp):
AAAATGTCTAATAACTAT
Found at i:281402 original size:27 final size:27
Alignment explanation
Indices: 281372--281430 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
281362 TACTTAAATA
281372 AATATAAAGATAAATCATACTTCCATC
1 AATATAAAGATAAATCATACTTCCATC
*
281399 AATATAAAGATAAATCGTACTTCCATC
1 AATATAAAGATAAATCATACTTCCATC
281426 AATAT
1 AATAT
281431 TTCAAACTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.31
Consensus pattern (27 bp):
AATATAAAGATAAATCATACTTCCATC
Found at i:283121 original size:16 final size:17
Alignment explanation
Indices: 283090--283121 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
283080 ATTTACGGGC
283090 TAAAATATATAATTTTT
1 TAAAATATATAATTTTT
283107 TAAAAT-TAT-ATTTTT
1 TAAAATATATAATTTTT
283122 GGTCCCTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAAAATATATAATTTTT
Found at i:285109 original size:29 final size:29
Alignment explanation
Indices: 285067--285152 Score: 147
Period size: 29 Copynumber: 3.0 Consensus size: 29
285057 AGTGTTGGTC
285067 GTAGGTCGCCATGC-CTTCCGGGCGACCTT
1 GTAGGTCGCCATGCAC-TCCGGGCGACCTT
*
285096 GTAGGTCACCATGCACTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
285125 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
285153 ACTCTTGCTC
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
29 53 0.98
30 1 0.02
ACGTcount: A:0.14, C:0.35, G:0.30, T:0.21
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:285188 original size:23 final size:23
Alignment explanation
Indices: 285158--285205 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
285148 GACCTACTCT
285158 TGCTCAAACAGAGAGAATGAACG
1 TGCTCAAACAGAGAGAATGAACG
285181 TGCTCAAACAGAGAGAATGAACG
1 TGCTCAAACAGAGAGAATGAACG
285204 TG
1 TG
285206 TTGCATGGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.42, C:0.17, G:0.27, T:0.15
Consensus pattern (23 bp):
TGCTCAAACAGAGAGAATGAACG
Found at i:285267 original size:29 final size:29
Alignment explanation
Indices: 285234--285318 Score: 143
Period size: 29 Copynumber: 2.9 Consensus size: 29
285224 TCCCAACACA
*
285234 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
* *
285263 TAGGTCGCCATGCACTCCGAGTGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
285292 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
285319 ACCCTCGGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.14, C:0.35, G:0.29, T:0.21
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:285356 original size:23 final size:23
Alignment explanation
Indices: 285324--285381 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
285314 GACCTACCCT
*
285324 CGGATTCCCTCGCATAGCTCGCA
1 CGGATGCCCTCGCATAGCTCGCA
**
285347 CGGATGCCCTCGCATAGCTCGTT
1 CGGATGCCCTCGCATAGCTCGCA
*
285370 CGGATGGCCTCG
1 CGGATGCCCTCG
285382 GATGCTCTCG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.14, C:0.36, G:0.28, T:0.22
Consensus pattern (23 bp):
CGGATGCCCTCGCATAGCTCGCA
Found at i:285394 original size:20 final size:20
Alignment explanation
Indices: 285369--285422 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
285359 CATAGCTCGT
285369 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCGGATGCTC
*
285389 TCGGATGGCCTCTGATGCTC
1 TCGGATGGCCTCGGATGCTC
*
285409 TCGGATAGCCTCGG
1 TCGGATGGCCTCGG
285423 TCGGATGGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.11, C:0.30, G:0.33, T:0.26
Consensus pattern (20 bp):
TCGGATGGCCTCGGATGCTC
Found at i:285439 original size:10 final size:9
Alignment explanation
Indices: 285369--285422 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 9
285359 CATAGCTCGT
285369 TCGGATGGCC
1 TCGGAT-GCC
285379 TCGGATGCTC
1 TCGGATGC-C
285389 TCGGATGGCC
1 TCGGAT-GCC
*
285399 TCTGATGCTC
1 TCGGATGC-C
285409 TCGGATAGCC
1 TCGGAT-GCC
285419 TCGG
1 TCGG
285423 TCGGATGGCC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 4 0.11
10 30 0.79
11 4 0.11
ACGTcount: A:0.11, C:0.30, G:0.33, T:0.26
Consensus pattern (9 bp):
TCGGATGCC
Found at i:285516 original size:29 final size:29
Alignment explanation
Indices: 285479--285536 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
