Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 2 of 120
Found at i:252442 original size:32 final size:32
Alignment explanation
Indices: 252374--252442 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
252364 CTCAAGTATC
* * *
252374 AACTAGATACTTTTTAAACAAATTCAAGTACT
1 AACTAAATACTTTTTAAACAAATTCAAGGACA
* *
252406 AACTAAATAC-TTTTGAATAAATTCAAAGGACA
1 AACTAAATACTTTTTAAACAAATTC-AAGGACA
252438 AACTA
1 AACTA
252443 TATGTTAACC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 12 0.39
32 19 0.61
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.30
Consensus pattern (32 bp):
AACTAAATACTTTTTAAACAAATTCAAGGACA
Found at i:261689 original size:23 final size:22
Alignment explanation
Indices: 261636--261689 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 22
261626 TTAAGAATTG
261636 AAAG-TTTAAAACATTTTTAGA
1 AAAGATTTAAAACATTTTTAGA
* * *
261657 AAATAATTAAAATATGTTTTAGA
1 AAAGATTTAAAACAT-TTTTAGA
*
261680 CAAGATTTAA
1 AAAGATTTAA
261690 GGTTTTAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 3 0.12
22 8 0.32
23 14 0.56
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.37
Consensus pattern (22 bp):
AAAGATTTAAAACATTTTTAGA
Found at i:264984 original size:22 final size:23
Alignment explanation
Indices: 264959--265001 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
264949 ATCTTAAAAC
264959 TTAAAAAATT-AAATTAAATATA
1 TTAAAAAATTAAAATTAAATATA
*
264981 TTAAAATATTAAAATTAAATA
1 TTAAAAAATTAAAATTAAATA
265002 AAAATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
TTAAAAAATTAAAATTAAATATA
Found at i:268323 original size:16 final size:16
Alignment explanation
Indices: 268277--268323 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
268267 AAAAAATATT
268277 TATATTGTTTTATTTTA
1 TATATT-TTTTATTTTA
* *
268294 -ATATTTAATAATTTTA
1 TATATTT-TTTATTTTA
268310 TATATTTTTTATTT
1 TATATTTTTTATTT
268324 ATTAAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 1 0.04
16 17 0.71
17 6 0.25
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
TATATTTTTTATTTTA
Found at i:269747 original size:59 final size:59
Alignment explanation
Indices: 269672--270043 Score: 507
Period size: 59 Copynumber: 6.4 Consensus size: 59
269662 TAGATACCCG
* *
269672 GGGGCAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTAGAAAGTTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCA
* ** *
269731 GGGGTAAAATAGTAATTTTTGGTGAAATCAAGGTTAAAAATGGAATTTTGG-AAGTTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCA
* * * * *
269789 AGGGCAAAATGGTAA-TTTTGGTAAAATCGGGGTTAAAAATGGGATTTTAGAAAGTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCA
* ** *
269847 GGGGTAAAATGATAATTTTTGGTGAAATTAGGGTTAAAAATGGGATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCA
* * * **
269906 GGGGTAAAATGGTAATTTTTGGTGAAAACGGGATTAAAAATGGAATTTTGGAAAGTTTT
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCA
* * **
269965 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGGA-TTTGGACAGTTTT
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCA
270023 GGGGTAAAATGGTAATTTTTG
1 GGGGTAAAATGGTAATTTTTG
270044 AACAGTCTAG
Statistics
Matches: 275, Mismatches: 36, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
57 30 0.11
58 70 0.25
59 175 0.64
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCA
Found at i:271282 original size:2 final size:2
Alignment explanation
Indices: 271275--271337 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
271265 TTAATAACTG
271275 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
271317 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
271338 TTTAAACATC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:271972 original size:6 final size:6
Alignment explanation
Indices: 271958--272014 Score: 55
Period size: 6 Copynumber: 9.8 Consensus size: 6
271948 GATTTTTTAA
* * * *
271958 TTAATT TTAAAT TTAAAT TCAAA- TTAAAT TTAAAC TT-AAT TAAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
272004 TTAAAC TTAAA
1 TTAAAT TTAAA
272015 AGAAAAGTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
5 7 0.17
6 34 0.83
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (6 bp):
TTAAAT
Found at i:271976 original size:17 final size:17
Alignment explanation
Indices: 271958--272013 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
271948 GATTTTTTAA
271958 TTAATTTTAAATTTAAA-
1 TTAA-TTTAAATTTAAAC
*
271975 TTCAAATTAAATTTAAAC
1 TT-AATTTAAATTTAAAC
*
271993 TTAATTAAAATTTAAAC
1 TTAATTTAAATTTAAAC
272010 TTAA
1 TTAA
272014 AAGAAAAGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 30 0.88
18 4 0.12
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
TTAATTTAAATTTAAAC
Found at i:272007 original size:23 final size:23
Alignment explanation
Indices: 271956--272014 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
271946 TGGATTTTTT
* * *
271956 AATTAATTTTAAATTTAAATTCA
1 AATTAAATTTAAACTTAAATTAA
271979 AATTAAATTTAAACTT-AATTAA
1 AATTAAATTTAAACTTAAATTAA
*
272001 AATTTAAACTTAAA
1 AA-TTAAATTTAAA
272015 AGAAAAGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 7 0.23
23 24 0.77
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (23 bp):
AATTAAATTTAAACTTAAATTAA
Found at i:272027 original size:19 final size:18
Alignment explanation
Indices: 271983--272033 Score: 68
Period size: 17 Copynumber: 2.8 Consensus size: 18
271973 AATTCAAATT
**
271983 AAATTTAAACTT-AATTA
1 AAATTTAAACTTAAAAGA
272000 AAATTTAAACTTAAAAGA
1 AAATTTAAACTTAAAAGA
272018 AAAGTTTAAACTTAAA
1 AAA-TTTAAACTTAAA
272034 CTAAATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 12 0.40
18 6 0.20
19 12 0.40
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (18 bp):
