Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 91 of 126
Found at i:28155277 original size:150 final size:147
Alignment explanation
Indices: 28155068--28155506 Score: 470
Period size: 150 Copynumber: 2.9 Consensus size: 147
28155058 TTTCCTTTTT
* ** * *
28155068 ATCTTCATGGTATCG-GATTCATCGTTACGACCTCAATCC-TTCCCATCGCATCTTCTTAGGTAC
1 ATCTTCATGGTACCGAG-TTCGCCGTTGCGACCTCAA-CCTTTCCCATCACATCTTCTTAGGTAC
**
28155131 AGGGTTCGTCGTTGCGGTCTCAACCTTTCCCTTCATATCTTTTTAGGTATCGAGTTCGCCGTTGC
64 -GGGTTCACCGTTGCGGTCTCAACCTTTCCCTTCATATCTTTTTAGGTATCG-GTTCGCCGTTGC
28155196 GGCCTCAACCTTTCCCATCAC
127 GGCCTCAACCTTTCCCATCAC
** ** * *
28155217 ATCTTTTTAGGTACCGAGTTCGCCGTTGCGACCTCAACCTTTCCTTTCATATCTTTTTAGGTATC
1 ATCTTCAT-GGTACCGAGTTCGCCGTTGCGACCTCAACCTTTCCCATCACATCTTCTTAGGTA-C
* * * *
28155282 GGGTTCACCGTTACGGTTTCAACCTTTCCCTTCATATCTTCTTAGGTATCGGGTTCGCCGTTACG
64 GGGTTCACCGTTGCGGTCTCAACCTTTCCCTTCATATCTTTTTAGGTATC-GGTTCGCCGTTGCG
* * *
28155347 GTCTCAACCTTTCCCTTTAC
128 GCCTCAACCTTTCCCATCAC
* * * *
28155367 ATCTTCATGGTACCGGGTTCGTCGTTGCGATCTCAACCTTTCCCATCACATCTTCTTAGGTACTC
1 ATCTTCATGGTACCGAGTTCGCCGTTGCGACCTCAACCTTTCCCATCACATCTTCTTAGGTAC-G
* * ** * * * * *
28155432 AGTTCACCGTTGTGACCTCAACCTTTCCCTTCA-ATCTTTTAAGGAATCGGATTCACTGTCGCGG
65 GGTTCACCGTTGCGGTCTCAACCTTTCCCTTCATATCTTTTTAGGTATCGG-TTCGCCGTTGCGG
28155496 CCTCAATCCTT
129 CCTCAA-CCTT
28155507 CCCTGTCAAA
Statistics
Matches: 238, Mismatches: 44, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
147 2 0.01
148 27 0.11
149 86 0.36
150 120 0.50
151 3 0.01
ACGTcount: A:0.17, C:0.30, G:0.17, T:0.36
Consensus pattern (147 bp):
ATCTTCATGGTACCGAGTTCGCCGTTGCGACCTCAACCTTTCCCATCACATCTTCTTAGGTACGG
GTTCACCGTTGCGGTCTCAACCTTTCCCTTCATATCTTTTTAGGTATCGGTTCGCCGTTGCGGCC
TCAACCTTTCCCATCAC
Found at i:28156434 original size:1 final size:1
Alignment explanation
Indices: 28156430--28156496 Score: 53
Period size: 1 Copynumber: 67.0 Consensus size: 1
28156420 TTTTTTCCTG
* * * * * * * * *
28156430 TTTTTTTTATTTTCTTTTTCTTTTTTTCTTTTTTCTTTTTTTTTTCTTCTTTTTCTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
28156495 TT
1 TT
28156497 CATTGAGTCC
Statistics
Matches: 48, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.01, C:0.12, G:0.00, T:0.87
Consensus pattern (1 bp):
T
Found at i:28156452 original size:30 final size:28
Alignment explanation
Indices: 28156418--28156496 Score: 97
Period size: 30 Copynumber: 2.7 Consensus size: 28
28156408 TCGACCTCTC
*
28156418 TCTTTTTTCCTGTTTTTTTTATTTTCTTT-T
1 TCTTTTTTTCT-TTTTTTTT-TTTT-TTTCT
28156448 TCTTTTTTTCTTTTTTCTTTTTTTTTTCT
1 TCTTTTTTTCTTTTTT-TTTTTTTTTTCT
28156477 TCTTTTTCTTCTTTTTTTTT
1 TCTTTTT-TTCTTTTTTTTT
28156497 CATTGAGTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
28 3 0.07
29 20 0.44
30 22 0.49
ACGTcount: A:0.01, C:0.14, G:0.01, T:0.84
Consensus pattern (28 bp):
TCTTTTTTTCTTTTTTTTTTTTTTTTCT
Found at i:28156456 original size:21 final size:19
Alignment explanation
Indices: 28156430--28156496 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 19
28156420 TTTTTTCCTG
*
28156430 TTTTTTTTATTTTCTTTTT
1 TTTTTTTTTTTTTCTTTTT
28156449 CTTTTTTTCTTTTTTCTTTTT
1 -TTTTTTT-TTTTTTCTTTTT
*
28156470 TTTTTCTTCTTTTTCTTCTTT
1 TTTTT-TTTTTTTTCTT-TTT
28156491 TTTTTT
1 TTTTTT
28156497 CATTGAGTCC
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 21 0.50
21 21 0.50
ACGTcount: A:0.01, C:0.12, G:0.00, T:0.87
Consensus pattern (19 bp):
TTTTTTTTTTTTTCTTTTT
Found at i:28156460 original size:38 final size:35
Alignment explanation
Indices: 28156418--28156496 Score: 106
Period size: 35 Copynumber: 2.2 Consensus size: 35
28156408 TCGACCTCTC
* *
28156418 TCTTTTTTCCTGTTTTTTTTATTTTCTTTTTCTTTTTT
1 TCTTTTTT-CT-TTTTTTTT-TCTTCTTTTTCTTCTTT
28156456 TCTTTTTTCTTTTTTTTTTCTTCTTTTTCTTCTTT
1 TCTTTTTTCTTTTTTTTTTCTTCTTTTTCTTCTTT
28156491 T-TTTTT
1 TCTTTTT
28156497 CATTGAGTCC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
34 5 0.13
35 16 0.41
36 8 0.21
37 2 0.05
38 8 0.21
ACGTcount: A:0.01, C:0.14, G:0.01, T:0.84
Consensus pattern (35 bp):
TCTTTTTTCTTTTTTTTTTCTTCTTTTTCTTCTTT
Found at i:28156468 original size:26 final size:27
Alignment explanation
Indices: 28156432--28156497 Score: 89
Period size: 26 Copynumber: 2.4 Consensus size: 27
28156422 TTTTCCTGTT
28156432 TTTTTTATTTTCTTTTTCTT-TTTTTC
1 TTTTTTATTTTCTTTTTCTTCTTTTTC
* *
28156458 TTTTTTCTTTTTTTTTTCTTCTTTTTC
1 TTTTTTATTTTCTTTTTCTTCTTTTTC
*
28156485 TTCTTTTTTTTTC
1 TT-TTTTATTTTC
28156498 ATTGAGTCCG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 18 0.53
27 8 0.24
28 8 0.24
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.85
Consensus pattern (27 bp):
TTTTTTATTTTCTTTTTCTTCTTTTTC
Found at i:28156496 original size:14 final size:13
Alignment explanation
Indices: 28156430--28156497 Score: 75
Period size: 14 Copynumber: 5.0 Consensus size: 13
28156420 TTTTTTCCTG
28156430 TTTTTTTTATTTTC
1 TTTTTTTT-TTTTC
28156444 TTTTTCTTTTTTTC
1 TTTTT-TTTTTTTC
28156458 TTTTTTCTTTTTT-
1 TTTTTT-TTTTTTC
*
28156471 TTTTCTTCTTTTTC
1 TTTT-TTTTTTTTC
*
28156485 TTCTTTTTTTTTC
1 TTTTTTTTTTTTC
28156498 ATTGAGTCCG
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
13 18 0.38
14 26 0.55
15 3 0.06
ACGTcount: A:0.01, C:0.13, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTTTTTTTC
Found at i:28161690 original size:29 final size:29
Alignment explanation
Indices: 28161637--28161844 Score: 135
Period size: 28 Copynumber: 7.3 Consensus size: 29
28161627 TCAAAAATGA
** *
28161637 AATTTTTGGATGCCCGAGGGG-AAAATGAT
1 AATTTTTGGATGTTCG-GGGGTAAAATGGT
28161666 AATTTTTGGATGTTCGGGGGTAAAATGGT
1 AATTTTTGGATGTTCGGGGGTAAAATGGT
*** *
28161695 AA-TTTTGGACACTCGAGGGTAAAATGGT
1 AATTTTTGGATGTTCGGGGGTAAAATGGT
* ***
28161723 AA-TTTTGAACACTCGGGGGTAAAATGGT
1 AATTTTTGGATGTTCGGGGGTAAAATGGT
* * * ***
28161751 AA-TTTTGAAATTTTAGGGTCAAAAAT-GT
1 AATTTTTG-GATGTTCGGGGGTAAAATGGT
** *
28161779 AATTTTTGGACATCCGAGGGGTAAAATGGT
1 AATTTTTGGATGTTCG-GGGGTAAAATGGT
* *
28161809 AA-TTTTGGTTGTT-TGGGGT-AAATGGT
1 AATTTTTGGATGTTCGGGGGTAAAATGGT
28161835 AATTTTTGGA
1 AATTTTTGGA
28161845 AAGTTCGAGG
Statistics
Matches: 143, Mismatches: 30, Indels: 14
0.76 0.16 0.07
Matches are distributed among these distances:
26 9 0.06
27 11 0.08
28 66 0.46
29 53 0.37
30 4 0.03
ACGTcount: A:0.30, C:0.07, G:0.29, T:0.35
Consensus pattern (29 bp):
AATTTTTGGATGTTCGGGGGTAAAATGGT
Found at i:28161729 original size:28 final size:28
Alignment explanation
Indices: 28161651--28161816 Score: 149
Period size: 28 Copynumber: 5.8 Consensus size: 28
28161641 TTTGGATGCC
* * ***
28161651 CGAGGGGAAAATGATAATTTTTGGATGTT
1 CGAGGGTAAAATGGTAA-TTTTGGACACT
*
28161680 CGGGGGTAAAATGGTAATTTTGGACACT
1 CGAGGGTAAAATGGTAATTTTGGACACT
*
28161708 CGAGGGTAAAATGGTAATTTTGAACACT
1 CGAGGGTAAAATGGTAATTTTGGACACT
* * *
28161736 CGGGGGTAAAATGGTAATTTT-GAAATT
1 CGAGGGTAAAATGGTAATTTTGGACACT
**
28161763 TTAGGGTCAAAAAT-GTAATTTTTGGACA-T
1 CGAGGGT--AAAATGGTAA-TTTTGGACACT
28161792 CCGAGGGGTAAAATGGTAATTTTGG
1 -CGA-GGGTAAAATGGTAATTTTGG
28161817 TTGTTTGGGG
Statistics
Matches: 112, Mismatches: 18, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
27 7 0.06
28 58 0.52
29 35 0.31
30 8 0.07
31 4 0.04
ACGTcount: A:0.32, C:0.07, G:0.29, T:0.32
Consensus pattern (28 bp):
CGAGGGTAAAATGGTAATTTTGGACACT
Found at i:28161755 original size:56 final size:56
Alignment explanation
Indices: 28161679--28161816 Score: 165
Period size: 56 Copynumber: 2.4 Consensus size: 56
28161669 TTTTGGATGT
*
28161679 TCGGGGGTAAAATGGTAATTTTGGACACTCGAGGGT-AAAATGGTAA-TTTTGAACA
1 TCGGGGGTAAAATGGTAATTTTGGAAACTCGAGGGTAAAAAT-GTAATTTTTGAACA
* ** *
28161734 CTCGGGGGTAAAATGGTAATTTT-GAAATTTTAGGGTCAAAAATGTAATTTTTGGACA
1 -TCGGGGGTAAAATGGTAATTTTGGAAACTCGAGGGT-AAAAATGTAATTTTTGAACA
28161791 TCCGAGGGGTAAAATGGTAATTTTGG
1 T-CG-GGGGTAAAATGGTAATTTTGG
28161817 TTGTTTGGGG
Statistics
Matches: 71, Mismatches: 5, Indels: 9
0.84 0.06 0.11
Matches are distributed among these distances:
55 9 0.13
56 27 0.38
57 15 0.21
58 19 0.27
59 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (56 bp):
TCGGGGGTAAAATGGTAATTTTGGAAACTCGAGGGTAAAAATGTAATTTTTGAACA
Found at i:28161877 original size:29 final size:28
Alignment explanation
Indices: 28161834--28161907 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 28
28161824 GGGTAAATGG
*
28161834 TAATTTTTGGAAAGTTCGAGGTCAAAAATA
1 TAATTTTTAG-AAGTTCGAGGT-AAAAATA
* * *
28161864 TAATTTTTAGAAGTTTGGGGGTAAAAATG
1 TAATTTTTAGAAG-TTCGAGGTAAAAATA
*
28161893 TAATTTTGAGAAGTT
1 TAATTTTTAGAAGTT
28161908 TAGGGTTACA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
28 2 0.05
29 21 0.55
30 15 0.39
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (28 bp):
TAATTTTTAGAAGTTCGAGGTAAAAATA
Found at i:28161913 original size:28 final size:27
Alignment explanation
Indices: 28161857--28161941 Score: 89
Period size: 29 Copynumber: 3.0 Consensus size: 27
28161847 GTTCGAGGTC
* *
28161857 AAAAATATAATTTTTAGAAGTTTGGGGGT
1 AAAAATGTAA-TTTTAGAAGTTT-AGGGT
28161886 AAAAATGTAATTTTGAGAAGTTTAGGGT
1 AAAAATGTAATTTT-AGAAGTTTAGGGT
* *
28161914 TACAATGTAATTTTAGAATAGTTTAGGG
1 AAAAATGTAATTTTAG-A-AGTTTAGGG
28161942 GTTAAAACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
27 2 0.04
28 21 0.43
29 26 0.53
ACGTcount: A:0.38, C:0.01, G:0.24, T:0.38
Consensus pattern (27 bp):
AAAAATGTAATTTTAGAAGTTTAGGGT
Found at i:28163733 original size:23 final size:23
Alignment explanation
Indices: 28163707--28163797 Score: 86
Period size: 23 Copynumber: 4.2 Consensus size: 23
28163697 AATTTAAGAA
28163707 TAAATTTAAACTTAAATTAAATT
1 TAAATTTAAACTTAAATTAAATT
28163730 TAAATTT--A---AAA-TAAATT
1 TAAATTTAAACTTAAATTAAATT
* *
28163747 TAAACTTAAACTTAAAATAAATT
1 TAAATTTAAACTTAAATTAAATT
** *
28163770 TAAATTTAAAAATAAATTTAAACT
1 TAAATTTAAACTTAAA-TTAAATT
28163794 TAAA
1 TAAA
28163798 ATAAATATAA
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
17 12 0.22
18 3 0.05
19 1 0.02
21 1 0.02
22 3 0.05
23 26 0.47
24 9 0.16
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (23 bp):
TAAATTTAAACTTAAATTAAATT
Found at i:28163808 original size:6 final size:6
Alignment explanation
Indices: 28163688--28163797 Score: 102
Period size: 6 Copynumber: 18.8 Consensus size: 6
28163678 CAAATTTAGG
* *
28163688 TTAAAT TTAAAT TTAAGA- ATAAAT TTAAAC TTAAA- TTAAAT TTAAAT
1 TTAAAT TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * * * *
28163735 TTAAA- ATAAAT TTAAAC TTAAAC TTAAA- ATAAAT TTAAAT TTAAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
28163781 ATAAAT TTAAAC TTAAA
1 TTAAAT TTAAAT TTAAA
28163798 ATAAATATAA
Statistics
Matches: 86, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
5 14 0.16
6 71 0.83
7 1 0.01
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:28163810 original size:18 final size:17
Alignment explanation
Indices: 28163689--28163808 Score: 123
Period size: 17 Copynumber: 6.6 Consensus size: 17
28163679 AAATTTAGGT
*
28163689 TAAATTTAAATTTAAGAA
1 TAAATTTAAACTTAA-AA
*
28163707 TAAATTTAAACTTAAAT
1 TAAATTTAAACTTAAAA
*
28163724 TAAATTTAAATTTAAAA
1 TAAATTTAAACTTAAAA
28163741 TAAATTTAAACTTAAACTTAAAA
1 TAAA--T----TTAAACTTAAAA
*
28163764 TAAATTTAAATTTAAAAA
1 TAAATTTAAACTT-AAAA
28163782 TAAATTTAAACTTAAAA
1 TAAATTTAAACTTAAAA
*
28163799 TAAATATAAA
1 TAAATTTAAA
28163809 ACAAAATGGG
Statistics
Matches: 87, Mismatches: 8, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
17 40 0.46
18 30 0.34
19 1 0.01
21 1 0.01
23 15 0.17
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (17 bp):
TAAATTTAAACTTAAAA
Found at i:28164820 original size:21 final size:20
Alignment explanation
Indices: 28164796--28164839 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
28164786 ACTTTCATCA
* *
28164796 TTAAGATTTAATTAAACATTT
1 TTAACATTT-ATTAAACATAT
*
28164817 TTAACCTTTATTAAACATAT
1 TTAACATTTATTAAACATAT
28164837 TTA
1 TTA
28164840 TAATCAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAACATTTATTAAACATAT
Found at i:28182169 original size:11 final size:12
Alignment explanation
Indices: 28182153--28182189 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
28182143 ATTTACTAAC
28182153 ATTTAATTT-TT
1 ATTTAATTTATT
28182164 ATTTAATTTATT
1 ATTTAATTTATT
28182176 A-TT-ATTTATT
1 ATTTAATTTATT
28182186 ATTT
1 ATTT
28182190 CTTTATGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 8 0.33
11 13 0.54
12 3 0.12
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
ATTTAATTTATT
Found at i:28183997 original size:7 final size:7
Alignment explanation
Indices: 28183985--28184010 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28183975 TGAACGAAAA
28183985 AATATTT
1 AATATTT
28183992 AATATTT
1 AATATTT
28183999 AATATTT
1 AATATTT
28184006 AATAT
1 AATAT
28184011 CATACATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
AATATTT