285469 GCTATCTCTT
**
285479 GTAGCTCGCGGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
* *
285508 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
285537 CGGCCAACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.22, C:0.26, G:0.38, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCGGAAGACATGGCGACCTA
Found at i:290509 original size:452 final size:452
Alignment explanation
Indices: 289660--290574 Score: 1778
Period size: 452 Copynumber: 2.0 Consensus size: 452
289650 TTGAAATAAA
*
289660 ATAAAATAAACACTTTAGAGGTATATTTTTGTTATTATTATTAGGTATGATATTTGATTATACAA
1 ATAATATAAACACTTTAGAGGTATATTTTTGTTATTATTATTAGGTATGATATTTGATTATACAA
289725 CTAAAGTAAAAATCCAAAATTTAAATTATACACAAACTCAAAATTAGGGGTGTTTAAAATTCGGT
66 CTAAAGTAAAAATCCAAAATTTAAATTATACACAAACTCAAAATTAGGGGTGTTTAAAATTCGGT
289790 TTTAACTCAGCTACCGAATTAGTTCGGCCGGGGAACGATTAAGATTTTTTTGAATATTCGGTTAA
131 TTTAACTCAGCTACCGAATTAGTTCGGCCGGGGAACGATTAAGATTTTTTTGAATATTCGGTTAA
*
289855 CGGTTAATTCGGTTCGGAATCGGTTAATTAACCGAAATAAAATTTTAAATTAATTATAAACTATT
196 CGGTTAATTCGGTTCGGAATCGGTTAATTAACCGAAATAAAAATTTAAATTAATTATAAACTATT
289920 TTTTTGAATTATAAAATATTTAATTTTTATATAAATTAGAAAATTTAAAAAAATTTCGGTTAATT
261 TTTTTGAATTATAAAATATTTAATTTTTATATAAATTAGAAAATTTAAAAAAATTTCGGTTAATT
* *
289985 CGAAAATTAACCGAAATTTATTCGGTTCAGTTAATATTTTTGAAAAAAAAATTCGGTTAATTTAG
326 CGAAAATTAACCGAAATTTATTCGGTTCAGTTAATATTTTCGAAAAAAAAATTCGGTTAATTTAA
290050 TTAATGGTAGTTCGGTTAGTTAGATCATCAAATTAACCGAATGAACAACGCTATTCAAAATT
391 TTAATGGTAGTTCGGTTAGTTAGATCATCAAATTAACCGAATGAACAACGCTATTCAAAATT
290112 ATAATATAAACACTTTAGAGGTATATTTTTGTTATTATTATTAGGTATGATATTTGATTATACAA
1 ATAATATAAACACTTTAGAGGTATATTTTTGTTATTATTATTAGGTATGATATTTGATTATACAA
290177 CTAAAGTAAAAATCCAAAATTTAAATTATACACAAACTCAAAATTAGGGGTGTTTAAAATTCGGT
66 CTAAAGTAAAAATCCAAAATTTAAATTATACACAAACTCAAAATTAGGGGTGTTTAAAATTCGGT
290242 TTTAACTCAGCTACCGAATTAGTTCGGCCGGGGAACGATTAAGATTTTTTTGAATATTCGGTTAA
131 TTTAACTCAGCTACCGAATTAGTTCGGCCGGGGAACGATTAAGATTTTTTTGAATATTCGGTTAA
290307 CGGTTAATTCGGTTCGGAATCGGTTAATTAACCGAAATAAAAATTTAAATTAATTATAAACTATT
196 CGGTTAATTCGGTTCGGAATCGGTTAATTAACCGAAATAAAAATTTAAATTAATTATAAACTATT
290372 TTTTTGAATTATAAAATATTTAATTTTTATATAAATTAGAAAATTTAAAAAAATTTCGGTTAATT
261 TTTTTGAATTATAAAATATTTAATTTTTATATAAATTAGAAAATTTAAAAAAATTTCGGTTAATT
290437 CGAAAATTAACCGAAATTTATTCGGTTCAGTTAATATTTTCGAAAAAAAAAATT-GGTTAATTTA
326 CGAAAATTAACCGAAATTTATTCGGTTCAGTTAATATTTTCG-AAAAAAAAATTCGGTTAATTTA
290501 ATTAATGGTAGTTCGGTTAGTTAGATCATCAAATTAACCGAATGAACAACGCTATTCAAAATT
390 ATTAATGGTAGTTCGGTTAGTTAGATCATCAAATTAACCGAATGAACAACGCTATTCAAAATT
290564 ATAATATAAAC
1 ATAATATAAAC
290575 CCTAAAATAC
Statistics
Matches: 458, Mismatches: 4, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
452 447 0.98
453 11 0.02
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.37
Consensus pattern (452 bp):
ATAATATAAACACTTTAGAGGTATATTTTTGTTATTATTATTAGGTATGATATTTGATTATACAA
CTAAAGTAAAAATCCAAAATTTAAATTATACACAAACTCAAAATTAGGGGTGTTTAAAATTCGGT
TTTAACTCAGCTACCGAATTAGTTCGGCCGGGGAACGATTAAGATTTTTTTGAATATTCGGTTAA
CGGTTAATTCGGTTCGGAATCGGTTAATTAACCGAAATAAAAATTTAAATTAATTATAAACTATT
TTTTTGAATTATAAAATATTTAATTTTTATATAAATTAGAAAATTTAAAAAAATTTCGGTTAATT
CGAAAATTAACCGAAATTTATTCGGTTCAGTTAATATTTTCGAAAAAAAAATTCGGTTAATTTAA
TTAATGGTAGTTCGGTTAGTTAGATCATCAAATTAACCGAATGAACAACGCTATTCAAAATT
Found at i:293692 original size:23 final size:24
Alignment explanation
Indices: 293648--293713 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 24
293638 TGATTAATTT
293648 ATGAATATATAAATAAACATGTTC
1 ATGAATATATAAATAAACATGTTC
* *
293672 ATGAAT-TTTAAATGAAA-ATGTTT
1 ATGAATATATAAAT-AAACATGTTC
* *
293695 ATAAATAT-TAAACAAACAT
1 ATGAATATATAAATAAACAT
293714 ATTTACGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
22 3 0.09
23 22 0.63
24 10 0.29
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.35
Consensus pattern (24 bp):
ATGAATATATAAATAAACATGTTC
Found at i:294779 original size:30 final size:33
Alignment explanation
Indices: 294720--294781 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 33
294710 AAAATTAAAG