AAATTTAAACTTAAAAGA
Found at i:273759 original size:2 final size:2
Alignment explanation
Indices: 273752--273789 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
273742 TGAGCTTTCA
273752 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
273790 CACAACCACC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:274904 original size:88 final size:88
Alignment explanation
Indices: 274755--274931 Score: 345
Period size: 88 Copynumber: 2.0 Consensus size: 88
274745 TTTCCTAAAA
274755 TAAGTTTTGGGCTTACATAATTTGCACTGTTAATTACAACCAATTGATAAGATAAAAGCACATTG
1 TAAGTTTTGGGCTTACATAATTTGCACTGTTAATTACAACCAATTGATAAGATAAAAGCACATTG
274820 AAATTGATGGAGTGGTGGTGCTT
66 AAATTGATGGAGTGGTGGTGCTT
*
274843 TAAGTTTTGGGCTTACATAATTTGCACTGTTAATTACAACCACTTGATAAGATAAAAGCACATTG
1 TAAGTTTTGGGCTTACATAATTTGCACTGTTAATTACAACCAATTGATAAGATAAAAGCACATTG
274908 AAATTGATGGAGTGGTGGTGCTT
66 AAATTGATGGAGTGGTGGTGCTT
274931 T
1 T
274932 TTATTGGGAA
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.34
Consensus pattern (88 bp):
TAAGTTTTGGGCTTACATAATTTGCACTGTTAATTACAACCAATTGATAAGATAAAAGCACATTG
AAATTGATGGAGTGGTGGTGCTT
Found at i:278707 original size:15 final size:15
Alignment explanation
Indices: 278687--278719 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
278677 GATATTAAAG
278687 ATATCCTATAGGGTA
1 ATATCCTATAGGGTA
278702 ATATCCTATAGGGTA
1 ATATCCTATAGGGTA
278717 ATA
1 ATA
278720 CATTAATGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.33
Consensus pattern (15 bp):
ATATCCTATAGGGTA
Found at i:280482 original size:2 final size:2
Alignment explanation
Indices: 280475--280533 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
280465 TACTTAAAAC
280475 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
280517 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
280534 AATCAAATGT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:282781 original size:59 final size:59
Alignment explanation
Indices: 282694--283006 Score: 434
Period size: 59 Copynumber: 5.3 Consensus size: 59
282684 CTTACGGGGC
* * * *
282694 AAAATGGTACTTTTCGGTGAAATCGAGGTCAAAAAGGGAATTTTGGAAAATTCGAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGT
* * *
282753 AACATAGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTT-TAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCGA-GGGT
* *
282812 AAAATGGTAATTTTTTGGTGAAATCGAGGTTAAAAATTGAATTTTGGAAAGTTCGAGGGT
1 AAAATGGTAA-TTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGT
* * *
282872 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGT
* *
282931 AAAATGGTAATTTTTGGTGAAATCGAGG-CTAAAAATATG-ATTTTGGAAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTC-AAAAAT-GGAATTTTGGAAAGTTCGAGGGT
*
282990 AAAATAGTAATTTTTGG
1 AAAATGGTAATTTTTGG
283007 ATAGTCTAAG
Statistics
Matches: 230, Mismatches: 19, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
58 1 0.00
59 173 0.75
60 55 0.24
61 1 0.00
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.32
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGT
Found at i:282868 original size:119 final size:117
Alignment explanation
Indices: 282689--283006 Score: 458
Period size: 119 Copynumber: 2.7 Consensus size: 117
282679 TTGGACTTAC
* * * * ** *
282689 GGGGCAAAATGGTACTTTTCGGTGAAATCGAGGTCAAAAAGGGAATTTTGGAAAATTCGAGGGTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATTGAATTTTGGAAAGTTCGAGGGTA
* *
282754 ACATAGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTTA
66 AAATAGTAATTTTTGGTGAAATCGAGGTCAAAAATAGAATTTTGGAAAG-TTA
282807 GGGGTAAAATGGTAATTTTTTGGTGAAATCGAGGTTAAAAATTGAATTTTGGAAAGTTCGAGGGT
1 GGGGTAAAATGGTAA-TTTTTGGTGAAATCGAGGTTAAAAATTGAATTTTGGAAAGTTCGAGGGT
* * * *
282872 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTC
65 AAAATAGTAATTTTTGGTGAAATCGAGGTCAAAAATAGAATTTTGGAAAGTTA
* *
282925 GAGGGTAAAATGGTAATTTTTGGTGAAATCGAGGCTAAAAATATG-ATTTTGGAAAGTTCGGGGG
1 G-GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAAT-TGAATTTTGGAAAGTTCGAGGG
282989 TAAAATAGTAATTTTTGG
64 TAAAATAGTAATTTTTGG
283007 ATAGTCTAAG
Statistics
Matches: 181, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
118 76 0.42
119 105 0.58
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (117 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATTGAATTTTGGAAAGTTCGAGGGTA
AAATAGTAATTTTTGGTGAAATCGAGGTCAAAAATAGAATTTTGGAAAGTTA
Found at i:282974 original size:30 final size:30
Alignment explanation
Indices: 282823--282974 Score: 106
Period size: 30 Copynumber: 5.1 Consensus size: 30
282813 AAATGGTAAT
*
282823 TTTTTGGTGAAATCGAGGTTAAAAAT-TGA
1 TTTTTGGTGAAATCGAGGGTAAAAATATGA
* * *
282852 ATTTT-G-GAAAGTTCGAGGGT-AAAATGGTAA
1 TTTTTGGTGAAA--TCGAGGGTAAAAAT-ATGA
282882 TTTTTGGTGAAATCG-GGGTTAAAAATA-GA
1 TTTTTGGTGAAATCGAGGG-TAAAAATATGA
* * *
282911 ATTTT-G-GAAAGTTCGAGGGT-AAAATGGTAA
1 TTTTTGGTGAAA--TCGAGGGTAAAAAT-ATGA
*
282941 TTTTTGGTGAAATCGAGGCTAAAAATATGA
1 TTTTTGGTGAAATCGAGGGTAAAAATATGA
282971 TTTT
1 TTTT
282975 GGAAAGTTCG
Statistics
Matches: 94, Mismatches: 13, Indels: 31
0.68 0.09 0.22
Matches are distributed among these distances:
27 8 0.09
28 12 0.13
29 23 0.24
30 31 0.33
31 12 0.13
32 8 0.09
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (30 bp):
TTTTTGGTGAAATCGAGGGTAAAAATATGA
Found at i:284858 original size:21 final size:21
Alignment explanation
Indices: 284834--284879 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
284824 TGGGCCTTTG
284834 TTTTGGACTTTGTAAATTTT-A
1 TTTTGGACTTT-TAAATTTTAA
* *
284855 TTTTGGGCTTTTTAATTTTAA
1 TTTTGGACTTTTAAATTTTAA
284876 TTTT
1 TTTT
284880 AAAATTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.20, C:0.04, G:0.13, T:0.63