Found at i:28186987 original size:31 final size:29
Alignment explanation
Indices: 28186952--28187032 Score: 99
Period size: 31 Copynumber: 2.7 Consensus size: 29
28186942 AATATTAAAA
*
28186952 TTATATATGAATTTTGATTTAATGTATAATG
1 TTATATATAAATTTTGATTT--TGTATAATG
* * *
28186983 TTATATACAAATTTTGATTTTGTGTAATT
1 TTATATATAAATTTTGATTTTGTATAATG
28187012 TTATATATAAAATTTTGATTT
1 TTATATAT-AAATTTTGATTT
28187033 GATTTAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
29 14 0.32
30 12 0.27
31 18 0.41
ACGTcount: A:0.35, C:0.01, G:0.10, T:0.54
Consensus pattern (29 bp):
TTATATATAAATTTTGATTTTGTATAATG
Found at i:28187041 original size:30 final size:29
Alignment explanation
Indices: 28186952--28187043 Score: 96
Period size: 30 Copynumber: 3.1 Consensus size: 29
28186942 AATATTAAAA
* * *
28186952 TTATATATGAATTTTGATTTAATGTATAATG
1 TTATATATAAATTTTGATTTGAT-T-TAATT
* *
28186983 TTATATACAAATTTTGATTTTG-TGTAATT
1 TTATATATAAATTTTGA-TTTGATTTAATT
28187012 TTATATATAAAATTTTGATTTGATTTAATT
1 TTATATAT-AAATTTTGATTTGATTTAATT
28187042 TT
1 TT
28187044 CATAAATTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
29 15 0.29
30 17 0.33
31 16 0.31
32 3 0.06
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.55
Consensus pattern (29 bp):
TTATATATAAATTTTGATTTGATTTAATT
Found at i:28188478 original size:6 final size:6
Alignment explanation
Indices: 28188456--28188518 Score: 65
Period size: 6 Copynumber: 10.2 Consensus size: 6
28188446 ACTTTTATGT
* * *
28188456 TTTAAA TTTTGAA TTTAAA TTT-AT TTTAAA TTTAAA TTCAACTA TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA--A TTTAAA
28188506 TTTAAA TTTAAA T
1 TTTAAA TTTAAA T
28188519 CAAATTATGA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
5 4 0.09
6 33 0.70
7 5 0.11
8 5 0.11
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:28188532 original size:26 final size:26
Alignment explanation
Indices: 28188480--28188544 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
28188470 TTAAATTTAT
**
28188480 TTTAAATTTAAATTCAACTATTTAAA
1 TTTAAATTTAAATTCAACTATGAAAA
*
28188506 TTTAAATTTAAA-TCAAATTATGAAAA
1 TTTAAATTTAAATTC-AACTATGAAAA
*
28188532 TACTAAATTTAAA
1 T-TTAAATTTAAA
28188545 CATTAAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 2 0.06
26 21 0.64
27 10 0.30
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (26 bp):
TTTAAATTTAAATTCAACTATGAAAA
Found at i:28189328 original size:24 final size:24
Alignment explanation
Indices: 28189283--28189329 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
28189273 GTTATAATAA
* * *
28189283 TAATAATAATAATAAATAAATTTT
1 TAATAAAAATAAAAAAGAAATTTT
*
28189307 TAATAAAAATAAAAAAGGAATTT
1 TAATAAAAATAAAAAAGAAATTT
28189330 GAAAGGACCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (24 bp):
TAATAAAAATAAAAAAGAAATTTT
Found at i:28190321 original size:162 final size:162
Alignment explanation
Indices: 28190134--28190472 Score: 588
Period size: 162 Copynumber: 2.1 Consensus size: 162
28190124 AGTTTTCAAT
* *
28190134 TTAGTCCTTTGACTGTTTTACTGCACCAGAGGTTGCCACGTGTCACTTTTTGGCTTATTCATGTA
1 TTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTCATGTA
* *
28190199 TCTGGTCCCTGTTATTTTTAATTTGTCGTAATTTAATCCCTAAATCAACTTTTATTTAATTACAA
66 TCTGATCCCTGTTATTTTTAATGTGTCGTAATTTAATCCCTAAATCAACTTTTATTTAATTACAA
*
28190264 AATTGGCCCAAGAATTTTTTAAGATTTATAAA
131 AATTGGCCCAAGAATTTTTTAAGATTTACAAA
*
28190296 TTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGTA
1 TTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTCATGTA
*
28190361 TCTGATCCCTGTTATTTTTAATGTGTCTTAATTTAATCCCTAAATCAACTTTTATTTAATTACAA
66 TCTGATCCCTGTTATTTTTAATGTGTCGTAATTTAATCCCTAAATCAACTTTTATTTAATTACAA
* *
28190426 AATTGGCCCAAGAATTTTTTAAGATTTACGAT
131 AATTGGCCCAAGAATTTTTTAAGATTTACAAA
*
28190458 TTAGTCCATTGACTG
1 TTAGTCCTTTGACTG
28190473 CTGGATGCCT
Statistics
Matches: 167, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
162 167 1.00
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (162 bp):
TTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTCATGTA
TCTGATCCCTGTTATTTTTAATGTGTCGTAATTTAATCCCTAAATCAACTTTTATTTAATTACAA
AATTGGCCCAAGAATTTTTTAAGATTTACAAA
Found at i:28190606 original size:29 final size:28
Alignment explanation
Indices: 28190573--28190912 Score: 104
Period size: 29 Copynumber: 11.6 Consensus size: 28
28190563 TGATTTCACT
28190573 AAAAATTACCATTTTACGCCCAAACTCTTC
1 AAAAATT-CCATTTTAC-CCCAAACTCTTC
*
28190603 -AAAA-TCTCATTTTTAACCCC-AA-TTTTACC
1 AAAAATTC-CA-TTTT-ACCCCAAACTCTT--C
28190632 AAAAATTACCATTTTACCCCCAAACTC-TC
1 AAAAATT-CCATTTTA-CCCCAAACTCTTC
** **
28190661 AAAAATTCCATTTTTAACCCCAATTTCACC
1 AAAAATTCCA-TTTT-ACCCCAAACTCTTC
* * *
28190691 AAAAATACCATTCTACCCCTGAACT-TTC
1 AAAAATTCCATTTTACCCC-AAACTCTTC
* * * *** ***
28190719 CAAAATTCTATTTTAACCTCAGTTTAACC
1 AAAAATTCCATTTT-ACCCCAAACTCTTC
28190748 AAAAATTACCATTTTACCCCTAAACTC-TC
1 AAAAATT-CCATTTTACCCC-AAACTCTTC
* * * ** *
28190777 TAAAATTCCCTTTTTAACCCCGATTTCATC
1 AAAAATT-CCATTTT-ACCCCAAACTCTTC
*
28190807 AAGAATTACCATTTTACCCCCAAACTC-TC
1 AAAAATT-CCATTTTA-CCCCAAACTCTTC
** * * * ** **
28190836 CCAAATTCCATTTTTAACTCGATTTCACC
1 AAAAATTCCA-TTTTACCCCAAACTCTTC
*
28190865 AAAAATTACCATTTTACCCCCGAACTC-TC
1 AAAAATT-CCATTTTA-CCCCAAACTCTTC
28190894 AAAAATTCCATTTTTACCC
1 AAAAATTCCA-TTTTACCC
28190913 TATTTTTACC
Statistics
Matches: 223, Mismatches: 60, Indels: 56
0.66 0.18 0.17
Matches are distributed among these distances:
27 4 0.02
28 39 0.17
29 105 0.47
30 67 0.30
31 6 0.03
32 2 0.01
ACGTcount: A:0.34, C:0.31, G:0.02, T:0.33
Consensus pattern (28 bp):
AAAAATTCCATTTTACCCCAAACTCTTC
Found at i:28190708 original size:58 final size:59
Alignment explanation
Indices: 28190565--28190942 Score: 446
Period size: 59 Copynumber: 6.5 Consensus size: 59
28190555 CTTGACCCTG
* *
28190565 ATTTCACTAAAAATTACCATTTTACGCCCAAACTCTTC-AAAA-TCTCATTTTTAACCCCA
1 ATTTCACCAAAAATTACCATTTTACCCCCAAACTC-TCAAAAATTC-CATTTTTAACCCCA
*
28190624 ATTTTACCAAAAATTACCATTTTACCCCCAAACTCTCAAAAATTCCATTTTTAACCCCA
1 ATTTCACCAAAAATTACCATTTTACCCCCAAACTCTCAAAAATTCCATTTTTAACCCCA
* ** * * * *
28190683 ATTTCACCAAAAA-TACCATTCTACCCCTGAACTTTCCAAAATTCTA-TTTTAACCTCA
1 ATTTCACCAAAAATTACCATTTTACCCCCAAACTCTCAAAAATTCCATTTTTAACCCCA
* * * * * *
28190740 GTTTAACCAAAAATTACCATTTTACCCCTAAACTCTCTAAAATTCCCTTTTTAACCCCG
1 ATTTCACCAAAAATTACCATTTTACCCCCAAACTCTCAAAAATTCCATTTTTAACCCCA
* * ** * *
28190799 ATTTCATCAAGAATTACCATTTTACCCCCAAACTCTCCCAAATTCCATTTTTAA-CTCG
1 ATTTCACCAAAAATTACCATTTTACCCCCAAACTCTCAAAAATTCCATTTTTAACCCCA
* *
28190857 ATTTCACCAAAAATTACCATTTTACCCCCGAACTCTCAAAAATTCCATTTTT-ACCCTA
1 ATTTCACCAAAAATTACCATTTTACCCCCAAACTCTCAAAAATTCCATTTTTAACCCCA
* * *
28190915 TTTTTACC-AAAATTACCATTTTGCCCCC
1 ATTTCACCAAAAATTACCATTTTACCCCC
28190943 GAGTATCCAA
Statistics
Matches: 273, Mismatches: 41, Indels: 12
0.84 0.13 0.04
Matches are distributed among these distances:
57 41 0.15
58 113 0.41
59 117 0.43
60 2 0.01
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.34
Consensus pattern (59 bp):
ATTTCACCAAAAATTACCATTTTACCCCCAAACTCTCAAAAATTCCATTTTTAACCCCA
Found at i:28190877 original size:175 final size:174
Alignment explanation
Indices: 28190573--28190941 Score: 487
Period size: 175 Copynumber: 2.1 Consensus size: 174
28190563 TGATTTCACT
*
28190573 AAAAATTACCATTTTACGCCCAAACTCTTCAAAATCTCATTTTTAACCCCAATTTTACCAAAAAT
1 AAAAATTACCATTTTAC-CCCAAACTCTTCAAAATCTCATTTTTAACCCCAATTTCACCAAAAAT
28190638 TACCATTTTACCCCCAAACTCTCAAAAATTCCATTTTTAACCCCAATTTCACCAAAAATACCATT
65 TACCATTTTACCCCCAAACTCTCAAAAATTCCATTTTTAACCCCAATTTCACCAAAAATACCATT
* * * *
28190703 CTACCCCTGAACTTTCCAAAATTCTATTTTAA-CCTCAGTTTAACC
130 CTACCCCCGAACTCTCAAAAATTCCATTTTAACCCT-AGTTTAACC
* * * *
28190748 AAAAATTACCATTTTACCCCTAAACTC-TCTAAAAT-TCCCTTTTTAACCCCGATTTCATCAAGA
1 AAAAATTACCATTTTACCCC-AAACTCTTC-AAAATCT-CATTTTTAACCCCAATTTCACCAAAA
** * *
28190811 ATTACCATTTTACCCCCAAACTCTCCCAAATTCCATTTTTAA-CTCGATTTCACCAAAAATTACC
63 ATTACCATTTTACCCCCAAACTCTCAAAAATTCCATTTTTAACCCCAATTTCACCAAAAA-TACC
* * * *
28190875 ATTTTACCCCCGAACTCTCAAAAATTCCATTTTTACCCTATTTTTACC
127 ATTCTACCCCCGAACTCTCAAAAATTCCATTTTAACCCTAGTTTAACC
*
28190923 -AAAATTACCATTTTGCCCC
1 AAAAATTACCATTTTACCCC
28190942 CGAGTATCCA
Statistics
Matches: 171, Mismatches: 18, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
174 39 0.23
175 129 0.75
176 3 0.02
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.34
Consensus pattern (174 bp):
AAAAATTACCATTTTACCCCAAACTCTTCAAAATCTCATTTTTAACCCCAATTTCACCAAAAATT
ACCATTTTACCCCCAAACTCTCAAAAATTCCATTTTTAACCCCAATTTCACCAAAAATACCATTC
TACCCCCGAACTCTCAAAAATTCCATTTTAACCCTAGTTTAACC
Found at i:28203144 original size:76 final size:76
Alignment explanation
Indices: 28203044--28203652 Score: 956
Period size: 76 Copynumber: 8.0 Consensus size: 76
28203034 CAGACCGCAC
28203044 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAATTGGATAACAAGTCTTTATCTCTGAAAT
1 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAATTGGATAACAAGTCTTTATCTCTGAAAT
28203109 TGAAGTAAGAG
66 TGAAGTAAGAG
* *
28203120 CAACG-TCATTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAA
1 CAA-GATCATTTCCTATCCTCTTGAAATTGAAGTAGAATTGGATAACAAGTCTTTATCTCTGAAA
28203184 TTGAAGTAAGAG
65 TTGAAGTAAGAG
* * *
28203196 CAACATCATTTCCTATCCTCTTGAAATTGAAGTA-AAGCTGGATATCAAGTCTTTATCTCTGAAA
1 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAA-TTGGATAACAAGTCTTTATCTCTGAAA
28203260 TTGAAGTAAGAG
65 TTGAAGTAAGAG
* * * *
28203272 CAAGATCTTTTCCTATCCCCTTGAAATCGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
1 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAATTGGATAACAAGTCTTTATCTCTGAAAT
28203337 TGAAGTAAGAG
66 TGAAGTAAGAG
* * *
28203348 CAACATCATTTCCTATCCTCTTGAAATTGAAGTA-AAGCTGGATATCAAGTCTTTATCTCTGAAA
1 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAA-TTGGATAACAAGTCTTTATCTCTGAAA
28203412 TTGAAGTAAGAG
65 TTGAAGTAAGAG
* * *
28203424 CAAGATCATATCCTATCCTCTTGAAATTGAAGTA-AAGCTGGATATCAAGTCTTTATCTCTGAAA
1 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAA-TTGGATAACAAGTCTTTATCTCTGAAA
28203488 TTGAAGTAAGAG
65 TTGAAGTAAGAG
* * **
28203500 CGAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACGCGTCTTTATCTCTGAAAT
1 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAATTGGATAACAAGTCTTTATCTCTGAAAT
28203565 TGAAGTAAGAG
66 TGAAGTAAGAG
** *
28203576 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGCGTTGGATAACGAGTCTTTATCTCTGAAAT
1 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAATTGGATAACAAGTCTTTATCTCTGAAAT
28203641 TGAAGTAAGAG
66 TGAAGTAAGAG
28203652 C
1 C
28203653 TAGACAAAGC
Statistics
Matches: 494, Mismatches: 33, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
75 2 0.00
76 489 0.99
77 3 0.01
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Consensus pattern (76 bp):
CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAATTGGATAACAAGTCTTTATCTCTGAAAT
TGAAGTAAGAG
Found at i:28203441 original size:228 final size:228
Alignment explanation
Indices: 28203044--28203652 Score: 1065
Period size: 228 Copynumber: 2.7 Consensus size: 228
28203034 CAGACCGCAC
*
28203044 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAATTGGATAACAAGTCTTTATCTCTGAAAT
1 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
* *
28203109 TGAAGTAAGAGCAACGTCATTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTT
66 TGAAGTAAGAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTT
*
28203174 ATCTCTGAAATTGAAGTAAGAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGAT
131 ATCTCTGAAATTGAAGTAAGAGCAACATCATATCCTATCCTCTTGAAATTGAAGTAAAGCTGGAT
28203239 ATCAAGTCTTTATCTCTGAAATTGAAGTAAGAG
196 ATCAAGTCTTTATCTCTGAAATTGAAGTAAGAG
* * *
28203272 CAAGATCTTTTCCTATCCCCTTGAAATCGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
1 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
* * *
28203337 TGAAGTAAGAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTT
66 TGAAGTAAGAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTT
*
28203402 ATCTCTGAAATTGAAGTAAGAGCAAGATCATATCCTATCCTCTTGAAATTGAAGTAAAGCTGGAT
131 ATCTCTGAAATTGAAGTAAGAGCAACATCATATCCTATCCTCTTGAAATTGAAGTAAAGCTGGAT
28203467 ATCAAGTCTTTATCTCTGAAATTGAAGTAAGAG
196 ATCAAGTCTTTATCTCTGAAATTGAAGTAAGAG
* **
28203500 CGAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACGCGTCTTTATCTCTGAAAT
1 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
* * *
28203565 TGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGCGTTGGATAACGAGTCTTT
66 TGAAGTAAGAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTT
28203630 ATCTCTGAAATTGAAGTAAGAGC
131 ATCTCTGAAATTGAAGTAAGAGC
28203653 TAGACAAAGC
Statistics
Matches: 358, Mismatches: 23, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
228 358 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Consensus pattern (228 bp):
CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
TGAAGTAAGAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTT
ATCTCTGAAATTGAAGTAAGAGCAACATCATATCCTATCCTCTTGAAATTGAAGTAAAGCTGGAT
ATCAAGTCTTTATCTCTGAAATTGAAGTAAGAG
Found at i:28203639 original size:38 final size:38
Alignment explanation
Indices: 28203065--28203647 Score: 210
Period size: 38 Copynumber: 15.3 Consensus size: 38
28203055 CCTATCCTCT
* *
28203065 TGAAATTGAAGTAGAATTGGATAACAAGTCTTTATCTC
1 TGAAATTGAAGTAGAGTTGGATAACGAGTCTTTATCTC
* * *
28203103 TGAAATTGAAGTA-AG--AG-CAAC--GTCATTTCCTATCCGC
1 TGAAATTGAAGTAGAGTTGGATAACGAGTC--TT--TAT-CTC
*
28203140 TTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTC
1 -TGAAATTGAAGTAGAGTTGGATAACGAGTCTTTATCTC
* *
28203179 TGAAATTGAAGTA-AG--AG-CAAC-A-TCATTTCCTATCCTC
1 TGAAATTGAAGTAGAGTTGGATAACGAGTC--TT--TAT-CTC
* * * *
28203216 TTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTC
1 -TGAAATTGAAGTAGAGTTGGATAACGAGTCTTTATCTC
*** *** * *
28203255 TGAAATTGAAGTAAGAGCAAGAT--CTTTTC-CTATCCCC
1 TGAAATTGAAGT-AGAGTTGGATAACGAGTCTTTAT-CTC
* *
28203292 TTGAAATCGAAGTAGAGTTGGATAACAAGTCTTTATCTC
1 -TGAAATTGAAGTAGAGTTGGATAACGAGTCTTTATCTC
* *
28203331 TGAAATTGAAGTA-AG--AG-CAAC-A-TCATTTCCTATCCTC
1 TGAAATTGAAGTAGAGTTGGATAACGAGTC--TT--TAT-CTC
* * * *
28203368 TTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTC
1 -TGAAATTGAAGTAGAGTTGGATAACGAGTCTTTATCTC
*** * * *
28203407 TGAAATTGAAGTAAGAGCAAGATCA-TA-TC-CTATCCTC
1 TGAAATTGAAGT-AGAGTTGGATAACGAGTCTTTAT-CTC
* * * *
28203444 TTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTC
1 -TGAAATTGAAGTAGAGTTGGATAACGAGTCTTTATCTC
*
28203483 TGAAATTGAAGTAAGAG-CGAGAT--C-A-T-TTCCTATCCTC
1 TGAAATTGAAGT-AGAGTTG-GATAACGAGTCTT--TAT-CTC
*
28203520 TTGAAATTGAAGTAGAGTTGGATAACGCGTCTTTATCTC
1 -TGAAATTGAAGTAGAGTTGGATAACGAGTCTTTATCTC
***
28203559 TGAAATTGAAGTAAGAGCAAGAT--C-A-T-TTCCTATCCTC
1 TGAAATTGAAGT-AGAGTTGGATAACGAGTCTT--TAT-CTC
*
28203596 TTGAAATTGAAGTAGCGTTGGATAACGAGTCTTTATCTC
1 -TGAAATTGAAGTAGAGTTGGATAACGAGTCTTTATCTC
28203635 TGAAATTGAAGTA
1 TGAAATTGAAGTA
28203648 AGAGCTAGAC
Statistics
Matches: 414, Mismatches: 61, Indels: 140
0.67 0.10 0.23
Matches are distributed among these distances:
32 7 0.02
33 2 0.00
34 19 0.05
35 5 0.01
36 22 0.05
37 58 0.14
38 189 0.46
39 59 0.14
40 22 0.05
41 5 0.01
42 17 0.04
43 2 0.00
44 7 0.02
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (38 bp):
TGAAATTGAAGTAGAGTTGGATAACGAGTCTTTATCTC
Found at i:28204023 original size:13 final size:13
Alignment explanation
Indices: 28204005--28204034 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
28203995 ACTTTTATGT
28204005 TTTAAATTTTGAA
1 TTTAAATTTTGAA
28204018 TTTAAATTTTGAA
1 TTTAAATTTTGAA
28204031 TTTA
1 TTTA
28204035 TTTAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (13 bp):
TTTAAATTTTGAA
Found at i:28204043 original size:6 final size:6
Alignment explanation
Indices: 28204005--28204101 Score: 76
Period size: 6 Copynumber: 16.2 Consensus size: 6
28203995 ACTTTTATGT
* * *
28204005 TTTAAA TTTTGAA TTTAAA TTTTGAA TTT--A TTTAAA TTTAAA TTT-AT
1 TTTAAA -TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
28204052 TTTAAA TTTAAA TTCAACTA TTCAAA TTT-AT TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAA--A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
28204101 T
1 T
28204102 CAAATTATGA
Statistics
Matches: 74, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
4 4 0.05
5 8 0.11
6 46 0.62
7 10 0.14
8 6 0.08
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:28204097 original size:17 final size:16
Alignment explanation
Indices: 28204017--28204098 Score: 78
Period size: 17 Copynumber: 5.1 Consensus size: 16
28204007 TAAATTTTGA
*
28204017 ATTTAAATTTTGAATTT
1 ATTTAAA-TTTAAATTT
28204034 ATTTAAATTTAAATTT
1 ATTTAAATTTAAATTT
*
28204050 ATTTTAAATTTAAATTC
1 A-TTTAAATTTAAATTT
** *
28204067 AACT--ATTCAAATTT
1 ATTTAAATTTAAATTT
28204081 ATTTTAAATTTAAATTT
1 A-TTTAAATTTAAATTT
28204098 A
1 A
28204099 AATCAAATTA
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
14 9 0.17
15 1 0.02
16 10 0.19
17 32 0.62
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (16 bp):
ATTTAAATTTAAATTT
Found at i:28204908 original size:24 final size:24
Alignment explanation
Indices: 28204863--28204909 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
28204853 ACGGTTATAA
* * *
28204863 TAATAATAATAATAAATAAATTTT
1 TAATAAAAATAAAAAAGAAATTTT
*
28204887 TAATAAAAATAAAAAAGGAATTT
1 TAATAAAAATAAAAAAGAAATTT
28204910 GAAAGGACCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (24 bp):
TAATAAAAATAAAAAAGAAATTTT
Found at i:28205982 original size:163 final size:162
Alignment explanation
Indices: 28205712--28206051 Score: 572
Period size: 163 Copynumber: 2.1 Consensus size: 162
28205702 AGTTTTCAAT
*
28205712 TTAGTCCTTTGACTGTTTTACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTCATGTA
1 TTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTCATGTA
*
28205777 TCTGGTCCCTGTTATTTTTAATTTGTCGTAATTTAATCCCTAAATCAACTTTTATTTAATTACAA
66 TCTGGTCCCTGTTATTTTTAATGTGTCGTAATTTAATCCCTAAATCAACTTTTATTTAATTACAA
* *
28205842 AATTGGCCCAAGAATTTTTTTAAGATTTATAAA
131 AATTGGCCCAAGAA-TTTTTCAAGATTTACAAA
*
28205875 TTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGTA
1 TTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTCATGTA
* *
28205940 TCTGGTCCCTGTTATTTTTAATGTGTCTTAATTTAATCCCTAAATCAACTTTTATTTAATTATAA
66 TCTGGTCCCTGTTATTTTTAATGTGTCGTAATTTAATCCCTAAATCAACTTTTATTTAATTACAA
* * *
28206005 AATTGGCCTAAGAATTTTTCAAGATTTACGAT
131 AATTGGCCCAAGAATTTTTCAAGATTTACAAA
*
28206037 TTAGTCCCTTGACTG
1 TTAGTCCTTTGACTG
28206052 CTGGATGCCT
Statistics
Matches: 166, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
162 28 0.17
163 138 0.83
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (162 bp):
TTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTCATGTA
TCTGGTCCCTGTTATTTTTAATGTGTCGTAATTTAATCCCTAAATCAACTTTTATTTAATTACAA
AATTGGCCCAAGAATTTTTCAAGATTTACAAA
Found at i:28206170 original size:29 final size:28
Alignment explanation
Indices: 28206125--28206403 Score: 121
Period size: 29 Copynumber: 9.6 Consensus size: 28
28206115 AATAGTCCAG
*
28206125 AAATTA-CATCTTGACCCCGATTTCACTAA
1 AAATTACCAT-TTTACCCCGATTTCAC-AA
* ** * *
28206154 AAATTACCATTTTACCCTCAAACTCTCCA
1 AAATTACCATTTTACCC-CGATTTCACAA
28206183 AAA-T-CTCATTTTTAACCCCGATTTCACCAA
1 AAATTAC-CA-TTTT-ACCCCGATTTCA-CAA
28206213 AAATTACC-TTTTACCCTCGAACTTTC-C-A
1 AAATTACCATTTTACCC-CG-A-TTTCACAA
* **
28206241 AAATT-CAATTTTTAACCCTAATTTCACCAA
1 AAATTACCA-TTTT-ACCCCGATTTCA-CAA
* * ** **
28206271 AAAATACCATTTTACCCCCAAACTCACCC
1 AAATTACCATTTTA-CCCCGATTTCACAA
28206300 AAATT-CCATTTTAACCCCCG-TTTCACCAA
1 AAATTACCATTTT-A-CCCCGATTTCA-CAA
**
28206329 AAATTACCATTTTACCCCCGAACTCTA-AA
1 AAATTACCATTTTA-CCCCGATTTC-ACAA
* *
28206358 AAATT-CCATTTTTACCCTGATTTCACCA
1 AAATTACCA-TTTTACCCCGATTTCACAA
*
28206386 AAATTACCATTTTGCCCC
1 AAATTACCATTTTACCCC
28206404 CGGGTATCCA
Statistics
Matches: 188, Mismatches: 35, Indels: 55
0.68 0.13 0.20
Matches are distributed among these distances:
27 7 0.04
28 47 0.25
29 76 0.40
30 48 0.26
31 9 0.05
32 1 0.01
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.32
Consensus pattern (28 bp):
AAATTACCATTTTACCCCGATTTCACAA
Found at i:28206252 original size:58 final size:59
Alignment explanation
Indices: 28206138--28206404 Score: 330
Period size: 58 Copynumber: 4.6 Consensus size: 59
28206128 TTACATCTTG
* *
28206138 ACCCCGATTTCACTAAAAATTACCATTTTACCCTCAAACTCTCCAAAA-TCTCATTTTTA
1 ACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAACTCTCCAAAATTC-CATTTTTA
* * * *
28206197 ACCCCGATTTCACCAAAAATTACC-TTTTACCCTCGAACTTTCCAAAATTCAATTTTTA
1 ACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAACTCTCCAAAATTCCATTTTTA
** * * *
28206255 ACCCTAATTTCACCAAAAAATACCATTTTACCCCCAAACTCACCCAAATTCCA-TTTTA
1 ACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAACTCTCCAAAATTCCATTTTTA
* **
28206313 ACCCCCG-TTTCACCAAAAATTACCATTTTACCCCCGAACTCTAAAAAATTCCATTTTT-
1 A-CCCCGATTTCACCAAAAATTACCATTTTACCCCCAAACTCTCCAAAATTCCATTTTTA
* *
28206371 ACCCTGATTTCACC-AAAATTACCATTTTGCCCCC
1 ACCCCGATTTCACCAAAAATTACCATTTTACCCCC
28206405 GGGTATCCAA
Statistics
Matches: 180, Mismatches: 23, Indels: 12
0.84 0.11 0.06
Matches are distributed among these distances:
57 23 0.13
58 103 0.57
59 54 0.30
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.31
Consensus pattern (59 bp):
ACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAACTCTCCAAAATTCCATTTTTA
Found at i:28206342 original size:117 final size:116
Alignment explanation
Indices: 28206144--28206404 Score: 350
Period size: 117 Copynumber: 2.2 Consensus size: 116
28206134 CTTGACCCCG
* * *
28206144 ATTTCACTAAAAATTACCATTTTACCCTCAAACTCTCCAAAATCTCATTTTTAACCCCGATTTCA
1 ATTTCACCAAAAATTACCATTTTACCCCCAAACTCCCCAAAATCTCATTTTTAACCCCGATTTCA
* * **
28206209 CCAAAAATTACCTTTTACCCTCGAACTTTCCAAAATTCAATTTTTAACCCTA
66 CCAAAAATTACCTTTTACCCCCGAACTCTAAAAAATTCAATTTTT-ACCCTA
* *
28206261 ATTTCACCAAAAAATACCATTTTACCCCCAAACTCACCCAAATTC-CA-TTTTAACCCCCG-TTT
1 ATTTCACCAAAAATTACCATTTTACCCCCAAACTC-CCCAAAATCTCATTTTTAA-CCCCGATTT
* *
28206323 CACCAAAAATTACCATTTTACCCCCGAACTCTAAAAAATTCCATTTTTACCCTG
64 CACCAAAAATTACC-TTTTACCCCCGAACTCTAAAAAATTCAATTTTTACCCTA
*
28206377 ATTTCACC-AAAATTACCATTTTGCCCCC
1 ATTTCACCAAAAATTACCATTTTACCCCC
28206405 GGGTATCCAA
Statistics
Matches: 128, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
115 18 0.14
116 36 0.28
117 67 0.52
118 7 0.05
ACGTcount: A:0.34, C:0.32, G:0.02, T:0.32
Consensus pattern (116 bp):
ATTTCACCAAAAATTACCATTTTACCCCCAAACTCCCCAAAATCTCATTTTTAACCCCGATTTCA
CCAAAAATTACCTTTTACCCCCGAACTCTAAAAAATTCAATTTTTACCCTA
Found at i:28206435 original size:58 final size:58
Alignment explanation
Indices: 28206138--28206439 Score: 256
Period size: 58 Copynumber: 5.2 Consensus size: 58
28206128 TTACATCTTG
* * * * ** *
28206138 ACCCCGATTTCACTAAAAATTACCATTTTACCCTCAAACTCTCCAAAATCTCATTTTTA
1 ACCCTGATTTCACCAAAAATTACCATTTTACCCCCGAACTCTAAAAAATCCCA-TTTTA
* * * ** * *
28206197 ACCCCGATTTCACCAAAAATTACC-TTTTACCCTCGAACTTTCCAAAATTCAATTTTTA
1 ACCCTGATTTCACCAAAAATTACCATTTTACCCCCGAACTCTAAAAAATCCCA-TTTTA
* * * ** *
28206255 ACCCTAATTTCACCAAAAAATACCATTTTACCCCCAAACTC-ACCCAAATTCCATTTTA
1 ACCCTGATTTCACCAAAAATTACCATTTTACCCCCGAACTCTA-AAAAATCCCATTTTA
* * *
28206313 ACCCCCG-TTTCACCAAAAATTACCATTTTACCCCCGAACTCTAAAAAATTCCATTTTT
1 A-CCCTGATTTCACCAAAAATTACCATTTTACCCCCGAACTCTAAAAAATCCCATTTTA
* * * *
28206371 ACCCTGATTTCACC-AAAATTACCATTTTGCCCCCGGGTA-TC-CAAAAGTCCCATTTTCA
1 ACCCTGATTTCACCAAAAATTACCATTTTACCCCC--GAACTCTAAAAAATCCCATTTT-A
28206429 ACCCTGATTTC
1 ACCCTGATTTC
28206440 GTCGTTTCTT
Statistics
Matches: 206, Mismatches: 29, Indels: 17
0.82 0.12 0.07
Matches are distributed among these distances:
57 35 0.17
58 121 0.59
59 50 0.24
ACGTcount: A:0.32, C:0.32, G:0.04, T:0.31
Consensus pattern (58 bp):
ACCCTGATTTCACCAAAAATTACCATTTTACCCCCGAACTCTAAAAAATCCCATTTTA
Found at i:28209407 original size:211 final size:211
Alignment explanation
Indices: 28209036--28209457 Score: 799
Period size: 211 Copynumber: 2.0 Consensus size: 211
28209026 ATATATTCCA
28209036 TCCAACCAAACATAATAATATTATTACAGTTACATTTCATTCCATTCGACCAAACAAGTGAATTA
1 TCCAACCAAACATAATAATATTATTACAGTTACATTTCATTCCATTCGACCAAACAAGTGAATTA
* *
28209101 TTGATTACAATTTTATTCCATTATAGCTTTATTTCATTACAACTCTATTACATTTCAGTAAACTA
66 CTGATTACAATTTTATTCCATTATAGCTTTATTTCATTACAACTCTATTACATTTCAATAAACTA
* *
28209166 AACATGTCGTTAGTTTGATTTTCGTCATAAATATACACATTTTATAAATGAAACATTAAAAAAGT
131 AACATATCGTTAGTTTGATTTTCATCATAAATATACACATTTTATAAATGAAACATTAAAAAAGT
28209231 TATTTGTGTTTTTGTC
196 TATTTGTGTTTTTGTC
28209247 TCCAACCAAACATAATAATATTATTACAGTTACATTTCATTCCATTCGACCAAACAAGTGAATTA
1 TCCAACCAAACATAATAATATTATTACAGTTACATTTCATTCCATTCGACCAAACAAGTGAATTA
*
28209312 CTGATTACAATTTTATTCCATTATAGCTTTATTTCATTACAACTCTATTACATTTCAATAAATTA
66 CTGATTACAATTTTATTCCATTATAGCTTTATTTCATTACAACTCTATTACATTTCAATAAACTA
28209377 AACATATCGTTAGTTTGATTTTCATCATAAATATACACATTTTATAAATGAAACATTAAAAAAGT
131 AACATATCGTTAGTTTGATTTTCATCATAAATATACACATTTTATAAATGAAACATTAAAAAAGT
28209442 TATTTGTGTTTTTGTC
196 TATTTGTGTTTTTGTC
28209458 ACATTGTGTG
Statistics
Matches: 206, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
211 206 1.00
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (211 bp):
TCCAACCAAACATAATAATATTATTACAGTTACATTTCATTCCATTCGACCAAACAAGTGAATTA
CTGATTACAATTTTATTCCATTATAGCTTTATTTCATTACAACTCTATTACATTTCAATAAACTA
AACATATCGTTAGTTTGATTTTCATCATAAATATACACATTTTATAAATGAAACATTAAAAAAGT
TATTTGTGTTTTTGTC
Found at i:28210154 original size:23 final size:24
Alignment explanation
Indices: 28210124--28210177 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
28210114 ATTGGTAAAA
* *
28210124 AAAAAAATTGG-TCTTTAAAAGTT
1 AAAAAAATTGGACCTTTAAAAATT