*
294720 TTATTTTTACTTTTTAAGAAATATATTTAATTA
1 TTATTATTACTTTTTAAGAAATATATTTAATTA
*
294753 TTATTATTA-TTTTTAATAAAT-T-TTTAATT
1 TTATTATTACTTTTTAAGAAATATATTTAATT
294782 TCTCTCATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 7 0.26
31 1 0.04
32 11 0.41
33 8 0.30
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (33 bp):
TTATTATTACTTTTTAAGAAATATATTTAATTA
Found at i:309400 original size:21 final size:20
Alignment explanation
Indices: 309375--309473 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
309365 AATCAGTTTC
309375 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
309396 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
309417 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
309437 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
309458 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
309474 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 15 0.25
21 44 0.75
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:309466 original size:20 final size:20
Alignment explanation
Indices: 309441--309593 Score: 75
Period size: 20 Copynumber: 7.7 Consensus size: 20
309431 GATTTTCCAG
* *
309441 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
309461 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
309481 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
309501 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
309521 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
309541 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
309561 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
309581 AATCGCAACGCGA
1 AATCGCAACGCGA
309594 TTTTTAAAAC
Statistics
Matches: 121, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
19 2 0.02
20 117 0.97
21 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:309488 original size:40 final size:40
Alignment explanation
Indices: 309441--309592 Score: 135
Period size: 40 Copynumber: 3.8 Consensus size: 40
309431 GATTTTCCAG
*
309441 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACACATA
1 AATCGCAACGCGAATACGAAAATCGCAACGCGTAAC-CATA
* * * * * *
309481 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGAATACGAAAATCGCAACGCGTAACCATA
* * * * * *
309521 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAAAATCGCAACGCGTAACCATA
* * * *
309561 TATCGCAACGCGTATCCGTAAATCGCAACGCG
1 AATCGCAACGCGAATACGAAAATCGCAACGCG
309593 ATTTTTAAAA
Statistics
Matches: 100, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 98 0.98
41 2 0.02
ACGTcount: A:0.34, C:0.28, G:0.20, T:0.19
Consensus pattern (40 bp):
AATCGCAACGCGAATACGAAAATCGCAACGCGTAACCATA
Found at i:309524 original size:60 final size:59
Alignment explanation
Indices: 309441--309593 Score: 207
Period size: 60 Copynumber: 2.6 Consensus size: 59
309431 GATTTTCCAG
* ** *
309441 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CATAAATCGCAACGCGTATCCGTA
* * * *
309501 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATAAATCGCAACGCGTATCCGTA
*
309561 TATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
309594 TTTTTAAAAC
Statistics
Matches: 82, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
59 1 0.01
60 79 0.96
61 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (59 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACCATAAATCGCAACGCGTATCCGTA
Found at i:310011 original size:33 final size:33
Alignment explanation
Indices: 309972--310042 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
309962 TTCACTTAGA
309972 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
310005 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
310038 TTTCA
1 TTTCA
310043 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:310148 original size:21 final size:20
Alignment explanation
Indices: 310122--310228 Score: 102
Period size: 21 Copynumber: 5.5 Consensus size: 20
310112 TGCAGAAGAG
310122 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
310143 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
310163 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