Consensus pattern (21 bp):
TTTTGGACTTTTAAATTTTAA
Found at i:284912 original size:6 final size:6
Alignment explanation
Indices: 284865--284986 Score: 85
Period size: 6 Copynumber: 21.0 Consensus size: 6
284855 TTTTGGGCTT
* * * *
284865 TTTAAT TTTAAT TTTAAA ATT--A TTTCAAA TTTAAA -CTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
* ** *
284911 TTTAAA -ATAAA TTTAAA TTTAAA AATGAA TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
284958 -GTAAA TTTAAT TTTAGAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA
284987 AATTATTTTT
Statistics
Matches: 89, Mismatches: 19, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
4 3 0.03
5 14 0.16
6 67 0.75
7 5 0.06
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:284946 original size:41 final size:41
Alignment explanation
Indices: 284901--284986 Score: 136
Period size: 41 Copynumber: 2.1 Consensus size: 41
284891 AAATTTAAAC
*
284901 TAAATTTAAATTTAAAATAAATTTAAATTTAAAAATGAATT
1 TAAATTTAAATTTAAAATAAATTTAAATTTAAAAATAAATT
* * *
284942 TAAATTTAAATTTAAAGTAAATTTAATTTTAGAAATAAATT
1 TAAATTTAAATTTAAAATAAATTTAAATTTAAAAATAAATT
284983 TAAA
1 TAAA
284987 AATTATTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (41 bp):
TAAATTTAAATTTAAAATAAATTTAAATTTAAAAATAAATT
Found at i:284967 original size:17 final size:17
Alignment explanation
Indices: 284871--284951 Score: 101
Period size: 17 Copynumber: 4.7 Consensus size: 17
284861 GCTTTTTAAT
* *
284871 TTTAATTTTAAAAT-TA
1 TTTAAATTTAAAATAAA
*
284887 TTTCAAATTTAAACTAAA
1 TTT-AAATTTAAAATAAA
284905 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
284922 TTTAAATTTAAAAATGAA
1 TTTAAATTT-AAAATAAA
284940 TTTAAATTTAAA
1 TTTAAATTTAAA
284952 TTTAAAGTAA
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.05
17 34 0.60
18 20 0.35
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:284972 original size:17 final size:18
Alignment explanation
Indices: 284942--284986 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
284932 AAAATGAATT
*
284942 TAAATTTAAATTTA-AAG
1 TAAATTTAAATTTAGAAA
*
284959 TAAATTTAATTTTAGAAA
1 TAAATTTAAATTTAGAAA
284977 TAAATTTAAA
1 TAAATTTAAA
284987 AATTATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (18 bp):
TAAATTTAAATTTAGAAA
Found at i:285004 original size:24 final size:24
Alignment explanation
Indices: 284918--285010 Score: 73
Period size: 24 Copynumber: 3.7 Consensus size: 24
284908 AAATTTAAAA
*
284918 TAAATTTAAATTTAAAAATGAA-TT
1 TAAA-TTAAATTTAAAAATTAATTT
284942 TAAATTTAAATTTAAAGTAAATTTAATTT
1 TAAA-TTAAATTT-AA--AAA-TTAATTT
* *
284971 TAGAAATAAATTTAAAAATTATTTT
1 TA-AATTAAATTTAAAAATTAATTT
*
284996 TAACTTAAA-TTAAAA
1 TAAATTAAATTTAAAA
285011 TTGACCCAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
23 6 0.10
24 18 0.31
25 10 0.17
26 3 0.05
27 3 0.05
28 5 0.09
29 11 0.19
30 2 0.03
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (24 bp):
TAAATTAAATTTAAAAATTAATTT
Found at i:287221 original size:18 final size:18
Alignment explanation
Indices: 287200--287241 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
287190 GTTATGTTAT
* *
287200 TTTAATTTAATATTTTTA
1 TTTAATTGAAAATTTTTA
287218 TTT-ATTGAAAATTTTTA
1 TTTAATTGAAAATTTTTA
*
287235 TATAATT
1 TTTAATT
287242 ATCTTAACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTAATTGAAAATTTTTA
Found at i:309880 original size:19 final size:17
Alignment explanation
Indices: 309843--309881 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
309833 ATATATATAT
*
309843 AAATTATTAAAATATTA
1 AAATTATAAAAATATTA
309860 AAATTATAAATAATCATTA
1 AAATTATAAA-AAT-ATTA
309879 AAA
1 AAA
309882 AATAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 3 0.16
19 7 0.37
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATTATAAAAATATTA
Found at i:311099 original size:15 final size:15
Alignment explanation
Indices: 311079--311109 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
311069 GTTTTATTTC
311079 AAAATAATAATAATA
1 AAAATAATAATAATA
*
311094 AAAATAATAATCATA
1 AAAATAATAATAATA
311109 A
1 A
311110 TTATTTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATAATAATAATA
Found at i:311646 original size:18 final size:20
Alignment explanation
Indices: 311615--311656 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
311605 AATAGAGTGG
311615 AAGCAACTTAAAG-ACAAAA
1 AAGCAACTTAAAGAACAAAA
311634 AAGCAAC-TAAAGAACAAAA
1 AAGCAACTTAAAGAACAAAA
311653 AAGC
1 AAGC
311657 CACAAGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.64, C:0.17, G:0.12, T:0.07
Consensus pattern (20 bp):
AAGCAACTTAAAGAACAAAA
Found at i:311664 original size:17 final size:18
Alignment explanation
Indices: 311624--311661 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
311614 GAAGCAACTT
311624 AAAG-ACAAAAAAGCAAC
1 AAAGAACAAAAAAGCAAC
*
311641 TAAAGAACAAAAAAGCCAC
1 -AAAGAACAAAAAAGCAAC
311660 AA
1 AA
311662 GAAAGCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.68, C:0.18, G:0.11, T:0.03
Consensus pattern (18 bp):
AAAGAACAAAAAAGCAAC
Found at i:331522 original size:11 final size:11
Alignment explanation
Indices: 331506--331531 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
331496 TTTGCATGTA
331506 AAAGTATTATG
1 AAAGTATTATG
331517 AAAGTATTATG
1 AAAGTATTATG
331528 AAAG
1 AAAG
331532 CTTCCATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (11 bp):
AAAGTATTATG
Found at i:334594 original size:12 final size:13
Alignment explanation
Indices: 334562--334594 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
334552 TAAAAGAGAG
334562 AGAGAGG-AGGAA
1 AGAGAGGAAGGAA
334574 AGAGAGGAAGGAA
1 AGAGAGGAAGGAA
334587 AG-GAGGAA