28210147 AAAAAAATTGGACCCTTTAAAAATT
1 AAAAAAATTGGA-CCTTTAAAAATT
28210172 AAAAAA
1 AAAAAA
28210178 CAATATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 11 0.41
25 16 0.59
ACGTcount: A:0.56, C:0.07, G:0.09, T:0.28
Consensus pattern (24 bp):
AAAAAAATTGGACCTTTAAAAATT
Found at i:28211135 original size:18 final size:18
Alignment explanation
Indices: 28211112--28211154 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
28211102 TTTTTAGTTG
28211112 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
28211130 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
28211148 TAATTAA
1 TAATTAA
28211155 AAATTTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:28218528 original size:18 final size:17
Alignment explanation
Indices: 28218494--28218534 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
28218484 GAATAGATTT
*
28218494 TTAATTAAATAAATTTAA
1 TTAA-TAAAAAAATTTAA
28218512 TTAATAAAAAAATTTTAA
1 TTAATAAAAAAA-TTTAA
28218530 TTAAT
1 TTAAT
28218535 TACACTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAATAAAAAAATTTAA
Found at i:28220233 original size:82 final size:82
Alignment explanation
Indices: 28220137--28220299 Score: 263
Period size: 82 Copynumber: 2.0 Consensus size: 82
28220127 TCTATTTTGA
*
28220137 TTGCGCTAATAATTCTCGAATCGATTAGATTAGTAATTGCTTAGCTAGTAATTAATTTGACAAAC
1 TTGCACTAATAATTCTCGAATCGATTAGATTAGTAATTGCTTAGCTAGTAATTAATTTGACAAAC
* *
28220202 ATGTTTACCAATTGACG
66 ACGTTTAACAATTGACG
* * *
28220219 TTGCACTAATAATTCTCGAATTGATTTGATTAGTAATTGCTTAGCTAGTAATTAGTTTGACAAAC
1 TTGCACTAATAATTCTCGAATCGATTAGATTAGTAATTGCTTAGCTAGTAATTAATTTGACAAAC
*
28220284 ACGTTTAACGATTGAC
66 ACGTTTAACAATTGAC
28220300 AATCCTTTGG
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 74 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (82 bp):
TTGCACTAATAATTCTCGAATCGATTAGATTAGTAATTGCTTAGCTAGTAATTAATTTGACAAAC
ACGTTTAACAATTGACG
Found at i:28226339 original size:18 final size:18
Alignment explanation
Indices: 28226302--28226341 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28226292 TCTTTAGAAT
* * *
28226302 TTTTTCAAAAAATTTTAA
1 TTTTTAAAAAAATATAAA
28226320 TTTTTAAAAAAATATAAA
1 TTTTTAAAAAAATATAAA
28226338 TTTT
1 TTTT
28226342 GGAATTGTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTTAAAAAAATATAAA
Found at i:28226408 original size:21 final size:21
Alignment explanation
Indices: 28226355--28226407 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
28226345 ATTGTATAAA
*
28226355 TATTTTGAA-ATTT-AAAATT
1 TATTTTGAATTTTTGAAAATT
28226374 TATTTTGAATTTTTGAAAA-T
1 TATTTTGAATTTTTGAAAATT
28226394 TATTTTGAATTTTT
1 TATTTTGAATTTTT
28226408 TTGTAACTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 9 0.29
20 18 0.58
21 4 0.13
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (21 bp):
TATTTTGAATTTTTGAAAATT
Found at i:28226791 original size:27 final size:27
Alignment explanation
Indices: 28226732--28226792 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
28226722 GTTTAGACTT
*
28226732 GTAAAATAAACATAATATTAGAAATAA
1 GTAAAATAAAAATAATATTAGAAATAA
** *
28226759 AAAAAATAAAAATAATATTA-AGATTAA
1 GTAAAATAAAAATAATATTAGA-AATAA
28226786 GTAAAAT
1 GTAAAAT
28226793 CGTGGGGGTG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.26
Consensus pattern (27 bp):
GTAAAATAAAAATAATATTAGAAATAA
Found at i:28233631 original size:23 final size:23
Alignment explanation
Indices: 28233605--28233657 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
28233595 TACTTTCATG
* *
28233605 TTATTTTTTATTTAGT-TTTATTT
1 TTATATTTTATTTA-TATTTATAT
28233628 TTATATTTTATTTATATTTATAT
1 TTATATTTTATTTATATTTATAT
28233651 TTATATT
1 TTATATT
28233658 CATATGCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.74
Consensus pattern (23 bp):
TTATATTTTATTTATATTTATAT
Found at i:28233641 original size:17 final size:17
Alignment explanation
Indices: 28233583--28233657 Score: 59
Period size: 17 Copynumber: 4.4 Consensus size: 17
28233573 ATGTTTTTGT
*
28233583 TTTTATTTA-TTTTA-C
1 TTTTATTTATTTTTATA
*
28233598 TTTCATGTTATTTTT-TA
1 TTTTAT-TTATTTTTATA
28233615 -TTTAGTTTTATTTTTATA
1 TTTTA--TTTATTTTTATA
*
28233633 TTTTATTTATATTTATA
1 TTTTATTTATTTTTATA
28233650 TTTATATT
1 TTT-TATT
28233658 CATATGCATA
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
15 5 0.10
16 6 0.12
17 26 0.54
18 7 0.15
19 4 0.08
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (17 bp):
TTTTATTTATTTTTATA
Found at i:28233641 original size:27 final size:27
Alignment explanation
Indices: 28233584--28233642 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
28233574 TGTTTTTGTT
* *
28233584 TTTATTTATTTTACTTTCATGTTATTT
1 TTTATTTATTTTACTTTCATATTATTA
* *
28233611 TTTATTTAGTTTTATTTTTATATT-TTA
1 TTTATTTA-TTTTACTTTCATATTATTA
28233638 TTTAT
1 TTTAT
28233643 ATTTATATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 15 0.56
28 12 0.44
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.73
Consensus pattern (27 bp):
TTTATTTATTTTACTTTCATATTATTA
Found at i:28233653 original size:12 final size:12
Alignment explanation
Indices: 28233621--28233712 Score: 73
Period size: 12 Copynumber: 7.8 Consensus size: 12
28233611 TTTATTTAGT
*
28233621 TTTATTTTTATA
1 TTTATATTTATA
28233633 TTT-TATTTATA
1 TTTATATTTATA
28233644 TTTATATTTATA
1 TTTATATTTATA
* **
28233656 TTCATATGCATA
1 TTTATATTTATA
28233668 TTCT-TATTCT-TA
1 TT-TATATT-TATA
* *
28233680 TTCATATTTCTA
1 TTTATATTTATA
* *
28233692 TTTCTATTTCTA
1 TTTATATTTATA
28233704 TTTATATTT
1 TTTATATTT
28233713 TACTACGCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
11 11 0.17
12 53 0.83
ACGTcount: A:0.25, C:0.09, G:0.01, T:0.65
Consensus pattern (12 bp):
TTTATATTTATA
Found at i:28233662 original size:6 final size:6
Alignment explanation
Indices: 28233636--28233687 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
28233626 TTTTATATTT
* * * * * *
28233636 TATTTA TATTTA TATTTA TATTCA TATGCA TATTCT TATTCT TATTCA
1 TATTCA TATTCA TATTCA TATTCA TATTCA TATTCA TATTCA TATTCA
28233684 TATT
1 TATT
28233688 TCTATTTCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.29, C:0.10, G:0.02, T:0.60
Consensus pattern (6 bp):
TATTCA
Found at i:28233712 original size:18 final size:19
Alignment explanation
Indices: 28233627--28233712 Score: 67
Period size: 18 Copynumber: 4.8 Consensus size: 19
28233617 TAGTTTTATT
28233627 TTTATATTT-TATTT-ATA
1 TTTATATTTATATTTCATA
28233644 TTTATATTTATA-TTCATA
1 TTTATATTTATATTTCATA
** *
28233662 TGCATATTCT-TA-TTCTTA
1 TTTATATT-TATATTTCATA
* *
28233680 TTCATATTTCTATTTC-TA
1 TTTATATTTATATTTCATA
*
28233698 TTTCTATTTATATTT
1 TTTATATTTATATTT
28233713 TACTACGCAC
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
17 12 0.21
18 41 0.72
19 4 0.07
ACGTcount: A:0.26, C:0.09, G:0.01, T:0.64
Consensus pattern (19 bp):
TTTATATTTATATTTCATA
Found at i:28241793 original size:8 final size:8
Alignment explanation
Indices: 28241782--28241851 Score: 51
Period size: 8 Copynumber: 8.9 Consensus size: 8
28241772 AGAAAAAAAT
28241782 AAAAAGGAA
1 AAAAAGG-A
28241791 AAAAACGGA
1 AAAAA-GGA
28241800 AAAAA-GA
1 AAAAAGGA
*
28241807 GAAAAA-CA
1 -AAAAAGGA
28241815 AAAAAGG-
1 AAAAAGGA
28241822 -AAAAGGA
1 AAAAAGGA
*
28241829 AAAAAAGA
1 AAAAAGGA
28241837 AGAAAA-GA
1 A-AAAAGGA
28241845 AAAAAGG
1 AAAAAGG
28241852 GGAGGTCGAG
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
6 6 0.12
7 11 0.22
8 17 0.33
9 15 0.29
10 2 0.04
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (8 bp):
AAAAAGGA
Found at i:28241834 original size:17 final size:16
Alignment explanation
Indices: 28241771--28241849 Score: 58
Period size: 15 Copynumber: 4.9 Consensus size: 16
28241761 GAAATTTCAC
*
28241771 AAGAAAAAAATAAAAAGG
1 AAGAAAAGAA-AAAAA-G
* *
28241789 AAAAAAACGGAAAAAAG
1 AAGAAAA-GAAAAAAAG
28241806 -AGAAAA-ACAAAAAAG
1 AAGAAAAGA-AAAAAAG
28241821 --GAAAAGGAAAAAAAG
1 AAGAAAA-GAAAAAAAG
28241836 AAGAAAAGAAAAAA
1 AAGAAAAGAAAAAA
28241850 GGGGAGGTCG
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
14 5 0.10
15 14 0.28
16 13 0.26
17 6 0.12
18 11 0.22
19 1 0.02
ACGTcount: A:0.78, C:0.03, G:0.18, T:0.01
Consensus pattern (16 bp):
AAGAAAAGAAAAAAAG
Found at i:28243273 original size:100 final size:100
Alignment explanation
Indices: 28243088--28243620 Score: 446
Period size: 100 Copynumber: 5.4 Consensus size: 100
28243078 AAACACGACA
* * * * * *
28243088 GGAAAGATCTAAGACCGCAACAACGAATCCAGTACTGCAAAGATGC-AAAGGGAAAGGTTTAAGT
1 GGAAAGATCTAAGACCGCAACAGCGGATCCAGTACCGCAAAGATACAAAAGGGAAAGATCTAAGT
*
28243152 CGTAACGGC-GAACCTTA-TACCTCAAAGACATGACG
66 CGTAACGGCAGATCC--AGTACCTCAAAGACATGACG
* * * * *
28243187 GGAAAGATCTAAGACTGCGACAGTGGATCCAGTACCGCAAAGATACAAAAGGGAAAGGTTTAAGT
1 GGAAAGATCTAAGACCGCAACAGCGGATCCAGTACCGCAAAGATACAAAAGGGAAAGATCTAAGT
* * *
28243252 CGTAACGGCGGA-CCGTGTACCTCAGAAGACATAACG
66 CGTAACGGCAGATCC-AGTACCTCA-AAGACATGACG
* * * *
28243288 GGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGCGAAG--ACACAAGGGAAAGATCTAATA
1 GGAAAGATCTAAGACCGCAACAGCGGATCCAGTACCGCAAAGATACAAAAGGGAAAGATCTAA-G
* * *
28243351 TCGCAACAGCAGATCCAGTACCAT-AAAGATACA-GAAG
65 TCGTAACGGCAGATCCAGTACC-TCAAAG--ACATGACG
** * *
28243388 GGAAAGATCTAAGACCGCAACAGCATATCCAGTACCACAAAGATACAGAAGGGAAAGATCTAAGA
1 GGAAAGATCTAAGACCGCAACAGCGGATCCAGTACCGCAAAGATACAAAAGGGAAAGATCTAAG-
* * * * *
28243453 CCGTAATGGCAGATCCAGTACCACAAAAACACGACG
65 TCGTAACGGCAGATCCAGTACCTCAAAGACATGACG
** * * *
28243489 GGAAAGATCTAAGACTC-CAATGGCAGATCCAGTACCGCGAAG--ACACAAGGGAAAGATCTAAG
1 GGAAAGATCTAAGAC-CGCAACAGCGGATCCAGTACCGCAAAGATACAAAAGGGAAAGATCTAAG
* ** * * * * *
28243551 CCGCGACGACGGATCCAGTACCAT-GAAGACA-CAAG
65 TCGTAACGGCAGATCCAGTACC-TCAAAGACATGACG
* * *
28243586 GGAAAGATCTAAG-CCGTAACGGCGGATTCAGTACC
1 GGAAAGATCTAAGACCGCAACAGCGGATCCAGTACC
28243621 ATGAAGATTT
Statistics
Matches: 358, Mismatches: 59, Indels: 37
0.79 0.13 0.08
Matches are distributed among these distances:
95 1 0.00
96 16 0.04
97 15 0.04
98 22 0.06
99 77 0.22
100 94 0.26
101 93 0.26
102 40 0.11
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.14
Consensus pattern (100 bp):
GGAAAGATCTAAGACCGCAACAGCGGATCCAGTACCGCAAAGATACAAAAGGGAAAGATCTAAGT
CGTAACGGCAGATCCAGTACCTCAAAGACATGACG
Found at i:28243291 original size:50 final size:48
Alignment explanation
Indices: 28243137--28243342 Score: 128
Period size: 50 Copynumber: 4.1 Consensus size: 48
28243127 AAGATGCAAA
* * *
28243137 GGGAAAGGTTTAAGTCGTAACGGCGAACCTTATACCTCAAAGACATGAC
1 GGGAAAGGTTTAAGTCGTAACGGCGGACC-TGTACCTCAAAGACATAAC
* * * ** * * * * *
28243186 GGGAAAGATCTAAGACTGCGACAGTGGATCCAGTACCGCAAAGATACA-AAA
1 GGGAAAGGTTTAAGTC-GTAACGGCGGA-CCTGTACCTCAAAG--ACATAAC
28243237 GGGAAAGGTTTAAGTCGTAACGGCGGACCGTGTACCTCAGAAGACATAAC
1 GGGAAAGGTTTAAGTCGTAACGGCGGACC-TGTACCTCA-AAGACATAAC
* * * * * * * *
28243287 GGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGCGAAGACACAA-
1 GGGAAAGGTTTAAG-TCGTAACGGCGGA-CCTGTACCTCAAAGACATAAC
28243336 GGGAAAG
1 GGGAAAG
28243343 ATCTAATATC
Statistics
Matches: 117, Mismatches: 31, Indels: 18
0.70 0.19 0.11
Matches are distributed among these distances:
49 25 0.21
50 51 0.44
51 36 0.31
52 5 0.04
ACGTcount: A:0.36, C:0.21, G:0.28, T:0.15
Consensus pattern (48 bp):
GGGAAAGGTTTAAGTCGTAACGGCGGACCTGTACCTCAAAGACATAAC
Found at i:28243323 original size:51 final size:49
Alignment explanation
Indices: 28243088--28243620 Score: 382
Period size: 51 Copynumber: 10.7 Consensus size: 49
28243078 AAACACGACA
** * *
28243088 GGAAAGATCTAAGACCGCAACAACGAATCCAGTACTGCAAAGATGCA-AAG
1 GGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGCAAAGA--CACAAG
* * * * * * * *
28243138 GGAAAGGTTTAAG-TCGTAACGGC-GAACCTTA-TACCTCAAAGACATGACG
1 GGAAAGATCTAAGACCGCAACGGCGGATCC--AGTACCGCAAAGACA-CAAG
* * * * *
28243187 GGAAAGATCTAAGACTGCGACAGTGGATCCAGTACCGCAAAGATACAAAAG
1 GGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGCAAAG--ACACAAG
* * * * * * *
28243238 GGAAAGGTTTAAG-TCGTAACGGCGGA-CCGTGTACCTCAGAAGACATAACG
1 GGAAAGATCTAAGACCGCAACGGCGGATCC-AGTACCGCA-AAGACACAA-G
*
28243288 GGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGCGAAGACACAAG
1 GGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGCAAAGACACAAG
* * * * ** *
28243337 GGAAAGATCTAATATCGCAACAGCAGATCCAGTACCATAAAGATACAGAAG
1 GGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGCAAAG--ACACAAG
* ** * *
28243388 GGAAAGATCTAAGACCGCAACAGCATATCCAGTACCACAAAGATACAGAAG
1 GGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGCAAAG--ACACAAG
* * * * * *
28243439 GGAAAGATCTAAGACCGTAATGGCAGATCCAGTACCACAAAAACACGACG
1 GGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGCAAAGACAC-AAG
* * *
28243489 GGAAAGATCTAAGACTC-CAATGGCAGATCCAGTACCGCGAAGACACAAG
1 GGAAAGATCTAAGAC-CGCAACGGCGGATCCAGTACCGCAAAGACACAAG
* * ***
28243538 GGAAAGATCTAAG-CCGCGACGACGGATCCAGTACCATGAAGACACAAG