310185 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
310199 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
310218 TCGCAACGAGA
1 TCGCAACGAGA
310229 GAATCGCAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 11 0.16
20 9 0.13
21 25 0.36
22 10 0.14
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:310202 original size:14 final size:14
Alignment explanation
Indices: 310183--310239 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
310173 GAAAAATGAA
310183 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
310197 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
310216 AATCGCAACGAGAG
1 AATCGCAACGAGAG
310230 AATCGCAACG
1 AATCGCAACG
310240 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:310214 original size:33 final size:33
Alignment explanation
Indices: 310176--310255 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
310166 GCAACGAGAA
310176 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
310209 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
310242 AAACCAAAATCGCA
1 AAATGAAAATCGCA
310256 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:310273 original size:19 final size:19
Alignment explanation
Indices: 310251--310315 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
310241 GAAACCAAAA
310251 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
310270 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
310286 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
310303 TCGCGTTGCGATT
1 TCGCATTGCGATT
310316 CTCTCGTTGC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 6 0.15
16 7 0.18
17 7 0.18
19 19 0.49
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:310294 original size:14 final size:14
Alignment explanation
Indices: 310275--310329 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
310265 TCATTTCGCA
310275 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
310289 TTGCGATTTTCATTTCGCG
1 TTGCGA--TTC---TCTCG
310308 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
310322 TTGCGATT
1 TTGCGATT
310330 TTCATTTCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:310298 original size:33 final size:33
Alignment explanation
Indices: 310256--310337 Score: 155
Period size: 33 Copynumber: 2.5 Consensus size: 33
310246 CAAAATCGCA
310256 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
310289 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
310322 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
310338 TCTCGTTGCG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:310340 original size:21 final size:21
Alignment explanation
Indices: 310314--310378 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
310304 CGCGTTGCGA
310314 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
310335 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
310355 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
310376 TTC
1 TTC
310379 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:312222 original size:93 final size:93
Alignment explanation
Indices: 312063--312471 Score: 782
Period size: 93 Copynumber: 4.4 Consensus size: 93
312053 TAGATTGCTT
* *
312063 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTATTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
312128 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
312156 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
312221 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
312249 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
312314 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
312342 AGTAAATTTGTTCAGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAAAAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
312407 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
312435 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
312472 AATACCCTGA
Statistics
Matches: 311, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 311 1.00
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:312606 original size:14 final size:14