1 AGAGAGGAA
334595 AGAGAAAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (13 bp):
AGAGAGGAAGGAA
Found at i:334609 original size:21 final size:20
Alignment explanation
Indices: 334554--334603 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
334544 GAAGAGGGTA
*
334554 AAAGAGAG-A-GAGAGGAGG
1 AAAGAGAGAAGGAAAGGAGG
334572 AAAGAGAGGAAGGAAAGGAGG
1 AAAGAGA-GAAGGAAAGGAGG
334593 AAAGAGA-AAGG
1 AAAGAGAGAAGG
334604 GAAAAGTGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 7 0.25
19 5 0.18
20 1 0.04
21 15 0.54
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (20 bp):
AAAGAGAGAAGGAAAGGAGG
Found at i:338897 original size:27 final size:27
Alignment explanation
Indices: 338866--338921 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
338856 AATATAAAAT
* *
338866 TTAATATTGATGAAATTATA-TATTAAC
1 TTAATAATCATGAAATTATAGT-TTAAC
338893 TTAATAATCATGAAATTATAGTTTAAC
1 TTAATAATCATGAAATTATAGTTTAAC
338920 TT
1 TT
338922 CTCAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (27 bp):
TTAATAATCATGAAATTATAGTTTAAC
Found at i:344673 original size:23 final size:23
Alignment explanation
Indices: 344629--344716 Score: 88
Period size: 23 Copynumber: 3.8 Consensus size: 23
344619 TTAATGTTCA
**
344629 CGAACATGTTCATTTAAC-TTAAT
1 CGAACATGTTCA-CGAACATTAAT
* * *
344652 CAAACATGTTCACGAGCATTAAA
1 CGAACATGTTCACGAACATTAAT
*
344675 CGAACATGTTCATGAACATATAAT
1 CGAACATGTTCACGAACAT-TAAT
*
344699 TGAACATGTTCACGAACA
1 CGAACATGTTCACGAACA
344717 ATGTTAATGA
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
22 2 0.04
23 31 0.60
24 19 0.37
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.28
Consensus pattern (23 bp):
CGAACATGTTCACGAACATTAAT
Found at i:349006 original size:2 final size:2
Alignment explanation
Indices: 348999--349024 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
348989 TACGAGTATC
348999 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
349025 CAGAAGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:354637 original size:13 final size:13
Alignment explanation
Indices: 354619--354678 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
354609 TTTATTAGAA
*
354619 AATTAATTTAATT
1 AATTAAATTAATT
354632 AATTAAATTAATTT
1 AATTAAATTAA-TT
** *
354646 TTTTGAAAAT-ATT
1 AATT-AAATTAATT
354659 AATTAAATTAATT
1 AATTAAATTAATT
*
354672 AAATAAA
1 AATTAAA
354679 CAAGATTTGG
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
12 4 0.11
13 23 0.64
14 5 0.14
15 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (13 bp):
AATTAAATTAATT
Found at i:354961 original size:20 final size:20
Alignment explanation
Indices: 354936--354973 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
354926 ATGGTCAAAA
354936 TTTATTTTCTT-AGAATAAAT
1 TTTATTTT-TTGAGAATAAAT
354956 TTTATTTTTTGAGAATAA
1 TTTATTTTTTGAGAATAA
354974 TAATTCCTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (20 bp):
TTTATTTTTTGAGAATAAAT
Found at i:362017 original size:50 final size:50
Alignment explanation
Indices: 361937--362032 Score: 113
Period size: 50 Copynumber: 1.9 Consensus size: 50
361927 ATTTGCAAGT
* * * * *
361937 AAATGTTGCCGATGGGTTGTGCATGTACAACATAGTTGTAGTTAAAAGAA
1 AAATATTGCCAATGGGTTGTGCATGCACAACAAAGTTGTAGATAAAAGAA
* *
361987 AAATATTGCCAAT-GGTTGTGGAGTGCACAACAAATTTGTAGATAAA
1 AAATATTGCCAATGGGTTGTGCA-TGCACAACAAAGTTGTAGATAAA
362033 CTGCCAATTC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
49 8 0.21
50 30 0.79
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.29
Consensus pattern (50 bp):
AAATATTGCCAATGGGTTGTGCATGCACAACAAAGTTGTAGATAAAAGAA
Found at i:362138 original size:34 final size:34
Alignment explanation
Indices: 362086--362277 Score: 206
Period size: 34 Copynumber: 5.6 Consensus size: 34
362076 ACATTGTGGC
* *
362086 ATGCTTATCACAGATCAATACAGTAGCAATTAAC
1 ATGCTTATAACAGATCAATACAGTAGCAATTAAT
* * *
362120 ATGCTTATAATAGCTCAATACAGTAGCAAATAAT
1 ATGCTTATAACAGATCAATACAGTAGCAATTAAT
** * * *
362154 ATGCTTATAATGGATTAATATAGT-GACAGTTAAT
1 ATGCTTATAACAGATCAATACAGTAG-CAATTAAT
* * *
362188 ATGCTTATAACAGATCAATACGGTAGTAAATAAT
1 ATGCTTATAACAGATCAATACAGTAGCAATTAAT
* * *
362222 ATTCTTATAACGGATCAATACAGTAACAATTAAT
1 ATGCTTATAACAGATCAATACAGTAGCAATTAAT
* *
362256 ATGTTTATAACAAATCAATACA
1 ATGCTTATAACAGATCAATACA
362278 ATAGTAAAAG
Statistics
Matches: 127, Mismatches: 29, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
33 1 0.01
34 125 0.98
35 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (34 bp):
ATGCTTATAACAGATCAATACAGTAGCAATTAAT
Found at i:362283 original size:68 final size:68
Alignment explanation
Indices: 362086--362285 Score: 247
Period size: 68 Copynumber: 2.9 Consensus size: 68
362076 ACATTGTGGC
* * * * * * *
362086 ATGCTTATCACAGATCAATACAGTAGCAATTAACATGCTTATAATAGCTCAATACAGTAGCAAAT
1 ATGCTTATAACGGATCAATACAGTAACAATTAATATGCTTATAACAGATCAATACAGTAGTAAAT
362151 AAT
66 AAT
* * * * * *
362154 ATGCTTATAATGGATTAATATAGTGACAGTTAATATGCTTATAACAGATCAATACGGTAGTAAAT
1 ATGCTTATAACGGATCAATACAGTAACAATTAATATGCTTATAACAGATCAATACAGTAGTAAAT
362219 AAT
66 AAT
* * * *
362222 ATTCTTATAACGGATCAATACAGTAACAATTAATATGTTTATAACAAATCAATACAATAGTAAA
1 ATGCTTATAACGGATCAATACAGTAACAATTAATATGCTTATAACAGATCAATACAGTAGTAAA
362286 AGACATGCTT
Statistics
Matches: 109, Mismatches: 23, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
68 109 1.00
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (68 bp):
ATGCTTATAACGGATCAATACAGTAACAATTAATATGCTTATAACAGATCAATACAGTAGTAAAT
AAT
Found at i:368755 original size:154 final size:156
Alignment explanation
Indices: 368504--368854 Score: 518
Period size: 154 Copynumber: 2.3 Consensus size: 156
368494 TGTTAATGAC