1 GGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGCAAAGACACAAG
* *
28243586 GGAAAGATCTAAG-CCGTAACGGCGGATTCAGTACC
1 GGAAAGATCTAAGACCGCAACGGCGGATCCAGTACC
28243621 ATGAAGATTT
Statistics
Matches: 388, Mismatches: 76, Indels: 40
0.77 0.15 0.08
Matches are distributed among these distances:
47 3 0.01
48 61 0.16
49 90 0.23
50 101 0.26
51 128 0.33
52 5 0.01
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.14
Consensus pattern (49 bp):
GGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGCAAAGACACAAG
Found at i:28243432 original size:201 final size:198
Alignment explanation
Indices: 28243186--28243621 Score: 513
Period size: 201 Copynumber: 2.2 Consensus size: 198
28243176 AAGACATGAC
* * ** * * *
28243186 GGGAAAGATCTAAGACTGCGACAGTGGATCCAGTACCGCAAAGATACAAAAGGGAAAGGTTTAAG
1 GGGAAAGATCTAAGACCGCAACAGCAGATCCAGTACCACAAAGATACAAAAGGGAAAGATCTAAG
* * * * * * *
28243251 -TCGTAACGGCGGA-CCGTGTACCTCAGAAGACATAACGGGAAAGATCTAAGAC-CGCAACGGCG
66 ACCGTAACGGCAGATCC-AGTACCACA-AAAACACAACGGGAAAGATCTAAGACTC-CAACGGCA
*
28243313 GATCCAGTACCGCGAAGACACAAGGGAAAGATCTAATATCGCAAC-AGCAGATCCAGTACCATAA
128 GATCCAGTACCGCGAAGACACAAGGGAAAGATCTAA-ACCGCAACGA-CAGATCCAGTACCATAA
*
28243377 AGATACAGAA
191 AG--ACACAA
* *
28243387 GGGAAAGATCTAAGACCGCAACAGCATATCCAGTACCACAAAGATACAGAAGGGAAAGATCTAAG
1 GGGAAAGATCTAAGACCGCAACAGCAGATCCAGTACCACAAAGATACAAAAGGGAAAGATCTAAG
* * *
28243452 ACCGTAATGGCAGATCCAGTACCACAAAAACACGACGGGAAAGATCTAAGACTCCAATGGCAGAT
66 ACCGTAACGGCAGATCCAGTACCACAAAAACACAACGGGAAAGATCTAAGACTCCAACGGCAGAT
* * * *
28243517 CCAGTACCGCGAAGACACAAGGGAAAGATCTAAGCCGCGACGACGGATCCAGTACCATGAAGACA
131 CCAGTACCGCGAAGACACAAGGGAAAGATCTAAACCGCAACGACAGATCCAGTACCATAAAGACA
28243582 CAA
196 CAA
* * * *
28243585 GGGAAAGATCTAAG-CCGTAACGGCGGATTCAGTACCA
1 GGGAAAGATCTAAGACCGCAACAGCAGATCCAGTACCA
28243622 TGAAGATTTG
Statistics
Matches: 201, Mismatches: 30, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
197 18 0.09
198 19 0.09
200 22 0.11
201 122 0.61
202 18 0.09
203 2 0.01
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.13
Consensus pattern (198 bp):
GGGAAAGATCTAAGACCGCAACAGCAGATCCAGTACCACAAAGATACAAAAGGGAAAGATCTAAG
ACCGTAACGGCAGATCCAGTACCACAAAAACACAACGGGAAAGATCTAAGACTCCAACGGCAGAT
CCAGTACCGCGAAGACACAAGGGAAAGATCTAAACCGCAACGACAGATCCAGTACCATAAAGACA
CAA
Found at i:28244048 original size:39 final size:39
Alignment explanation
Indices: 28244004--28244130 Score: 129
Period size: 39 Copynumber: 3.3 Consensus size: 39
28243994 AACCAGTCTA
* *
28244004 TTACCCCGAGCCTGGGGTAGGTTGCAACCATTTGATCTT
1 TTACCCCGAGCCTGGGGCAGATTGCAACCATTTGATCTT
* * *
28244043 TTACCCCGAG-TTGGGGCAGATCATCATCAACCA----ATCTC
1 TTACCCCGAGCCTGGGGCAGAT--T--GCAACCATTTGATCTT
*
28244081 TTACCCCGAGCCTGGGGCAGATTGTAACCATTTGATCTT
1 TTACCCCGAGCCTGGGGCAGATTGCAACCATTTGATCTT
28244120 TTACCCCGAGC
1 TTACCCCGAGC
28244131 TCGAGGCAGA
Statistics
Matches: 70, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
35 5 0.07
37 1 0.01
38 22 0.31
39 35 0.50
40 1 0.01
42 6 0.09
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (39 bp):
TTACCCCGAGCCTGGGGCAGATTGCAACCATTTGATCTT
Found at i:28244114 original size:77 final size:78
Alignment explanation
Indices: 28243987--28244167 Score: 265
Period size: 77 Copynumber: 2.3 Consensus size: 78
28243977 AGTGAAGTTG
* * *
28243987 CATCATCAACCAGTCTATTACCCCGAGCCTGGGGTAGGTTGCAACCATTTGATCTTTTACCCCGA
1 CATCATCAACCAATCTATTACCCCGAGCCTGGGGCAGATTGCAACCATTTGATCTTTTACCCCGA
* *
28244052 G-TTGGGGCAGAT
66 GCTCGAGGCAGAT
* *
28244064 CATCATCAACCAATCTCTTACCCCGAGCCTGGGGCAGATTGTAACCATTTGATCTTTTACCCCGA
1 CATCATCAACCAATCTATTACCCCGAGCCTGGGGCAGATTGCAACCATTTGATCTTTTACCCCGA
28244129 GCTCGAGGCAGAT
66 GCTCGAGGCAGAT
* * *
28244142 CATCGTCAACCAATCTACTATCCCGA
1 CATCATCAACCAATCTATTACCCCGA
28244168 TCACAGGGCA
Statistics
Matches: 92, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
77 61 0.66
78 31 0.34
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.26
Consensus pattern (78 bp):
CATCATCAACCAATCTATTACCCCGAGCCTGGGGCAGATTGCAACCATTTGATCTTTTACCCCGA
GCTCGAGGCAGAT
Found at i:28244573 original size:206 final size:204
Alignment explanation
Indices: 28244204--28244654 Score: 586
Period size: 206 Copynumber: 2.2 Consensus size: 204
28244194 AAACAGAGAG
** * * * *
28244204 ACGGTCATCTTCCTGATGAGATAAAGAGAAGTATACCAACT---CGACGCTCGATGCGAGCAAAT
1 ACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAACTCAACCACGCTCGATACGAGCAAAT
**
28244266 CTTCGAACCTTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTC
66 CTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTC
* * * * * * **
28244331 CTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGGATTGAA
131 CTGATGAGATACTGAGAAGTGAACCAAATCCGTCTTCCTGATGAAACACAAAGAAGCGGATCAAA
28244396 ACAAACGAT
196 ACAAACGAT
*
28244405 ACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAACTCAAACTCACGCTCGATATGAGCAA
1 ACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAACTC-AAC-CACGCTCGATACGAGCAA
* *
28244470 ATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGTGGTTTGCT
64 ATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCT
* *
28244535 TCCTGATGAGATAC-GAGGAAGTGAACTAAATCCGTCTTCCTGATGAAACACAAAGAAGTGGATC
129 TCCTGATGAGATACTGA-GAAGTGAACCAAATCCGTCTTCCTGATGAAACACAAAGAAGCGGATC
**
28244599 AAAACAAGGGAT
193 AAAACAAACGAT
** * * * *
28244611 GTGGTCATCTACCTGATGAGATACTAAGAAGAAGGCCAAGTCAA
1 ACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAACTCAA
28244655 TGAAACCGGA
Statistics
Matches: 215, Mismatches: 29, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
201 37 0.17
205 5 0.02
206 173 0.80
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.22
Consensus pattern (204 bp):
ACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAACTCAACCACGCTCGATACGAGCAAAT
CTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTC
CTGATGAGATACTGAGAAGTGAACCAAATCCGTCTTCCTGATGAAACACAAAGAAGCGGATCAAA
ACAAACGAT
Found at i:28244986 original size:18 final size:17
Alignment explanation
Indices: 28244945--28245051 Score: 108
Period size: 17 Copynumber: 6.3 Consensus size: 17
28244935 CCAAACTCAT
* *
28244945 TTTAAATTTCTTTTAAG
1 TTTAAATTTATTTTAAA
* *
28244962 GTTAAATTTGTTTTAAAA
1 TTTAAATTTATTTT-AAA
28244980 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
28244997 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
* *
28245014 TTTAAATTTA-CTCAAA
1 TTTAAATTTATTTTAAA
* *
28245030 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
28245047 TTTAA
1 TTTAA
28245052 GTACAAACAC
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
16 12 0.16
17 48 0.65
18 14 0.19
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:28244988 original size:6 final size:6
Alignment explanation
Indices: 28244977--28245023 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
28244967 ATTTGTTTTA
* *
28244977 AAATTT AAATTT -ATTTT AAATTT AAATTT -AATTT AAGTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
28245023 A
1 A
28245024 CTCAAATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 9 0.26
6 26 0.74
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:28244994 original size:11 final size:12
Alignment explanation
Indices: 28244977--28245023 Score: 62
Period size: 11 Copynumber: 4.1 Consensus size: 12
28244967 ATTTGTTTTA
28244977 AAATTTAAATTT
1 AAATTTAAATTT
*
28244989 -ATTTTAAATTT
1 AAATTTAAATTT
28245000 AAATTT-AATTT
1 AAATTTAAATTT
*
28245011 AAGTTTAAATTT
1 AAATTTAAATTT
28245023 A
1 A
28245024 CTCAAATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 20 0.67
12 10 0.33
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (12 bp):
AAATTTAAATTT
Found at i:28244994 original size:35 final size:34
Alignment explanation
Indices: 28244945--28245023 Score: 95
Period size: 35 Copynumber: 2.3 Consensus size: 34
28244935 CCAAACTCAT
* * **
28244945 TTTAAATTTCTTTTAAGGTTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAAAGTTAAATTTAATTT-AAA
* *
28244980 TTTAAATTTATTTTAAATTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAAGTTAAATTTAATTTAAA
28245014 TTTAAATTTA
1 TTTAAATTTA
28245024 CTCAAATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
34 12 0.32
35 26 0.68
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.56
Consensus pattern (34 bp):
TTTAAATTTATTTTAAAGTTAAATTTAATTTAAA
Found at i:28245737 original size:6 final size:6
Alignment explanation
Indices: 28245721--28245750 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
28245711 TTAATAGTAG
28245721 TAATAAT TAATAT TAATAT TAATAT TAATA
1 TAAT-AT TAATAT TAATAT TAATAT TAATA
28245751 ATGACTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
TAATAT
Found at i:28245775 original size:36 final size:35
Alignment explanation
Indices: 28245710--28245808 Score: 94
Period size: 36 Copynumber: 2.8 Consensus size: 35
28245700 CATTACTATT
* * * *
28245710 ATTAATAGTAGTAA-TAATTAATATTAATAT-TAAT
1 ATTAATAATACTAATTAA-TAATAATAATATATAAC
*
28245744 ATTAATAATGACTATTTTAATAATAATAATATGATAAC
1 ATTAATAAT-ACTA-ATTAATAATAATAATAT-ATAAC
*
28245782 ATTAATAATATTAATTAATAATAATAA
1 ATTAATAATACTAATTAATAATAATAA
28245809 AAAAGAATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
34 8 0.15
35 3 0.06
36 24 0.45
37 6 0.11
38 12 0.23
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (35 bp):
ATTAATAATACTAATTAATAATAATAATATATAAC
Found at i:28246825 original size:30 final size:29
Alignment explanation
Indices: 28246782--28247159 Score: 194
Period size: 30 Copynumber: 12.9 Consensus size: 29
28246772 GAGGTTCCCG
*
28246782 AACTTCCTAAAAATTATATTTTGACCCCAA
1 AACTTCCTAAAAATTACATTTTGACCCC-A
* * *
28246812 AACTTCTTGAAAATTACATTTTTACCCTCA
1 AACTTCCTAAAAATTACATTTTGACCC-CA
*
28246842 AACTTCCTAAAAATTACATTTTGACCCCTG
1 AACTTCCTAAAAATTACATTTTGACCCC-A
* * *
28246872 AACTTTC-AAAAATTACATTTTTATCCTCA
1 AACTTCCTAAAAATTACATTTTGA-CCCCA
* * *
28246901 AACTTCC-AAAAATTTCATTTTTAACCCAA
1 AACTTCCTAAAAATTACA-TTTTGACCCCA
* * *
28246930 AACTTTC-AAAAATTACATTTTTACCCTTA
1 AACTTCCTAAAAATTACATTTTGACCC-CA
* *
28246959 AACTTTCC--AAAATTTCATTTTTGA-CCCG
1 AAC-TTCCTAAAAATTACA-TTTTGACCCCA
* *
28246987 ATCTTTCC-AAAAATTACCATTTTTACCCCCA
1 AAC-TTCCTAAAAATTA-CATTTTGA-CCCCA
* * ***
28247018 AA-TTTCTAAAAATTCCATTTTTGACCTTG
1 AACTTCCTAAAAATTACA-TTTTGACCCCA
*
28247047 ATCTTTCC-AAAAATTACCATTTT-ACCCTCA
1 AAC-TTCCTAAAAATTA-CATTTTGACCC-CA
* * ***
28247077 AACTTCC--GAAATTCCATTTTTGACCTTG
1 AACTTCCTAAAAATTACA-TTTTGACCCCA
*
28247105 ATCTTTCC-AAAAATTACCATTTT-ACCCCCA
1 AAC-TTCCTAAAAATTA-CATTTTGA-CCCCA
*
28247135 AACTT-CTAAAAATTCCA-TTTGACCC
1 AACTTCCTAAAAATTACATTTTGACCC
28247160 AGATTTTTCC
Statistics
Matches: 266, Mismatches: 57, Indels: 53
0.71 0.15 0.14
Matches are distributed among these distances:
27 8 0.03
28 30 0.11
29 106 0.40
30 110 0.41
31 12 0.05
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.37
Consensus pattern (29 bp):
AACTTCCTAAAAATTACATTTTGACCCCA
Found at i:28246883 original size:29 final size:28
Alignment explanation
Indices: 28246790--28247159 Score: 205
Period size: 29 Copynumber: 12.7 Consensus size: 28
28246780 CGAACTTCCT
* * *
28246790 AAAAATTATATTTTGACCCCAAAACTTCTT
1 AAAAATTACATTTTGA-CCCTAAACTT-TC
* * *
28246820 GAAAATTACATTTTTACCCTCAAACTTCC
1 AAAAATTACATTTTGACCCT-AAACTTTC
*
28246849 TAAAAATTACATTTTGACCCCTGAACTTTC
1 -AAAAATTACATTTTGA-CCCTAAACTTTC
* * *
28246879 AAAAATTACATTTTTATCCTCAAACTTCC
1 AAAAATTACATTTTGACCCT-AAACTTTC
* * *
28246908 AAAAATTTCATTTTTAACCCAAAACTTTC
1 AAAAATTACA-TTTTGACCCTAAACTTTC
*
28246937 AAAAATTACATTTTTACCCTTAAACTTTC
1 AAAAATTACATTTTGACCC-TAAACTTTC
* * * *
28246966 CAAAATTTCATTTTTGACCC-GATCTTTCC
1 AAAAATTACA-TTTTGACCCTAAACTTT-C
* *
28246995 AAAAATTACCATTTTTACCCCCAAA-TTTC
1 AAAAATTA-CATTTTGA-CCCTAAACTTTC
* * * *
28247024 TAAAAATTCCATTTTTGACCTTGATCTTTCC
1 -AAAAATTACA-TTTTGACCCTAAACTTT-C
28247055 AAAAATTACCATTTT-ACCCTCAAAC-TTC
1 AAAAATTA-CATTTTGACCCT-AAACTTTC
** * * * *
28247083 CGAAATTCCATTTTTGACCTTGATCTTTCC
1 AAAAATTACA-TTTTGACCCTAAACTTT-C
*
28247113 AAAAATTACCATTTT-ACCCCCAAAC-TTC
1 AAAAATTA-CATTTTGA-CCCTAAACTTTC
*
28247141 TAAAAATTCCA-TTTGACCC
1 -AAAAATTACATTTTGACCC
28247160 AGATTTTTCC
Statistics
Matches: 259, Mismatches: 56, Indels: 53
0.70 0.15 0.14
Matches are distributed among these distances:
27 8 0.03
28 32 0.12
29 105 0.41
30 104 0.40
31 10 0.04
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.37
Consensus pattern (28 bp):
AAAAATTACATTTTGACCCTAAACTTTC
Found at i:28246940 original size:58 final size:60
Alignment explanation
Indices: 28246821--28247222 Score: 377
Period size: 58 Copynumber: 6.9 Consensus size: 60
28246811 AAACTTCTTG
* * *
28246821 AAAATTA-CATTTTTACCCTCAAACTTCCTAAAAATTACATTTTGACCCCTGAACTTT-CA
1 AAAATTACCATTTTTACCCTCAAACTTCC-AAAAATTCCATTTTTAACCCTGAACTTTCCA
* * **
28246880 AAAATTA-CATTTTTATCCTCAAACTTCCAAAAATTTCATTTTTAACCCAAAACTTT-CA