Alignment explanation
Indices: 312587--312643 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
312577 CGAAACTTAA
312587 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
312601 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
312620 AATCGCAACGACAG
1 AATCGCAACGAGAG
312634 AATCGCAACG
1 AATCGCAACG
312644 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:312627 original size:33 final size:33
Alignment explanation
Indices: 312569--312662 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 33
312559 TAGTTTACTT
* * *
312569 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAA-TCAAAATCGCAACGACAGAA
*
312603 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAATCAAAATCGCAACGACAGAA
*
312636 TCGCAACGCGAAACCAAAATCGCAACG
1 TCGCAACGCGAAATCAAAATCGCAACG
312663 CGAAACCAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 43 0.78
34 12 0.22
ACGTcount: A:0.45, C:0.27, G:0.19, T:0.10
Consensus pattern (33 bp):
TCGCAACGCGAAATCAAAATCGCAACGACAGAA
Found at i:312684 original size:19 final size:19
Alignment explanation
Indices: 312601--312678 Score: 94
Period size: 19 Copynumber: 4.4 Consensus size: 19
312591 GCAACGAGAG
**
312601 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
*
312620 AATCGCAA--CG--A-CAG
1 AATCGCAACGCGAAACCAA
312634 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
312653 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
312672 AATCGCA
1 AATCGCA
312679 TTGCGATTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
14 9 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 36 0.71
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:312696 original size:19 final size:19
Alignment explanation
Indices: 312674--312827 Score: 139
Period size: 19 Copynumber: 8.6 Consensus size: 19
312664 GAAACCAAAA
*
312674 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
312693 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
312707 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
312726 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
312742 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
312759 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
312778 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
312797 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
312817 TCGTGTTGCGA
1 TCGCGTTGCGA
312828 AAGTAAACTA
Statistics
Matches: 107, Mismatches: 17, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
14 17 0.16
16 8 0.07
17 8 0.07
19 62 0.58
20 12 0.11
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:312715 original size:14 final size:14
Alignment explanation
Indices: 312696--312752 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
312686 TTTCATTTCG
312696 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
312710 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
312727 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
312743 CGTTGCGATT
1 CGTTGCGATT
312753 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:312721 original size:33 final size:33
Alignment explanation
Indices: 312679--312809 Score: 181
Period size: 33 Copynumber: 3.8 Consensus size: 33
312669 CAAAATCGCA
312679 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
312712 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
312745 TTGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGA---T--TCTCTCG
*
312783 TTGCGATTCTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
312810 TTAAGTTTCG
Statistics
Matches: 87, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
33 56 0.64
35 1 0.01
36 1 0.01
38 29 0.33
ACGTcount: A:0.10, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:314769 original size:14 final size:14
Alignment explanation
Indices: 314750--314785 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
314740 ATTGTTTAAT
314750 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
314764 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
314778 TGATTTGT
1 TGATTTGT
314786 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Done.