* * *
368504 TTTAATCCGACCCACTT--AACTTCAAGGGTATAGGATTTG-TTCTTGTAGTTACATCTTTGCTC
1 TTTAATCCGACCC-TTTACAACTTTAGGGGTATAGGATTTGCTTCTTGTAGTTACATCTTTGCTC
368566 TACTACAACTTCAAAGAGATAACGATTCACCTTCGTAGCTTCACTCTATTTCTTTGCAACTTCAG
65 TACTACAACTTCAAAGAGATAACGATTCACCTTCGTAGCTTCACTCTATTTCTTTGCAACTTCAG
*
368631 TGAAGATCGAGGTCTACTATTGTGAGT
130 TGAAGATCGAGGTCTACTACTGTGAGT
* *
368658 TTTAATCC-ACCTTTCTACAACTTTAGGGGTATAAGATTTGCTTC-TGTAGCTT-CATC-TTGCT
1 TTTAATCCGACCCTT-TACAACTTTAGGGGTATAGGATTTGCTTCTTGTAG-TTACATCTTTGCT
* * * * *
368719 CTACTGCAACTTCAGAGAGATAAGGATTCGCTTTCGTAGCTTCACTCTATTTCTTTGCAACTTCA
64 CTACTACAACTTCAAAGAGATAACGATTCACCTTCGTAGCTTCACTCTATTTCTTTGCAACTTCA
368784 GTGAAGATCGAGGTCTACTACTGTGAGT
129 GTGAAGATCGAGGTCTACTACTGTGAGT
*
368812 TTTAATCCGCCCCTTTACAACTTTAGGGGTATAGGATTTGCTT
1 TTTAATCCGACCCTTTACAACTTTAGGGGTATAGGATTTGCTT
368855 TTATAATTTT
Statistics
Matches: 177, Mismatches: 14, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
152 1 0.01
153 4 0.02
154 135 0.76
155 32 0.18
156 5 0.03
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.37
Consensus pattern (156 bp):
TTTAATCCGACCCTTTACAACTTTAGGGGTATAGGATTTGCTTCTTGTAGTTACATCTTTGCTCT
ACTACAACTTCAAAGAGATAACGATTCACCTTCGTAGCTTCACTCTATTTCTTTGCAACTTCAGT
GAAGATCGAGGTCTACTACTGTGAGT
Found at i:368997 original size:39 final size:40
Alignment explanation
Indices: 368889--369219 Score: 230
Period size: 40 Copynumber: 8.3 Consensus size: 40
368879 TAACTTTAAA
* * *
368889 GGTAAAAGATTGAATTGT-TTTAATCTG-CCTCATGG-TCG
1 GGTAAAAGATTGGATTGTCTTCAATCTGCCCTC-TGGTTAG
* * *
368927 AGGTAAGAA-ATTTGATAGTCTTTAATCTGCCCTCTGGTTAG
1 -GGTAA-AAGATTGGATTGTCTTCAATCTGCCCTCTGGTTAG
* * * *
368968 GGTAAAAGACTGGATTG-CTTCAATATGCCCTTTGGTTAA
1 GGTAAAAGATTGGATTGTCTTCAATCTGCCCTCTGGTTAG
* * *
369007 GGTAAAAGATTAGATTGT-TTTAATCTG-TCTCATGGTT-G
1 GGTAAAAGATTGGATTGTCTTCAATCTGCCCTC-TGGTTAG
* * * * **
369045 AGGTAAGAGATTAGATTG-CTTTCAATTTACCCTCTAATTAG
1 -GGTAAAAGATTGGATTGTC-TTCAATCTGCCCTCTGGTTAG
* * * * * *
369086 GGTAAAAGATTAGATGGTCTTCAATATACCCTTTGATTAG
1 GGTAAAAGATTGGATTGTCTTCAATCTGCCCTCTGGTTAG
* * * * *
369126 GGTAAAAGATTGGATAGTTTTCAATCTGCCCTATGATTGG
1 GGTAAAAGATTGGATTGTCTTCAATCTGCCCTCTGGTTAG
* * * *
369166 GGTAAGAGATCGGATGGTCTTCAATCTACCCTCTGGTTAG
1 GGTAAAAGATTGGATTGTCTTCAATCTGCCCTCTGGTTAG
*
369206 GGTAAGAGATTGGA
1 GGTAAAAGATTGGA
369220 GGTTGTAACT
Statistics
Matches: 233, Mismatches: 46, Indels: 25
0.77 0.15 0.08
Matches are distributed among these distances:
38 2 0.01
39 75 0.32
40 145 0.62
41 11 0.05
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (40 bp):
GGTAAAAGATTGGATTGTCTTCAATCTGCCCTCTGGTTAG
Found at i:369050 original size:78 final size:79
Alignment explanation
Indices: 368947--369134 Score: 184
Period size: 79 Copynumber: 2.4 Consensus size: 79
368937 TTTGATAGTC
* * * **
368947 TTTAATCTGCCCTCTGGTTAGGGTAAAAGACTGGATTGC-TTCAATATGCCCTTTGGTTAAGGTA
1 TTTAATCTGCCCTCTGGTTAGGGTAAAAGACTAGATTGCTTTCAATATACCCTCTAATTAAGGTA
369011 AAAGATTAGATTGT
66 AAAGATTAGATTGT
* * * * *
369025 TTTAATCTG-TCTCATGGTT-GAGGTAAGAGATTAGATTGCTTTCAATTTACCCTCTAATTAGGG
1 TTTAATCTGCCCTC-TGGTTAG-GGTAAAAGACTAGATTGCTTTCAATATACCCTCTAATTAAGG
*
369088 TAAAAGATTAGATGGT
64 TAAAAGATTAGATTGT
* * * * *
369104 CTTCAATATACCCTTTGATTAGGGTAAAAGA
1 -TTTAATCTGCCCTCTGGTTAGGGTAAAAGA
369135 TTGGATAGTT
Statistics
Matches: 86, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
77 4 0.05
78 29 0.34
79 32 0.37
80 18 0.21
81 3 0.03
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.36
Consensus pattern (79 bp):
TTTAATCTGCCCTCTGGTTAGGGTAAAAGACTAGATTGCTTTCAATATACCCTCTAATTAAGGTA
AAAGATTAGATTGT
Found at i:369327 original size:50 final size:50
Alignment explanation
Indices: 369273--369379 Score: 142
Period size: 50 Copynumber: 2.1 Consensus size: 50
369263 GTCCTTGAGA
* *
369273 CTTCAATATGCCCCTCTACAGCTTTAGGTGAATGAGATTTGCCATTGCGG
1 CTTCAATATGCCCCTCTACAACTTTAGGTGAATGAAATTTGCCATTGCGG
* * * * *
369323 CTTCATTCTTCCCTTCTACAACTTTAGGTGTATGAAATTTGCCATTGCGG
1 CTTCAATATGCCCCTCTACAACTTTAGGTGAATGAAATTTGCCATTGCGG
*
369373 TTTCAAT
1 CTTCAAT
369380 TTGCACCTTC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.37
Consensus pattern (50 bp):
CTTCAATATGCCCCTCTACAACTTTAGGTGAATGAAATTTGCCATTGCGG
Found at i:369521 original size:39 final size:39
Alignment explanation
Indices: 369399--369532 Score: 117
Period size: 39 Copynumber: 3.4 Consensus size: 39
369389 CATATCTTTA
* * * * *
369399 GGGGTAAAAGATTGAATTACTTCAATCTACCCTC-TGGTT
1 GGGGTAAAAGATTGGAGTACTTCAATCTGCCC-CATGATC
* * * * * *
369438 AGGGTAAAAGATCTGAATTACTTCAATCTGCCTCATGGTT
1 GGGGTAAAAGAT-TGGAGTACTTCAATCTGCCCCATGATC
* *
369478 GGGGTAAAAGATTGGAGTGCTTCAATTTGCCCCATGATC
1 GGGGTAAAAGATTGGAGTACTTCAATCTGCCCCATGATC
*
369517 GGGGTAAGAGATTGGA
1 GGGGTAAAAGATTGGA
369533 TGGTCTTCAA
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 47 0.58
40 34 0.42
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (39 bp):
GGGGTAAAAGATTGGAGTACTTCAATCTGCCCCATGATC
Found at i:369569 original size:40 final size:40
Alignment explanation
Indices: 369400--369614 Score: 151
Period size: 40 Copynumber: 5.4 Consensus size: 40
369390 ATATCTTTAG
* * * *
369400 GGGTAAAAGATTGAAT--TACTTCAATCTACCCTCTGGTTA
1 GGGTAAAAGATTGGATGGT-CTTCAATATGCCCTCTGATTA
* * * *
369439 GGGTAAAAGATCTGAAT--TACTTCAATCTG-CCTCATGGTTG
1 GGGTAAAAGAT-TGGATGGT-CTTCAATATGCCCTC-TGATTA
* **
369479 GGGTAAAAGATTGGA--GTGCTTCAATTTGCCC-CATGATCG
1 GGGTAAAAGATTGGATGGT-CTTCAATATGCCCTC-TGATTA
* **
369518 GGGTAAGAGATTGGATGGTCTTCAATATGTTCTCT-AGTTA
1 GGGTAAAAGATTGGATGGTCTTCAATATGCCCTCTGA-TTA
* * *
369558 GGGTCAAAGATTTGATGGTCTTCAATCTGCCCTCTGATTA
1 GGGTAAAAGATTGGATGGTCTTCAATATGCCCTCTGATTA