1 AAAATTACCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCCTGAACTTTCCA
* * * *
28246938 AAAATTA-CATTTTTACCCTTAAACTTTCC-AAAATTTCATTTTTGACCC-GATCTTTCCA
1 AAAATTACCATTTTTACCCTCAAAC-TTCCAAAAATTCCATTTTTAACCCTGAACTTTCCA
* * * * * *
28246996 AAAATTACCATTTTTACCCCCAAATTTCTAAAAATTCCATTTTTGACCTTGATCTTTCCA
1 AAAATTACCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCCTGAACTTTCCA
* * * *
28247056 AAAATTACCA-TTTTACCCTCAAACTTCC-GAAATTCCATTTTTGACCTTGATCTTTCCA
1 AAAATTACCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCCTGAACTTTCCA
* * * * **
28247114 AAAATTACCA-TTTTACCCCCAAACTTCTAAAAATTCCA--TTTGACCCAGATTTTTCC-
1 AAAATTACCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCCTGAACTTTCCA
* *
28247170 AAAATTACCA-TTTTACCCCCCAAA-TATCCAAAAA-TCACATTTTCAAACCCTGA
1 AAAATTACCATTTTTA-CCCTCAAACT-TCCAAAAATTC-CATTTT-TAACCCTGA
28247223 TTATTTTATT
Statistics
Matches: 300, Mismatches: 31, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
56 18 0.06
57 37 0.12
58 132 0.44
59 87 0.29
60 26 0.09
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (60 bp):
AAAATTACCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCCTGAACTTTCCA
Found at i:28247008 original size:117 final size:116
Alignment explanation
Indices: 28246782--28247154 Score: 414
Period size: 117 Copynumber: 3.2 Consensus size: 116
28246772 GAGGTTCCCG
** * * **
28246782 AACTTCCTAAAAATTATATTTTGACCCCAAAACTTCTTGAAAATTACATTTTTACCCTCAAACTT
1 AACTTCC-AAAAATTCCATTTTTAACCCAAAACTT-TCAAAAATTACATTTTTACCCTCAAACTT
* * *
28246847 CCTAAAAATTACA-TTTTGACCCCTGAACTTT-CAAAAATTA-CATTTTTATCCTCA
64 CC--AAAATTACATTTTTGA-CCC-GATCTTTCCAAAAATTACCATTTTTACCCCCA
* *
28246901 AACTTCCAAAAATTTCATTTTTAACCCAAAACTTTCAAAAATTACATTTTTACCCTTAAACTTTC
1 AACTTCCAAAAATTCCATTTTTAACCCAAAACTTTCAAAAATTACATTTTTACCCTCAAAC-TTC
*
28246966 CAAAATTTCATTTTTGACCCGATCTTTCCAAAAATTACCATTTTTACCCCCA
65 CAAAATTACATTTTTGACCCGATCTTTCCAAAAATTACCATTTTTACCCCCA
* * * *** *
28247018 AATTTCTAAAAATTCCATTTTTGACCTTGATCTTTCCAAAAATTACCA-TTTTACCCTCAAACTT
1 AACTTCCAAAAATTCCATTTTTAACCCAAAACTTT-CAAAAATTA-CATTTTTACCCTCAAACTT
* * *
28247082 CCGAAATTCCATTTTTGACCTTGATCTTTCCAAAAATTACCA-TTTTACCCCCA
64 CCAAAATTACATTTTTGACC-CGATCTTTCCAAAAATTACCATTTTTACCCCCA
*
28247135 AACTTCTAAAAATTCCATTT
1 AACTTCCAAAAATTCCATTT
28247155 GACCCAGATT
Statistics
Matches: 223, Mismatches: 24, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
115 6 0.03
116 20 0.09
117 119 0.53
118 69 0.31
119 9 0.04
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (116 bp):
AACTTCCAAAAATTCCATTTTTAACCCAAAACTTTCAAAAATTACATTTTTACCCTCAAACTTCC
AAAATTACATTTTTGACCCGATCTTTCCAAAAATTACCATTTTTACCCCCA
Found at i:28252963 original size:5 final size:5
Alignment explanation
Indices: 28252955--28252991 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
28252945 TAATTAAATT
28252955 ATTTA ATTTA ATTTA ATTTA ATTT- ATATT- ATTTA ATT
1 ATTTA ATTTA ATTTA ATTTA ATTTA AT-TTA ATTTA ATT
28252992 ATATTGTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
ATTTA
Found at i:28252975 original size:15 final size:14
Alignment explanation
Indices: 28252952--28252996 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
28252942 AGTTAATTAA
28252952 ATTATTTAATTTA-
1 ATTATTTAATTTAT
28252965 ATTTAATTTAATTTAT
1 A-TT-ATTTAATTTAT
28252981 ATTATTTAA-TTAT
1 ATTATTTAATTTAT
28252994 ATT
1 ATT
28252997 GTACATTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 8 0.28
14 8 0.28
15 12 0.41
16 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTATTTAATTTAT
Found at i:28254232 original size:20 final size:20
Alignment explanation
Indices: 28254207--28254252 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
28254197 CAAGGTATCG
* * *
28254207 AGAAGTGGAGTTGTATCGGT
1 AGAAGTGAAGTTCTACCGGT
28254227 AGAAGTGAAGTTCTACCGGT
1 AGAAGTGAAGTTCTACCGGT
28254247 AGAAGT
1 AGAAGT
28254253 CTCACTGGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.35, T:0.26
Consensus pattern (20 bp):
AGAAGTGAAGTTCTACCGGT
Found at i:28256091 original size:18 final size:18
Alignment explanation
Indices: 28256068--28256105 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
28256058 AACACTTATC
28256068 TTTTTTTTTCTCTTTCTG
1 TTTTTTTTTCTCTTTCTG
28256086 TTTTTTTTTCTCTTTCTG
1 TTTTTTTTTCTCTTTCTG
28256104 TT
1 TT
28256106 CTCTCCCCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (18 bp):
TTTTTTTTTCTCTTTCTG
Found at i:28258352 original size:21 final size:23
Alignment explanation
Indices: 28258327--28258376 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
28258317 ATGTTTAATT
*
28258327 TTTTTAT-TATTTAATG-AAATA
1 TTTTTATGTAATTAATGTAAATA
*
28258348 TTTTTATGTAATTAATGTACATA
1 TTTTTATGTAATTAATGTAAATA
28258371 TTTTTA
1 TTTTTA
28258377 CACTAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 7 0.28
22 8 0.32
23 10 0.40
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (23 bp):
TTTTTATGTAATTAATGTAAATA
Found at i:28259661 original size:16 final size:16
Alignment explanation
Indices: 28259641--28259683 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
28259631 AAATTTAAAG
28259641 TTTTTATTTAA-ATAA
1 TTTTTATTTAAGATAA
*
28259656 TATTTTAATTAAGATAA
1 T-TTTTATTTAAGATAA
28259673 TTTTTATTTAA
1 TTTTTATTTAA
28259684 TAAATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 1 0.04
16 18 0.75
17 5 0.21
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
TTTTTATTTAAGATAA
Found at i:28265661 original size:15 final size:15
Alignment explanation
Indices: 28265641--28265672 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
28265631 TAGTAGTGGC
28265641 CATGGAATGCTTTAG
1 CATGGAATGCTTTAG
28265656 CATGGAATGCTTTAG
1 CATGGAATGCTTTAG
28265671 CA
1 CA
28265673 GTTTTGGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (15 bp):
CATGGAATGCTTTAG
Found at i:28267892 original size:23 final size:23
Alignment explanation
Indices: 28267861--28267906 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
28267851 GATTTTTTCG
28267861 TTTTGGTCCC-TATGTTGTGACAT
1 TTTTGGTCCCGT-TGTTGTGACAT
*
28267884 TTTTTGTCCCGTTGTTGTGACAT
1 TTTTGGTCCCGTTGTTGTGACAT
28267907 AGGGATCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.11, C:0.17, G:0.22, T:0.50
Consensus pattern (23 bp):
TTTTGGTCCCGTTGTTGTGACAT
Found at i:28275269 original size:536 final size:536
Alignment explanation
Indices: 28274257--28275325 Score: 2005
Period size: 536 Copynumber: 2.0 Consensus size: 536
28274247 TTATTTGGAA
28274257 GAATCGGAACGAGTCTATTTTTTTGCATTTTCATAAACCAGCAGAGGTTATTATTTCTACCGCAA
1 GAATCGGAACGAGTCTATTTTTTTGCATTTTCATAAACCAGCAGAGGTTATTATTTCTACCGCAA
28274322 GTGCTTGGGCGAAATCTCTTCAAGTGTGCAGTTTCAAAAACAATTGGGCAACCACGTCTATGTCT
66 GTGCTTGGGCGAAATCTCTTCAAGTGTGCAGTTTCAAAAACAATTGGGCAACCACGTCTATGTCT
* *
28274387 CGGAATATATGGCAAAAAGCGTAGCATGGATGGATTAAACTGAACGTGGATGGCTCTTTATCAAG
131 CAGAATATATGGCAAAAAGCGTAGCATGGATGGATTAAACTGAACGTAGATGGCTCTTTATCAAG
28274452 TGATGGTCTATTGGCTTCCATTGGTGGCTTAGGGCGGGATTCTAATGGTCATTGGCTTTTTAGAT
196 TGATGGTCTATTGGCTTCCATTGGTGGCTTAGGGCGGGATTCTAATGGTCATTGGCTTTTTAGAT
28274517 TTAAAATGAAGCTATTCACTTCTGAAATTTTGTAGATAGAAGCAATGGCTATTATTGCTGGACTG
261 TTAAAATGAAGCTATTCACTTCTGAAATTTTGTAGATAGAAGCAATGGCTATTATTGCTGGACTG
28274582 AAAGTTGCTTGGAACAAAGGATACAGAAGGGTGGAGCTTGAATGTGATAATGCGCACCTTGTTGA
326 AAAGTTGCTTGGAACAAAGGATACAGAAGGGTGGAGCTTGAATGTGATAATGCGCACCTTGTTGA
* * *
28274647 CATTTTATATTTCGGGTTGGCATCAATAAGTAAGATCTTCGACATCCAAAGAATCCATGATCTGT
391 CATTTTATATTCCGGGTTGGCATCAATAAGTAAGATCTCCGACATCCAAAGAATCCATGATCTAT
* *
28274712 GTTGTCGAGAGTGGTCAGTCGAGGTTCGGTGTATTCCTCGAAAGTTTAGCCAAAAGGAGTAATAT
456 GTTGTCGAGAGTGGTCAGTCGAGGTTCGATGTATTCCTCGAAAGTTTAGCCAAAAGGAGTAACAT
28274777 GCAGATGGGACAAATG
521 GCAGATGGGACAAATG
28274793 GAATCGGAACGAGTCTATTTTTTTGCATTTTCATAAACCAGCAGAGGTTATTATTTCTACCGCAA
1 GAATCGGAACGAGTCTATTTTTTTGCATTTTCATAAACCAGCAGAGGTTATTATTTCTACCGCAA
28274858 GTGCTTGGGCGAAATCTCTTCAAGTGTGCAGTTTCAAAAACAATTGGGCAACCACGTCTATGTCT
66 GTGCTTGGGCGAAATCTCTTCAAGTGTGCAGTTTCAAAAACAATTGGGCAACCACGTCTATGTCT
* *
28274923 CAGAATATATGGCAAAAAGCGTAGGATGGATGGATTAAACTGAATGTAGATGGCTCTTTATCAAG
131 CAGAATATATGGCAAAAAGCGTAGCATGGATGGATTAAACTGAACGTAGATGGCTCTTTATCAAG
28274988 TGATGGTCTATTGGCTTCCATTGGTGGCTTAGGGCGGGATTCTAATGGTCATTGGCTTTTTAGAT
196 TGATGGTCTATTGGCTTCCATTGGTGGCTTAGGGCGGGATTCTAATGGTCATTGGCTTTTTAGAT
* *
28275053 TTAAAATGAAGCTATTCACTTCTGAAATTTTGTAGATAGAAGCAGTGGCTATTGTTGCTGGACT-
261 TTAAAATGAAGCTATTCACTTCTGAAATTTTGTAGATAGAAGCAATGGCTATTATTGCTGGACTG
28275117 AGAAGTTGCTTGGAACAAAGGATACAGAAGGGTGGAGCTTGAATGTGATAATGCGCACCTTGTTG
326 A-AAGTTGCTTGGAACAAAGGATACAGAAGGGTGGAGCTTGAATGTGATAATGCGCACCTTGTTG
28275182 ACATTTTATATTCCGGGTTGGCATCAATAAGTAAGATCTCCGACATCCAAAGAATCCATGATCTA
390 ACATTTTATATTCCGGGTTGGCATCAATAAGTAAGATCTCCGACATCCAAAGAATCCATGATCTA
* *
28275247 TGTTGTTGAGAGTGGTCAGTCGAGGTTCGATGTATTCTTCGAAAGTTTAGCCAAAAGGAGTAACA
455 TGTTGTCGAGAGTGGTCAGTCGAGGTTCGATGTATTCCTCGAAAGTTTAGCCAAAAGGAGTAACA
28275312 TGCAGATGGGACAA
520 TGCAGATGGGACAA
28275326 TTGGTTTTAT
Statistics
Matches: 519, Mismatches: 13, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
535 1 0.00
536 518 1.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (536 bp):
GAATCGGAACGAGTCTATTTTTTTGCATTTTCATAAACCAGCAGAGGTTATTATTTCTACCGCAA
GTGCTTGGGCGAAATCTCTTCAAGTGTGCAGTTTCAAAAACAATTGGGCAACCACGTCTATGTCT
CAGAATATATGGCAAAAAGCGTAGCATGGATGGATTAAACTGAACGTAGATGGCTCTTTATCAAG
TGATGGTCTATTGGCTTCCATTGGTGGCTTAGGGCGGGATTCTAATGGTCATTGGCTTTTTAGAT
TTAAAATGAAGCTATTCACTTCTGAAATTTTGTAGATAGAAGCAATGGCTATTATTGCTGGACTG
AAAGTTGCTTGGAACAAAGGATACAGAAGGGTGGAGCTTGAATGTGATAATGCGCACCTTGTTGA
CATTTTATATTCCGGGTTGGCATCAATAAGTAAGATCTCCGACATCCAAAGAATCCATGATCTAT
GTTGTCGAGAGTGGTCAGTCGAGGTTCGATGTATTCCTCGAAAGTTTAGCCAAAAGGAGTAACAT
GCAGATGGGACAAATG
Found at i:28293465 original size:30 final size:30
Alignment explanation
Indices: 28293417--28293740 Score: 197
Period size: 30 Copynumber: 10.9 Consensus size: 30
28293407 ATTTTTTTAG
*
28293417 AATTTTGGGAAAGA-TTAGGGGTTAAAATGT
1 AATTTT-GGAAAAATTTAGGGGTTAAAATGT
* *
28293447 AATATTGGAAAAATTTAGGGG-TCAAATGT
1 AATTTTGGAAAAATTTAGGGGTTAAAATGT
* * * * *
28293476 AATTTT-TAGAAAGTTTAAGGGTCAAATTGT
1 AATTTTGGA-AAAATTTAGGGGTTAAAATGT
* *
28293506 AATTTTGGAAAAA-TTAGAGGTTGAAATGT
1 AATTTTGGAAAAATTTAGGGGTTAAAATGT
* *
28293535 AATTTTTGG-AAAGTTTAGGGGTCAAAATGT
1 AA-TTTTGGAAAAATTTAGGGGTTAAAATGT
* *
28293565 AACTTTTGG-AAAGTTTAGGGGTTGAAATGT
1 AA-TTTTGGAAAAATTTAGGGGTTAAAATGT
* * *
28293595 AATTTAT--ATAAAGTTCAAGGG-TAGAAATGT
1 AATTT-TGGA-AAAATTTAGGGGTTA-AAATGT
* *
28293625 AATTTATGG-AAAATTTA-GGGTCAAAATGA
1 AATTT-TGGAAAAATTTAGGGGTTAAAATGT
* * **
28293654 AATTTTAGAAAAATTT-GCGGCCAAAATGT
1 AATTTTGGAAAAATTTAGGGGTTAAAATGT
* * *
28293683 GATTTTGG-GAAATTTTGAGGGTTAAAATGT
1 AATTTTGGAAAAATTTAG-GGGTTAAAATGT
* * * * *
28293713 GATTTAGGGAAAATTTAGAGGTCAAAAT
1 AATTTTGGAAAAATTTAGGGGTTAAAAT
28293741 ATATTTTTAG
Statistics
Matches: 230, Mismatches: 46, Indels: 36
0.74 0.15 0.12
Matches are distributed among these distances:
28 9 0.04
29 84 0.37
30 129 0.56
31 8 0.03
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.34
Consensus pattern (30 bp):
AATTTTGGAAAAATTTAGGGGTTAAAATGT
Found at i:28293608 original size:60 final size:59
Alignment explanation
Indices: 28293425--28293717 Score: 265
Period size: 59 Copynumber: 4.9 Consensus size: 59
28293415 AGAATTTTGG
* * * * *
28293425 GAAAGATTAGGGGTTAAAATGTAATATTGGAAAAATTTAGGGG-TCAAATGTAATTTTTA
1 GAAAGTTTAAGGGTCAAAATGTAATTTTGG-AAAATTTAGGGGTTGAAATGTAATTTTTA
* * * *
28293484 GAAAGTTTAAGGGTCAAATTGTAATTTTGGAAAAATTAGAGGTTGAAATGTAATTTTTG
1 GAAAGTTTAAGGGTCAAAATGTAATTTTGGAAAATTTAGGGGTTGAAATGTAATTTTTA
* * *
28293543 GAAAGTTTAGGGGTCAAAATGTAACTTTTGGAAAGTTTAGGGGTTGAAATGTAATTTATA
1 GAAAGTTTAAGGGTCAAAATGTAA-TTTTGGAAAATTTAGGGGTTGAAATGTAATTTTTA
* * ** *
28293603 TAAAGTTCAAGGGT-AGAAATGTAATTTATGGAAAATTTA-GGGTCAAAATG-AAATTTTA
1 GAAAGTTTAAGGGTCA-AAATGTAATTT-TGGAAAATTTAGGGGTTGAAATGTAATTTTTA
* * * * * * *
28293661 GAAAAATTT--GCGGCCAAAATGTGATTTTGGGAAATTTTGAGGGTTAAAATGTGATTT
1 G-AAAGTTTAAG-GGTCAAAATGTAATTTTGGAAAATTTAG-GGGTTGAAATGTAATTT
28293718 AGGGAAAATT
Statistics
Matches: 190, Mismatches: 34, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
57 10 0.05
58 28 0.15
59 90 0.47
60 62 0.33
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (59 bp):
GAAAGTTTAAGGGTCAAAATGTAATTTTGGAAAATTTAGGGGTTGAAATGTAATTTTTA
Found at i:28295687 original size:85 final size:85
Alignment explanation
Indices: 28295542--28295701 Score: 230
Period size: 85 Copynumber: 1.9 Consensus size: 85
28295532 TCGCTTCATT
* * *
28295542 GATTTGGTCTACTTCTCTATATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTC
1 GATTTGGTCCACTTCTCTATAACTCATCAGGAAGATGACCGCTTCATTGATTTAACCCACTTCTC
*
28295607 TGTATCTCATTTGAAAGACA
66 TATATCTCATTTGAAAGACA
* * * * * *
28295627 GATTTGGTCCACTTCTCTGTAACTCATCAGGAAGATGGCCTCTTTATTGCTTTGACCCACTTCTC
1 GATTTGGTCCACTTCTCTATAACTCATCAGGAAGATGACCGCTTCATTGATTTAACCCACTTCTC
28295692 TATATCTCAT
66 TATATCTCAT
28295702 CAGGAAGATG
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
85 65 1.00
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.38
Consensus pattern (85 bp):
GATTTGGTCCACTTCTCTATAACTCATCAGGAAGATGACCGCTTCATTGATTTAACCCACTTCTC
TATATCTCATTTGAAAGACA
Found at i:28295806 original size:208 final size:208
Alignment explanation
Indices: 28295421--28296664 Score: 1573
Period size: 208 Copynumber: 6.0 Consensus size: 208
28295411 GCTTCATCTA
* * * *
28295421 TTGGTCCACTTCTCTGTATCTCAACAGGAAGATGACCGCTTTATTACTTCGACCCACTTCTCTAT
1 TTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTACTTTGACCCACTTCTCTGT
* * *
28295486 ATCTCATCAGGAATATAGGGGTTTGAAGT-TCCACTCGCATTGAGTTTCGCTTCATTGATTTGGT
66 ATCTCATCAGGAAGAT-GGGGTTTGAAGTCT-CACTCACATTGAGCTTCGCTTCATTGATTTGGT
* *
28295550 CTACTTCTCTATATCTCATCAGGAAGATGACCGCTTCATTGA-TTTAATCCACTTCTCTGTATCT
129 CTACTTCTCTGTATCTCATCAGGAAGATGACTGCTTCATT-ATTTTAATCCACTTCTCTGTATCT
** *
28295614 CATTTGAAAGACAGAT
193 CATCAGGAAGACAGAT
* * * * *
28295630 TTGGTCCACTTCTCTGTAACTCATCAGGAAGATGGCCTCTTTATTGCTTTGACCCACTTCTCTAT
1 TTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTACTTTGACCCACTTCTCTGT
* * * * *
28295695 ATCTCATCAGGAAGATGGGGTTTGGAAGTTTCACT-ACATTAAGCTTTGCTTCATTAAATTGGTC
66 ATCTCATCAGGAAGATGGGGTTT-GAAGTCTCACTCACATTGAGCTTCGCTTCATTGATTTGGTC
* *
28295759 TGCTTCTCTGTATCTCATCAGGAAGATGATTGCTTCATTATTTTAATCCACTTCTCTGTATCTCA
130 TACTTCTCTGTATCTCATCAGGAAGATGACTGCTTCATTATTTTAATCCACTTCTCTGTATCTCA
28295824 TCAGGAAGACAGAT
195 TCAGGAAGACAGAT
* ** *
28295838 TTGGTTCACTTCTCTACATCTCGTCAGGAAGATGACCACTTTATTACTTTGACCCACTTCTCTGT
1 TTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTACTTTGACCCACTTCTCTGT
* * * ** * *
28295903 ACCTCATCAGGAAGATTGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCCTCATTTATTTGGTCT
66 ATCTCATCAGGAAGATGGGGTTTGAAGTCTCACTCACATTGAGCTTCGCTTCATTGATTTGGTCT
* * * * *
28295968 ACTTCTTTGTATCTTATCAGGAAGATGACTGCCTCATTGTTTCAATCCACTTCTCTGTATCTCAT
131 ACTTCTCTGTATCTCATCAGGAAGATGACTGCTTCATTATTTTAATCCACTTCTCTGTATCTCAT
* *
28296033 TAAGAAGACAGAT
196 CAGGAAGACAGAT
* * *
28296046 TTGGTCAACTTCTCTGTATCTCATCAGGAAGATGATCGCTTTATTACTTTGACCCACTTCTCTGT
1 TTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTACTTTGACCCACTTCTCTGT
* * * * *
28296111 ATCTAATTAGGAAGATGGGGTTTGAAGTCTCATTCATATTGAGCTTCGCTTCATTAATTTGGTCT
66 ATCTCATCAGGAAGATGGGGTTTGAAGTCTCACTCACATTGAGCTTCGCTTCATTGATTTGGTCT
* * * * * *
28296176 ACTTTTCTGTATATCATCAGGAAGATGACCGCCTCATTGTTTCAATCCACTTCTCTGTATCTCAT
131 ACTTCTCTGTATCTCATCAGGAAGATGACTGCTTCATTATTTTAATCCACTTCTCTGTATCTCAT
28296241 CAGGAAGAC-GAAT
196 CAGGAAGACAG-AT
* * * * * * * *
28296254 TTGGTCTACTTCTCTGTATTTTATTAGAAAGATGATCACTTTCTTGCTTTGACCCACTTCTCTGT
1 TTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTACTTTGACCCACTTCTCTGT
* * * * *
28296319 ATCTCATCAGGAAGGTGGTGTTTGAAGTTTCACTCGCATTGAACTTCGCTTCATTGATTTGGTCT
66 ATCTCATCAGGAAGATGGGGTTTGAAGTCTCACTCACATTGAGCTTCGCTTCATTGATTTGGTCT
* * *
28296384 ACTTCTTTGTTTCTCATCAAGAAGATGACTGCTTCATTGA-TTTAATCCACTTCTCTGTATCTCA
131 ACTTCTCTGTATCTCATCAGGAAGATGACTGCTTCATT-ATTTTAATCCACTTCTCTGTATCTCA
*
28296448 TCAGGAAGACGGAT
195 TCAGGAAGACAGAT
* * * *
28296462 TTGGTCTACTTCTCTATATCTTATCAGGAAGATGACCTCTTTATTACTTTGACCCACTTCTCTGT
1 TTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTACTTTGACCCACTTCTCTGT
* * * *
28296527 ATCTCATCAGGAAGATGGGGTTCGAAGACTCATTCATATTGAGCTTCGCTTCATTGATTTGGTCT
66 ATCTCATCAGGAAGATGGGGTTTGAAGTCTCACTCACATTGAGCTTCGCTTCATTGATTTGGTCT
* * * ** ** *
28296592 ACTTCTCTGTATCTCATC-GAGAAGATGACCGTTTTATTGCTTCGACCCACTTCTCTGTATCTCA
131 ACTTCTCTGTATCTCATCAG-GAAGATGACTGCTTCATTATTTTAATCCACTTCTCTGTATCTCA
*
28296656 TCAGAAAGA
195 TCAGGAAGA
28296665 TGAGGGTTTG
Statistics
Matches: 901, Mismatches: 125, Indels: 19
0.86 0.12 0.02
Matches are distributed among these distances:
207 11 0.01
208 805 0.89
209 84 0.09
210 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (208 bp):
TTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTACTTTGACCCACTTCTCTGT
ATCTCATCAGGAAGATGGGGTTTGAAGTCTCACTCACATTGAGCTTCGCTTCATTGATTTGGTCT
ACTTCTCTGTATCTCATCAGGAAGATGACTGCTTCATTATTTTAATCCACTTCTCTGTATCTCAT
CAGGAAGACAGAT
Found at i:28295896 original size:85 final size:85
Alignment explanation
Indices: 28295761--28295917 Score: 215
Period size: 85 Copynumber: 1.8 Consensus size: 85
28295751 AATTGGTCTG
** *** * * *
28295761 CTTCTCTGTATCTCATCAGGAAGATGATTGCTTCATTATTTTAATCCACTTCTCTGTATCTCATC
1 CTTCTCTACATCTCATCAGGAAGATGACCACTTCATTACTTTAACCCACTTCTCTGTACCTCATC
28295826 AGGAAGACAGATTTGGTTCA
66 AGGAAGACAGATTTGGTTCA
* * *
28295846 CTTCTCTACATCTCGTCAGGAAGATGACCACTTTATTACTTTGACCCACTTCTCTGTACCTCATC
1 CTTCTCTACATCTCATCAGGAAGATGACCACTTCATTACTTTAACCCACTTCTCTGTACCTCATC
28295911 AGGAAGA
66 AGGAAGA
28295918 TTGGGTTTGA
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
85 61 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.36
Consensus pattern (85 bp):
CTTCTCTACATCTCATCAGGAAGATGACCACTTCATTACTTTAACCCACTTCTCTGTACCTCATC
AGGAAGACAGATTTGGTTCA
Found at i:28296103 original size:85 final size:85
Alignment explanation
Indices: 28295959--28296125 Score: 212
Period size: 85 Copynumber: 2.0 Consensus size: 85
28295949 CGCCTCATTT
* * * * *
28295959 ATTTGGTCTACTTCTTTGTATCTTATCAGGAAGATGACTGCCTCATTGTTTCAATCCACTTCTCT
1 ATTTGGTCAACTTCTCTGTATCTCATCAGGAAGATGACTGCCTCATTCTTTCAACCCACTTCTCT
*
28296024 GTATCTCATTAAGAAGACAG
66 GTATCTAATTAAGAAGACAG
* * *
28296044 ATTTGGTCAACTTCTCTGTATCTCATCAGGAAGATGA-TCGCTTTATTACTTT-GACCCACTTCT
1 ATTTGGTCAACTTCTCTGTATCTCATCAGGAAGATGACT-GCCTCATT-CTTTCAACCCACTTCT
*
28296107 CTGTATCTAATTAGGAAGA
64 CTGTATCTAATTAAGAAGA
28296126 TGGGGTTTGA
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
84 1 0.01
85 66 0.94
86 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (85 bp):
ATTTGGTCAACTTCTCTGTATCTCATCAGGAAGATGACTGCCTCATTCTTTCAACCCACTTCTCT
GTATCTAATTAAGAAGACAG
Found at i:28296463 original size:37 final size:37
Alignment explanation
Indices: 28296422--28296493 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
28296412 CTGCTTCATT
*
28296422 GATTTAATCCACTTCTCTGTATCTCATCAGGAAGACG
1 GATTTAATCCACTTCTCTATATCTCATCAGGAAGACG
** * *
28296459 GATTTGGTCTACTTCTCTATATCTTATCAGGAAGA
1 GATTTAATCCACTTCTCTATATCTCATCAGGAAGA
28296494 TGACCTCTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (37 bp):
GATTTAATCCACTTCTCTATATCTCATCAGGAAGACG
Found at i:28296520 original size:85 final size:85
Alignment explanation
Indices: 28296374--28296541 Score: 232
Period size: 85 Copynumber: 2.0 Consensus size: 85
28296364 TCGCTTCATT
* * * *
28296374 GATTTGGTCTACTTCTTTGTTTCTCATCAAGAAGATGACTGCTTCATTGATTTAATCCACTTCTC
1 GATTTGGTCTACTTCTCTATATCTCATCAAGAAGATGACTGCTTCATTGATTTAACCCACTTCTC
28296439 TGTATCTCATCAGGAAGACG
66 TGTATCTCATCAGGAAGACG
* * * *
28296459 GATTTGGTCTACTTCTCTATATCTTATCAGGAAGATGACCT-CTTTATT-ACTTTGACCCACTTC
1 GATTTGGTCTACTTCTCTATATCTCATCAAGAAGATGA-CTGCTTCATTGA-TTTAACCCACTTC
28296522 TCTGTATCTCATCAGGAAGA
64 TCTGTATCTCATCAGGAAGA
28296542 TGGGGTTCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
84 1 0.01
85 70 0.96
86 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (85 bp):
GATTTGGTCTACTTCTCTATATCTCATCAAGAAGATGACTGCTTCATTGATTTAACCCACTTCTC
TGTATCTCATCAGGAAGACG
Found at i:28296628 original size:123 final size:124
Alignment explanation
Indices: 28296459--28296747 Score: 415
Period size: 123 Copynumber: 2.3 Consensus size: 124
28296449 CAGGAAGACG
* * *
28296459 GATTTGGTCTACTTCTCTATATCTTATCAGGAAGATGACCTCTTTATTACTTTGACCCACTTCTC
1 GATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCTCTTTATTACTTCGACCCACTTCTC
* * *
28296524 TGTATCTCATCAGGAAGATG-GGGTTCGAAGACTCA-TTCATATTGAGCTTCGCTTCATT
66 TGTATCTCATCAGAAAGATGAGGGTTCGAAGACTCACTT-ATATTGAGCTCCACTTCATT
*
28296582 GATTTGGTCTACTTCTCTGTATCTCATC-GAGAAGATGACCGT-TTTATTGCTTCGACCCACTTC
1 GATTTGGTCTACTTCTCTGTATCTCATCAG-GAAGATGACC-TCTTTATTACTTCGACCCACTTC
* **
28296645 TCTGTATCTCATCAGAAAGATGAGGGTTTGAAGTTTCACTTATATTGAGCTCCACTTCATT
64 TCTGTATCTCATCAGAAAGATGAGGGTTCGAAGACTCACTTATATTGAGCTCCACTTCATT
* *
28296706 GAATTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCTC
1 GATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCTC
28296748 AATTTGCCCC
Statistics
Matches: 148, Mismatches: 12, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
122 1 0.01
123 77 0.52
124 67 0.45
125 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (124 bp):
GATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCTCTTTATTACTTCGACCCACTTCTC
TGTATCTCATCAGAAAGATGAGGGTTCGAAGACTCACTTATATTGAGCTCCACTTCATT
Found at i:28296933 original size:46 final size:44
Alignment explanation
Indices: 28296746--28297066 Score: 416
Period size: 43 Copynumber: 7.2 Consensus size: 44
28296736 GAAGATGACC
* * * *
28296746 TCAATTTGCCCCTCTTGGCTTAGGGGTAAAAGATTGGAAAGGTCT
1 TCAATCTGCCCCTCTTGACTTAGAGGTAAAAGATTGGAATGG-CT
* * *
28296791 TCAATCTACCCCTCTTGA-TTAGTGGTAAAAGATTGGAATGACT
1 TCAATCTGCCCCTCTTGACTTAGAGGTAAAAGATTGGAATGGCT
*
28296834 TCAATCTGCCCCTCTTGA-TTAGGGGTAAAAGATTGGAATGGCT
1 TCAATCTGCCCCTCTTGACTTAGAGGTAAAAGATTGGAATGGCT
* *
28296877 TCAATTTGCCCCTTTTGACTTAGAGGTAAAAGATTGGATGATGGCT
1 TCAATCTGCCCCTCTTGACTTAGAGGTAAAAGATTGGA--ATGGCT
*
28296923 TCAATCTGCCCCTCTTGACTTAGAGGTAAAAGATTGGAATGTGGGT
1 TCAATCTGCCCCTCTTGACTTAGAGGTAAAAGATTGGAA--TGGCT
* *
28296969 TCAATCTGCCTCTCTTGACTTAGAGGTAAAACATTGGAA-GGTCT
1 TCAATCTGCCCCTCTTGACTTAGAGGTAAAAGATTGGAATGG-CT
* *
28297013 TCAATCTGCCCCTCTTGAC-TAGGGGTAAAAGATTGGAATGGAT
1 TCAATCTGCCCCTCTTGACTTAGAGGTAAAAGATTGGAATGGCT
*
28297056 GCAATCTGCCC
1 TCAATCTGCCC
28297067 TATGATCGAG
Statistics
Matches: 246, Mismatches: 23, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
43 88 0.36
44 60 0.24
45 15 0.06
46 83 0.34
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (44 bp):
TCAATCTGCCCCTCTTGACTTAGAGGTAAAAGATTGGAATGGCT
Found at i:28303605 original size:13 final size:13
Alignment explanation
Indices: 28303580--28303622 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
28303570 CTTTTATTTA
28303580 TTTATTATTTTTGT
1 TTTATT-TTTTTGT
28303594 TTTATTTTTTTGGT
1 TTTATTTTTTT-GT
*
28303608 TTT-TTTTTTGGT
1 TTTATTTTTTTGT
28303620 TTT
1 TTT
28303623 GAATGGGCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 5 0.19
13 11 0.41
14 11 0.41
ACGTcount: A:0.07, C:0.00, G:0.12, T:0.81
Consensus pattern (13 bp):
TTTATTTTTTTGT
Found at i:28303613 original size:12 final size:12
Alignment explanation
Indices: 28303587--28303622 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
28303577 TTATTTATTA
*
28303587 TTTTTGTTTTATT
1 TTTTTGGTTT-TT
28303600 TTTTTGGTTTTT
1 TTTTTGGTTTTT
28303612 TTTTTGGTTTT
1 TTTTTGGTTTT
28303623 GAATGGGCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.59
13 9 0.41
ACGTcount: A:0.03, C:0.00, G:0.14, T:0.83
Consensus pattern (12 bp):
TTTTTGGTTTTT
Found at i:28308837 original size:50 final size:50
Alignment explanation
Indices: 28308729--28308839 Score: 120
Period size: 50 Copynumber: 2.2 Consensus size: 50
28308719 AGATCTAATA
* **
28308729 TTTTAA-ATAAATATAAATATTTATTTAAACTGATTTGTTTAAATCTGACT
1 TTTTAATATAAAAATAAATATTTATTTAAACTGATTTGTACAAATCTGA-T
* * * *
28308779 TGTT-ATATAAAAATAAATATTTATTTATATTGTTTTGTACAAATCTTG-T
1 TTTTAATATAAAAATAAATATTTATTTAAACTGATTTGTACAAATC-TGAT
28308828 TTTTAATATAAA
1 TTTTAATATAAA
28308840 TATTTATATT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
49 5 0.10
50 43 0.86
51 2 0.04
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.50
Consensus pattern (50 bp):
TTTTAATATAAAAATAAATATTTATTTAAACTGATTTGTACAAATCTGAT
Found at i:28309939 original size:11 final size:11
Alignment explanation
Indices: 28309923--28309964 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
28309913 TAACCATTTA
28309923 TAATAAAATAT
1 TAATAAAATAT
28309934 TAATAAAATATCT
1 TAATAAAATA--T
*
28309947 TATTAAAATAT
1 TAATAAAATAT
28309958 TAATAAA
1 TAATAAA
28309965 GTAATATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 17 0.63
13 10 0.37
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:28310359 original size:20 final size:20
Alignment explanation
Indices: 28310331--28310371 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
28310321 TATAATACTA
*
28310331 TATATTTTATTT-TGTTATTT
1 TATAATTTATTTAT-TTATTT
28310351 TATAATTTATTTATTTATTT
1 TATAATTTATTTATTTATTT
28310371 T
1 T
28310372 TGGACCTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (20 bp):
TATAATTTATTTATTTATTT
Found at i:28317047 original size:19 final size:19
Alignment explanation
Indices: 28317025--28317068 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
28317015 TTTATTAGGT
28317025 TTTAATATTTAAGATAT-TA
1 TTTAATATTTAA-ATATGTA
* *