369598 GGGTAAAAGATTGGATG
1 GGGTAAAAGATTGGATG
369615 ATTGTAACTT
Statistics
Matches: 146, Mismatches: 21, Indels: 17
0.79 0.11 0.09
Matches are distributed among these distances:
39 49 0.34
40 93 0.64
41 4 0.03
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (40 bp):
GGGTAAAAGATTGGATGGTCTTCAATATGCCCTCTGATTA
Found at i:369951 original size:49 final size:49
Alignment explanation
Indices: 369898--370015 Score: 155
Period size: 49 Copynumber: 2.4 Consensus size: 49
369888 AAGATTCGTT
** * * * *
369898 GTTGCGGCCCCAATCTTTCCCTTCACATCTTTAGGGTACAAGGTTCACC
1 GTTGCGGCTTCAATCTTTCCCTCCACAACTCTAGGGTACAAGATTCACC
* *
369947 GTTGCAGCTTCAATCTTTCCCTCCATAACTCTAGGGTACAAGATTCACC
1 GTTGCGGCTTCAATCTTTCCCTCCACAACTCTAGGGTACAAGATTCACC
*
369996 GTCGCGGCTTCAATCTTTCC
1 GTTGCGGCTTCAATCTTTCC
370016 TATCATGTCC
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 59 1.00
ACGTcount: A:0.19, C:0.32, G:0.17, T:0.31
Consensus pattern (49 bp):
GTTGCGGCTTCAATCTTTCCCTCCACAACTCTAGGGTACAAGATTCACC
Found at i:371029 original size:22 final size:22
Alignment explanation
Indices: 370981--371029 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
370971 GACCTCCCCT
*
370981 TTTTTCTTTTCTTATTTTTTTC
1 TTTTTCTTTTCTTATTTTTCTC
* *
371003 CTTTTCTTTT-TCTCTTTTTCTC
1 TTTTTCTTTTCT-TATTTTTCTC
371025 TTTTT
1 TTTTT
371030 TCCTTTTTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTTCTTTTCTTATTTTTCTC
Found at i:376656 original size:91 final size:91
Alignment explanation
Indices: 376501--376685 Score: 325
Period size: 91 Copynumber: 2.0 Consensus size: 91
376491 TCAAGATAAA
* *
376501 TTGGGATGCTACAAGCTCTTTTAGAGCATCAGTAAGGTTGGCTTCTTTTTCTACTAAGGAGTAGT
1 TTGGGATGCTACAAGCTCCTTTAGAGCATCACTAAGGTTGGCTTCTTTTTCTACTAAGGAGTAGT
376566 CTTTCTTTTAGATATTCGTCAAAAGG
66 CTTTCTTTTAGATATTCGTCAAAAGG
*
376592 TTGGGATGCTGCAAGCTCCTTTAGAGCATCACTAAGGTTGGCTTCTTTTTCTACTAAGGAGTAGT
1 TTGGGATGCTACAAGCTCCTTTAGAGCATCACTAAGGTTGGCTTCTTTTTCTACTAAGGAGTAGT
* *
376657 CTTTCTTTTTGATATTCTTCAAAAGG
66 CTTTCTTTTAGATATTCGTCAAAAGG
376683 TTG
1 TTG
376686 TGATTTTCCT
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 89 1.00
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (91 bp):
TTGGGATGCTACAAGCTCCTTTAGAGCATCACTAAGGTTGGCTTCTTTTTCTACTAAGGAGTAGT
CTTTCTTTTAGATATTCGTCAAAAGG
Found at i:379270 original size:19 final size:19
Alignment explanation
Indices: 379246--379284 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
379236 ATCGCACTAA
379246 TTGTCTTGCTGTTATGATT
1 TTGTCTTGCTGTTATGATT
* *
379265 TTGTCTTTCTTTTATGATT
1 TTGTCTTGCTGTTATGATT
379284 T
1 T
379285 ATCAAAACGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.10, C:0.10, G:0.15, T:0.64
Consensus pattern (19 bp):
TTGTCTTGCTGTTATGATT
Found at i:383390 original size:29 final size:29
Alignment explanation
Indices: 383348--383436 Score: 126
Period size: 29 Copynumber: 3.1 Consensus size: 29
383338 GGATGGGGTA
383348 ATCATGTCTGCATCTGTAACTGTATCTGT
1 ATCATGTCTGCATCTGTAACTGTATCTGT
* *
383377 ATCATGTCTGCATCCGTAACTATATCTGT
1 ATCATGTCTGCATCTGTAACTGTATCTGT
* *
383406 GA-CATGACTGCATCTGTAACTGTATTTGT
1 -ATCATGTCTGCATCTGTAACTGTATCTGT
383435 AT
1 AT
383437 TATTTCTATA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
28 1 0.02
29 50 0.96
30 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (29 bp):
ATCATGTCTGCATCTGTAACTGTATCTGT
Found at i:384606 original size:29 final size:29
Alignment explanation
Indices: 384504--384607 Score: 75
Period size: 31 Copynumber: 3.4 Consensus size: 29
384494 ATTTCTTTAA
* * *
384504 ATATATAAAATTTAATCGCAATTAAAATTTT
1 ATATATTAAATTAAATC-AAATTAAAA-TTT
* * * * *
384535 ATGTATTTATTTAAACTAAAATCAAAATTT
1 ATATATTAAATTAAA-TCAAATTAAAATTT
*
384565 -TAAATATATAATTAAATCAAATTAAAATTT
1 ATATAT-TA-AATTAAATCAAATTAAAATTT
384595 ATATATTAAATTA
1 ATATATTAAATTA
384608 CAATTCACGT
Statistics
Matches: 54, Mismatches: 15, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
29 8 0.15
30 18 0.33
31 27 0.50
32 1 0.02
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (29 bp):
ATATATTAAATTAAATCAAATTAAAATTT
Found at i:384906 original size:12 final size:12
Alignment explanation
Indices: 384890--384919 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
384880 TTTAAATCTA
384890 ATTATTAAATTT
1 ATTATTAAATTT
*
384902 TTTATTAAATTT
1 ATTATTAAATTT
384914 ATTATT
1 ATTATT
384920 GTGATATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
ATTATTAAATTT
Found at i:388428 original size:17 final size:17
Alignment explanation
Indices: 388402--388439 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
388392 TTAAATGAAA
388402 ATTATCTCAATTAAAAT-
1 ATTATCTCAA-TAAAATG
*
388419 ATTATTTCAATAAAATG
1 ATTATCTCAATAAAATG
388436 ATTA
1 ATTA
388440 AATTTCATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (17 bp):
ATTATCTCAATAAAATG
Found at i:392707 original size:92 final size:92
Alignment explanation
Indices: 392549--392722 Score: 222
Period size: 92 Copynumber: 1.9 Consensus size: 92
392539 CCAATATTAG
*
392549 GTACCATAATAAAACACATATTGATAATTCAAGTACCACATTAAAAATTTTCAAAGTACAAGTAT
1 GTACCATAATAAAACACATATTGATAATTCAAGTACCACATTAAAAATTTTCAAAGTACAAATAT
392614 CACATTGAACATTTTATGAAAGTATGT
66 CACATTGAACATTTTATGAAAGTATGT
* * * * ** * * * * *
392641 GTACCATTATGAAACGCATATTGATGATTCGGGTACTATATTGAACATTTTCAAAGTATAAATAT
1 GTACCATAATAAAACACATATTGATAATTCAAGTACCACATTAAAAATTTTCAAAGTACAAATAT
* *
392706 CACGTTGAATATTTTAT
66 CACATTGAACATTTTAT
392723 AAAAATACAA
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
92 68 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (92 bp):
GTACCATAATAAAACACATATTGATAATTCAAGTACCACATTAAAAATTTTCAAAGTACAAATAT