28317044 TTTATTATTTAAATTTGTA
1 TTTAATATTTAAATATGTA
28317063 TTTAAT
1 TTTAAT
28317069 TTATTTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTAATATTTAAATATGTA
Found at i:28326147 original size:27 final size:27
Alignment explanation
Indices: 28326109--28326167 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
28326099 TGTAAATATG
28326109 GTTAGTTGGTTAGAAAGTTAGTTTAGT
1 GTTAGTTGGTTAGAAAGTTAGTTTAGT
28326136 GTTAGTTGGTTAGAAAGTTAGTTTAGT
1 GTTAGTTGGTTAGAAAGTTAGTTTAGT
28326163 -TTAGT
1 GTTAGT
28326168 AAACTTTGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 5 0.16
27 27 0.84
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (27 bp):
GTTAGTTGGTTAGAAAGTTAGTTTAGT
Found at i:28328363 original size:14 final size:15
Alignment explanation
Indices: 28328346--28328380 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
28328336 TTTAAGAAGG
28328346 GAAAAAGAAGAA-AA
1 GAAAAAGAAGAAGAA
28328360 GAAAAAGAAGAAGAA
1 GAAAAAGAAGAAGAA
28328375 GAAAAA
1 GAAAAA
28328381 AGGAGGAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
GAAAAAGAAGAAGAA
Found at i:28329064 original size:27 final size:27
Alignment explanation
Indices: 28329034--28329096 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
28329024 GGCCAAACGT
* * * *
28329034 CAAAATGTTTGCAAAAGATAGGAATGG
1 CAAAATATTTACAAAAGAAAGGAATGA
* *
28329061 CAAACTATTTACAAAATAAAGGAATGA
1 CAAAATATTTACAAAAGAAAGGAATGA
*
28329088 CAAACTATT
1 CAAAATATT
28329097 GCCAAATTTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.24
Consensus pattern (27 bp):
CAAAATATTTACAAAAGAAAGGAATGA
Found at i:28330362 original size:21 final size:21
Alignment explanation
Indices: 28330336--28330398 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
28330326 CTTGGGAAAG
28330336 TTCTACCGAAACAAGTGTAAC
1 TTCTACCGAAACAAGTGTAAC
*
28330357 TTCTACCGATACAAGTGTAAC
1 TTCTACCGAAACAAGTGTAAC
* *
28330378 TTCTACCGAAGCAAGTCTAAC
1 TTCTACCGAAACAAGTGTAAC
28330399 CGATACTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.25
Consensus pattern (21 bp):
TTCTACCGAAACAAGTGTAAC
Found at i:28330382 original size:42 final size:41
Alignment explanation
Indices: 28330302--28330398 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 41
28330292 AAGCAATTTA
** *
28330302 GAAAC-AGTGTAGACTTCTACGATACTTGGGAAAGTTCTACC
1 GAAACAAGTGTA-ACTTCTACGATACAAGGGAAACTTCTACC
* *
28330343 GAAACAAGTGTAACTTCTACCGATACAAGTGTAACTTCTACC
1 GAAACAAGTGTAACTTCTA-CGATACAAGGGAAACTTCTACC
* *
28330385 GAAGCAAGTCTAAC
1 GAAACAAGTGTAAC
28330399 CGATACTAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
41 12 0.26
42 35 0.74
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.25
Consensus pattern (41 bp):
GAAACAAGTGTAACTTCTACGATACAAGGGAAACTTCTACC
Found at i:28331128 original size:36 final size:36
Alignment explanation
Indices: 28331063--28331131 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
28331053 ATGATTGTTA
* * *
28331063 TTCATTTTACTCCCTGTTGACTCAAAGGTCATGATG
1 TTCATTTTACTCCCTATTCACCCAAAGGTCATGATG
* *
28331099 TTCATTTTACTCCTTATTCACCCAGAGGTCATG
1 TTCATTTTACTCCCTATTCACCCAAAGGTCATG
28331132 TCTATTACTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.39
Consensus pattern (36 bp):
TTCATTTTACTCCCTATTCACCCAAAGGTCATGATG
Found at i:28334465 original size:15 final size:15
Alignment explanation
Indices: 28334453--28334487 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28334443 GTTTCAGATA
28334453 CATCACTAACAGAAC
1 CATCACTAACAGAAC
* *
28334468 CATCACTATCAGACC
1 CATCACTAACAGAAC
28334483 CATCA
1 CATCA
28334488 AAATCAGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.40, C:0.37, G:0.06, T:0.17
Consensus pattern (15 bp):
CATCACTAACAGAAC
Found at i:28335210 original size:45 final size:45
Alignment explanation
Indices: 28335112--28335215 Score: 145
Period size: 45 Copynumber: 2.3 Consensus size: 45
28335102 TAAATGGCAT
28335112 ACAATAAACAATATTTAAGGTTTCATAACATACAAAAAACAATAA
1 ACAATAAACAATATTTAAGGTTTCATAACATACAAAAAACAATAA
* * * * *
28335157 ATAATAAACAATATTTAAGGTTTCATAGCATACAATAAATAATTA
1 ACAATAAACAATATTTAAGGTTTCATAACATACAAAAAACAATAA
**
28335202 ACCCTAAACAATAT
1 ACAATAAACAATAT
28335216 ATGTCATTCA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.54, C:0.13, G:0.05, T:0.28
Consensus pattern (45 bp):
ACAATAAACAATATTTAAGGTTTCATAACATACAAAAAACAATAA
Found at i:28335265 original size:11 final size:11
Alignment explanation
Indices: 28335249--28335282 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
28335239 ACCAAAATAT
28335249 AAAATGAAATC
1 AAAATGAAATC
28335260 AAAATG-AATAC
1 AAAATGAAAT-C
28335271 AAAATGAAATC
1 AAAATGAAATC
28335282 A
1 A
28335283 GACTCTAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
10 3 0.14
11 15 0.71
12 3 0.14
ACGTcount: A:0.65, C:0.09, G:0.09, T:0.18
Consensus pattern (11 bp):
AAAATGAAATC
Found at i:28336715 original size:26 final size:25
Alignment explanation
Indices: 28336686--28336768 Score: 71
Period size: 26 Copynumber: 3.3 Consensus size: 25
28336676 GCTGGCGAGA
28336686 GTAAACGCATATATAAGCTGATGAGC
1 GTAAACGCATATATAAGCTGA-GAGC
* ** *
28336712 GTAAACG--TGTGCAATCTGGAGAGC
1 GTAAACGCATATATAAGCT-GAGAGC
* *
28336736 ATAAACGCATATATAAGTTGACGAGC
1 GTAAACGCATATATAAGCTGA-GAGC
28336762 GTAAACG
1 GTAAACG
28336769 TGTGCAAGTT
Statistics
Matches: 42, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
24 16 0.38
25 4 0.10
26 22 0.52
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (25 bp):
GTAAACGCATATATAAGCTGAGAGC
Found at i:28336741 original size:50 final size:50
Alignment explanation
Indices: 28336669--28336799 Score: 176
Period size: 50 Copynumber: 2.6 Consensus size: 50
28336659 TATCTGGATA
* *
28336669 TGTGCAAGCTGGCGAG-AGTAAACGCATATATAAGCTGATGAGCGTAAACG
1 TGTGCAATCTGGCGAGCA-TAAACGCATATATAAGCTGACGAGCGTAAACG
* *
28336719 TGTGCAATCTGGAGAGCATAAACGCATATATAAGTTGACGAGCGTAAACG
1 TGTGCAATCTGGCGAGCATAAACGCATATATAAGCTGACGAGCGTAAACG
* *
28336769 TGTGCAAGT-TGGCGAGCGTAAATGCATATAT
1 TGTGCAA-TCTGGCGAGCATAAACGCATATAT
28336800 TATAACAGTC
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
50 70 0.97
51 2 0.03
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.23
Consensus pattern (50 bp):
TGTGCAATCTGGCGAGCATAAACGCATATATAAGCTGACGAGCGTAAACG
Found at i:28336784 original size:24 final size:24
Alignment explanation
Indices: 28336708--28336790 Score: 78
Period size: 24 Copynumber: 3.4 Consensus size: 24
28336698 ATAAGCTGAT
*
28336708 GAGCGTAAACGTGTGCAA-TCTGGA
1 GAGCGTAAACGTGTGCAAGT-TGGC
* * ** *
28336732 GAGCATAAACGCATATATAAGTTGAC
1 GAGCGTAAACG--TGTGCAAGTTGGC
28336758 GAGCGTAAACGTGTGCAAGTTGGC
1 GAGCGTAAACGTGTGCAAGTTGGC
28336782 GAGCGTAAA
1 GAGCGTAAA
28336791 TGCATATATT
Statistics
Matches: 45, Mismatches: 11, Indels: 6
0.73 0.18 0.10
Matches are distributed among these distances:
24 28 0.62
26 16 0.36
27 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.30, T:0.20
Consensus pattern (24 bp):
GAGCGTAAACGTGTGCAAGTTGGC
Found at i:28347468 original size:24 final size:24
Alignment explanation
Indices: 28347439--28347500 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
28347429 TTACATATAT
* *
28347439 AGCTGACGAGTGTAAATGTGTGCA
1 AGCTGACGAGTGTAAATGTATGAA
*
28347463 AGCTGACGAGCGTAAATGTATGAA
1 AGCTGACGAGTGTAAATGTATGAA
28347487 AGCT--CGAGTGTAAA
1 AGCTGACGAGTGTAAA
28347501 ACGCAATGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 9 0.26
24 25 0.74
ACGTcount: A:0.34, C:0.13, G:0.31, T:0.23
Consensus pattern (24 bp):
AGCTGACGAGTGTAAATGTATGAA
Found at i:28355105 original size:49 final size:49
Alignment explanation
Indices: 28355048--28355145 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
28355038 ATAGTTATTG
*
28355048 GAACACTATAAATATTTGAAAATGTTTAAATAATAGTAAGGGTCTCACC
1 GAACACTATAAATATTTGAAAATGTTTAAATAATAGTAAGGATCTCACC
28355097 GAACACTATAAATATTTGAAAATGTTTAAATAATAGTAAGGATCTCACC
1 GAACACTATAAATATTTGAAAATGTTTAAATAATAGTAAGGATCTCACC
28355146 TACCTTAACT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (49 bp):
GAACACTATAAATATTTGAAAATGTTTAAATAATAGTAAGGATCTCACC
Found at i:28355584 original size:30 final size:30
Alignment explanation
Indices: 28355559--28355618 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
28355549 ATAAAATATT
28355559 ATTA-AAATTAGT-GAAAAATTATAAAAAAA
1 ATTAGAAATTA-TAGAAAAATTATAAAAAAA
28355588 ATTAGAAATTATAGAAAAATTATAAAAAAA
1 ATTAGAAATTATAGAAAAATTATAAAAAAA
28355618 A
1 A
28355619 AACTATAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 5 0.17
30 24 0.83
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (30 bp):
ATTAGAAATTATAGAAAAATTATAAAAAAA
Found at i:28356836 original size:22 final size:23
Alignment explanation
Indices: 28356789--28356837 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
28356779 TTTTGAGCAA
* *
28356789 TTTAACTTTTTCTTTTATTTTCT
1 TTTAACTTTTGCTTTTATTTTAT
28356812 TTTAAC-TTTGCTTTT-TCTTTAT
1 TTTAACTTTTGCTTTTAT-TTTAT
28356834 TTTA
1 TTTA
28356838 CATTCTCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 1 0.04
22 16 0.70
23 6 0.26
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.71
Consensus pattern (23 bp):
TTTAACTTTTGCTTTTATTTTAT
Found at i:28364393 original size:21 final size:20
Alignment explanation
Indices: 28364348--28364399 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
28364338 TGTGCTAGTT
*
28364348 CTACCGATACAAGTATGATTT
1 CTACCGATACAAGTATGA-TA
28364369 CTACCGATACAAGTCATGCA-A
1 CTACCGATACAAGT-ATG-ATA
28364390 CTACCGATAC
1 CTACCGATAC
28364400 CAAAAACTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 24 0.86
22 3 0.11
23 1 0.04
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.25
Consensus pattern (20 bp):
CTACCGATACAAGTATGATA
Found at i:28368117 original size:36 final size:36
Alignment explanation
Indices: 28368070--28368162 Score: 134
Period size: 36 Copynumber: 2.6 Consensus size: 36
28368060 AGTAAGTACT
*
28368070 TCTGTTCCACCTGA-TGTGTCTGAGTCTGCATCCTCA
1 TCTGTTCCACCT-ATTGTGTCTGAGTCTACATCCTCA
*
28368106 TCTGTTCCACCTATTGTGTCTGAGTCTACATCCTTA
1 TCTGTTCCACCTATTGTGTCTGAGTCTACATCCTCA
* *
28368142 TCTGCTCCATCTATTGTGTCT
1 TCTGTTCCACCTATTGTGTCT
28368163 CTTCCACCTA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
35 1 0.02
36 51 0.98
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (36 bp):
TCTGTTCCACCTATTGTGTCTGAGTCTACATCCTCA
Found at i:28370592 original size:3 final size:3
Alignment explanation
Indices: 28370534--28370578 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
28370524 AAATAAATAC
*
28370534 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28370579 CCATAGAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:28370885 original size:26 final size:24
Alignment explanation
Indices: 28370839--28370887 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
28370829 AGGACTTAAT
* *
28370839 TAAAATTAAAAATAAATTAAAGGC
1 TAAAATTAAAAAAAAAATAAAGGC
28370863 TAAAATTAAAAAAACAGAATAAAGG
1 TAAAATTAAAAAAA-A-AATAAAGG
28370888 ATTAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 13 0.62
25 1 0.05
26 7 0.33
ACGTcount: A:0.65, C:0.04, G:0.10, T:0.20
Consensus pattern (24 bp):
TAAAATTAAAAAAAAAATAAAGGC
Found at i:28381631 original size:24 final size:23
Alignment explanation
Indices: 28381604--28381667 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
28381594 TCATTAACAT
28381604 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTA-A
** * **
28381628 TGTTTATGAATATGTTCGTTTAA
1 TGTTCGTGAACATGTTCAATTAA
*
28381651 TGTTCGTAAACATGTTC
1 TGTTCGTGAACATGTTC
28381668 GATTGAGTTA
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
23 14 0.45
24 17 0.55
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.45
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:28390421 original size:37 final size:36
Alignment explanation
Indices: 28390325--28390435 Score: 127
Period size: 36 Copynumber: 3.1 Consensus size: 36
28390315 GGTAATAGGC
* * *
28390325 ATGACCTTTAGGTCAACAGGGAGAAAAATGAGCATA
1 ATGACCTTTGGGTCAACAGGGAGTAAAACGAGCATA
* * *
28390361 ATGACCTTTGGGTCAACAAGGAGTAAAACGAGTATC
1 ATGACCTTTGGGTCAACAGGGAGTAAAACGAGCATA
* *
28390397 ATGATCTTTGGGGTCAATAGGGAGTAAAACGA--ATA
1 ATGACCTTT-GGGTCAACAGGGAGTAAAACGAGCATA
28390432 ATGA
1 ATGA
28390436 TCACTGAAGT
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
35 6 0.09
36 38 0.59
37 20 0.31
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.23
Consensus pattern (36 bp):
ATGACCTTTGGGTCAACAGGGAGTAAAACGAGCATA
Found at i:28391187 original size:12 final size:12
Alignment explanation
Indices: 28391170--28391200 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
28391160 AGAAGTCTAC
28391170 ATTGTTTGATGA
1 ATTGTTTGATGA
28391182 ATTGTTTGATGA
1 ATTGTTTGATGA
28391194 ATTGTTT
1 ATTGTTT
28391201 ACTGACTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (12 bp):
ATTGTTTGATGA
Done.