CACATTGAACATTTTATGAAAGTATGT
Found at i:392738 original size:92 final size:92
Alignment explanation
Indices: 392550--392742 Score: 199
Period size: 92 Copynumber: 2.1 Consensus size: 92
392540 CAATATTAGG
*
392550 TACCATAATAAAACACATATTGATAATTCAAGTACCACATTAAAAATTTTCAAAGTACAAGTATC
1 TACCATAATAAAACACATATTGATAATTCAAGTACCACATTAAAAATTTTCAAAGTACAAATATC
* * ****
392615 ACATTGAACATTTTATGAAAGTATGTG
66 ACATTGAACATTTTATAAAAATACAAA
* * * * ** * * * * *
392642 TACCATTATGAAACGCATATTGATGATTCGGGTACTATATTGAACATTTTCAAAGTATAAATATC
1 TACCATAATAAAACACATATTGATAATTCAAGTACCACATTAAAAATTTTCAAAGTACAAATATC
* *
392707 ACGTTGAATATTTTATAAAAATACAAA
66 ACATTGAACATTTTATAAAAATACAAA
392734 TACCA-AATA
1 TACCATAATA
392743 TGATATTATC
Statistics
Matches: 79, Mismatches: 22, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
91 2 0.03
92 77 0.97
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (92 bp):
TACCATAATAAAACACATATTGATAATTCAAGTACCACATTAAAAATTTTCAAAGTACAAATATC
ACATTGAACATTTTATAAAAATACAAA
Found at i:395100 original size:22 final size:22
Alignment explanation
Indices: 395075--395146 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
395065 TATGTTATAA
395075 GATATGCTCCGATATGAAATCT
1 GATATGCTCCGATATGAAATCT
** ** *
395097 GATATGCTATGATATGTTAT-A
1 GATATGCTCCGATATGAAATCT
* *
395118 AATTATGCTCCGTTATGAAATCT
1 GA-TATGCTCCGATATGAAATCT
395141 GATATG
1 GATATG
395147 TTATTATATG
Statistics
Matches: 35, Mismatches: 13, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (22 bp):
GATATGCTCCGATATGAAATCT
Found at i:395115 original size:44 final size:44
Alignment explanation
Indices: 395060--395233 Score: 210
Period size: 44 Copynumber: 4.0 Consensus size: 44
395050 GGGTAGTAGT
*
395060 TATGCTATGTTATAAGATATGCTCCGATATGAAATCTGATATGC
1 TATGATATGTTATAAGATATGCTCCGATATGAAATCTGATATGC
* *
395104 TATGATATGTTATAA-ATTATGCTCCGTTATGAAATCTGATATGT
1 TATGATATGTTATAAGA-TATGCTCCGATATGAAATCTGATATGC
* * *
395148 TATTATATGTTATAAGATTTG-TGCC-ATTATGAAATTTGATATGC
1 TATGATATGTTATAAGATATGCT-CCGA-TATGAAATCTGATATGC
* * * *
395192 TATGATATGTTGTAAGATATGCACCAATATGAAATATGATAT
1 TATGATATGTTATAAGATATGCTCCGATATGAAATCTGATAT
395234 ATTCTGACAT
Statistics
Matches: 111, Mismatches: 13, Indels: 12
0.82 0.10 0.09
Matches are distributed among these distances:
43 2 0.02
44 107 0.96
45 2 0.02
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (44 bp):
TATGATATGTTATAAGATATGCTCCGATATGAAATCTGATATGC
Found at i:400147 original size:23 final size:24
Alignment explanation
Indices: 400121--400165 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
400111 AAACTCGCTC
*
400121 ATATTAT-TTTTTTTAAAATTTTT
1 ATATTATATTATTTTAAAATTTTT
*
400144 ATATTATATTATTTTAATATTT
1 ATATTATATTATTTTAAAATTT
400166 AATAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
ATATTATATTATTTTAAAATTTTT
Found at i:408547 original size:16 final size:16
Alignment explanation
Indices: 408526--408561 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
408516 CGAGAAATGT
408526 TTTTGTTTAAAAAAAA
1 TTTTGTTTAAAAAAAA
* *
408542 TTTTGTTTAGAAATAA
1 TTTTGTTTAAAAAAAA
408558 TTTT
1 TTTT
408562 ATCAAAGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (16 bp):
TTTTGTTTAAAAAAAA
Found at i:410739 original size:48 final size:48
Alignment explanation
Indices: 410683--410865 Score: 357
Period size: 48 Copynumber: 3.8 Consensus size: 48
410673 TTGGGGGTGA
410683 TGGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGGTGCAGGAGC
1 TGGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGGTGCAGGAGC
410731 TGGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGGTGCAGGAGC
1 TGGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGGTGCAGGAGC
*
410779 TGGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGCGGTGCAGGAGC
1 TGGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGGTGCAGGAGC
410827 TGGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGG
1 TGGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGG
410866 CTTATATGGT
Statistics
Matches: 133, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 133 1.00
ACGTcount: A:0.14, C:0.10, G:0.48, T:0.27
Consensus pattern (48 bp):
TGGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGGTGCAGGAGC
Found at i:410746 original size:27 final size:27
Alignment explanation
Indices: 410716--410853 Score: 79
Period size: 27 Copynumber: 5.6 Consensus size: 27
410706 GAGCCTTGGT
*
410716 TGGTGGTGCAGGAGCTGGGGGCTTATA
1 TGGTGGAGCAGGAGCTGGGGGCTTATA
* *
410743 TGGTGGAGTAGGAGC------CTTGGT-
1 TGGTGGAGCAGGAGCTGGGGGCTT-ATA
*
410764 TGGTGGTGCAGGAGCTGGGGGCTTATA
1 TGGTGGAGCAGGAGCTGGGGGCTTATA
* *
410791 TGGTGGAGTAGGAGC------CTTGGT-
1 TGGTGGAGCAGGAGCTGGGGGCTT-ATA
* *
410812 TGGCGGTGCAGGAGCTGGGGGCTTATA
1 TGGTGGAGCAGGAGCTGGGGGCTTATA
*
410839 TGGTGGAGTAGGAGC
1 TGGTGGAGCAGGAGC
410854 CTTGGTTGGT
Statistics
Matches: 79, Mismatches: 16, Indels: 32
0.62 0.13 0.25
Matches are distributed among these distances:
21 31 0.39
22 2 0.03
26 2 0.03
27 44 0.56
ACGTcount: A:0.15, C:0.11, G:0.49, T:0.25
Consensus pattern (27 bp):
TGGTGGAGCAGGAGCTGGGGGCTTATA
Found at i:410873 original size:33 final size:33
Alignment explanation
Indices: 410827--410956 Score: 206
Period size: 33 Copynumber: 3.9 Consensus size: 33
410817 GTGCAGGAGC
* *
410827 TGGGGGCTTATATGGTGGAGTAGGAGCCTTGGT
1 TGGGGGCTTATATGGTGGAGTGGGGGCCTTGGT
*
410860 TGGTGGCTTATATGGTGGAGTGGGGGCCTTGGT
1 TGGGGGCTTATATGGTGGAGTGGGGGCCTTGGT
* *
410893 TGGGGGTTTGTATGGTGGAGTGGGGGCCTTGGT
1 TGGGGGCTTATATGGTGGAGTGGGGGCCTTGGT
*
410926 TGGGGGTTTATATGGTGGAGTGGGGGCCTTG
1 TGGGGGCTTATATGGTGGAGTGGGGGCCTTG
410957 TACGGCGGTG
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.10, C:0.08, G:0.50, T:0.32
Consensus pattern (33 bp):
TGGGGGCTTATATGGTGGAGTGGGGGCCTTGGT
Found at i:412510 original size:2 final size:2
Alignment explanation
Indices: 412505--412571 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
412495 ATAAGCTAAT
412505 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
412547 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
412572 TTGAAAGTTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:413529 original size:25 final size:25
Alignment explanation
Indices: 413500--413553 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
413490 TCATTATTCT
* *
413500 AAATATTGAAATATTT-ATAATTATA
1 AAATATTGAAAAATTTCA-AAATATA
*
413525 AAATATTTAAAAATTTCAAAATATA
1 AAATATTGAAAAATTTCAAAATATA
413550 AAAT
1 AAAT
413554 TAAAAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 24 0.96
26 1 0.04
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (25 bp):
AAATATTGAAAAATTTCAAAATATA
Found at i:413808 original size:19 final size:18
Alignment explanation
Indices: 413769--413810 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
413759 GATTTTTATT
413769 AAATAAAATAAAACTATA
1 AAATAAAATAAAACTATA
*
413787 AAATATAAATATAAAGTA-A
1 AAATA-AAATA-AAACTATA
413806 AAATA
1 AAATA
413811 CATGTGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 11 0.52
20 5 0.24
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (18 bp):
AAATAAAATAAAACTATA
Found at i:413809 original size:13 final size:13
Alignment explanation
Indices: 413771--413810 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
413761 TTTTTATTAA
*
413771 ATAAAATAAAACT
1 ATAAAATAAAAAT
*
413784 ATAAAATATAAAT
1 ATAAAATAAAAAT
*
413797 ATAAAGTAAAAAT
1 ATAAAATAAAAAT
413810 A
1 A
413811 CATGTGAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (13 bp):
ATAAAATAAAAAT
Found at i:419097 original size:20 final size:20
Alignment explanation
Indices: 419041--419100 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
419031 AAATTACTTC
*
419041 ATTTTAAAAATTTAAAAATA
1 ATTTTTAAAATTTAAAAATA
**
419061 ATTTTTTAAAAAATAAAAAT-
1 A-TTTTTAAAATTTAAAAATA
419081 ATTTTTAAAATCTTAAAAAT
1 ATTTTTAAAAT-TTAAAAAT
419101 TTAATTAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 9 0.27
20 9 0.27
21 15 0.45
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTTTTAAAATTTAAAAATA
Found at i:423823 original size:30 final size:30
Alignment explanation
Indices: 423772--423834 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
423762 AGAAACAGAC
* * *
423772 TCTTGTTCAGCGAAAGTTGTTTCTCCTTGT
1 TCTTGTTCAACGAAAGCTGTTTCTCCTTCT
*
423802 TCTTGTTCAAC-AACAGCTGTTTCTTCTTCT
1 TCTTGTTCAACGAA-AGCTGTTTCTCCTTCT
423832 TCT
1 TCT
423835 GCAGACTTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 2 0.07
30 26 0.93
ACGTcount: A:0.14, C:0.24, G:0.14, T:0.48
Consensus pattern (30 bp):
TCTTGTTCAACGAAAGCTGTTTCTCCTTCT
Found at i:435475 original size:24 final size:26
Alignment explanation
Indices: 435409--435480 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 26
435399 GTAATTAAAA
*
435409 TAAATAAAACTAATTAATATATTTTAAT
1 TAAATAAAA--AATTAATATATATTAAT
435437 TAAAATTAAAAAATTAA-AT-TATTAAT
1 T-AAA-TAAAAAATTAATATATATTAAT
435463 TAAATAAAAAATTGAATA
1 TAAATAAAAAATT-AATA
435481 ATTCAAATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
24 9 0.23
25 5 0.13
26 8 0.21
27 2 0.05
28 7 0.18
29 3 0.08
30 5 0.13
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (26 bp):
TAAATAAAAAATTAATATATATTAAT
Found at i:435874 original size:24 final size:24
Alignment explanation
Indices: 435847--435892 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
435837 TCAAATAATA
435847 TATTAATTA-ATAATAATAATATTT
1 TATTAATTATATAATAA-AATATTT
* *
435871 TATTATTTATATTATAAAATAT
1 TATTAATTATATAATAAAATAT
435893 AAAGAAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TATTAATTATATAATAAAATATTT
Found at i:439687 original size:6 final size:6
Alignment explanation
Indices: 439678--439717 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
439668 AAAGTTACGT
* * *
439678 CCGACA CCGACA CCGACA CCGACC CCGACC CCGACC CCGA
1 CCGACA CCGACA CCGACA CCGACA CCGACA CCGACA CCGA
439718 AACAACACTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.25, C:0.57, G:0.17, T:0.00
Consensus pattern (6 bp):
CCGACA
Found at i:439695 original size:12 final size:12
Alignment explanation
Indices: 439678--439717 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
439668 AAAGTTACGT
*
439678 CCGACACCGACA
1 CCGACACCGACC
439690 CCGACACCGACC
1 CCGACACCGACC
*
439702 CCGACCCCGACC
1 CCGACACCGACC
439714 CCGA
1 CCGA
439718 AACAACACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.25, C:0.57, G:0.17, T:0.00
Consensus pattern (12 bp):
CCGACACCGACC
Found at i:441301 original size:33 final size:32
Alignment explanation
Indices: 441256--441317 Score: 106
Period size: 33 Copynumber: 1.9 Consensus size: 32
441246 AATAAAATAA
*
441256 GAAAGCCTCCAATAATCCACTTAGATTGCTCT
1 GAAAGCCGCCAATAATCCACTTAGATTGCTCT
441288 GAAAGGCCGCCAATAATCCACTTAGATTGC
1 GAAA-GCCGCCAATAATCCACTTAGATTGC
441318 GTTGAATCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 4 0.14
33 24 0.86
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (32 bp):
GAAAGCCGCCAATAATCCACTTAGATTGCTCT
Found at i:442968 original size:9 final size:10
Alignment explanation
Indices: 442954--443006 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
442944 ATTAAAATCA
442954 TTTTTAAT-T
1 TTTTTAATAT
442963 TTTTT-ATGA-
1 TTTTTAAT-AT
*
442972 TTTTTAATAA
1 TTTTTAATAT
442982 TTTTT-ATAGT
1 TTTTTAATA-T
442992 TTTTTAATAT
1 TTTTTAATAT
443002 TTTTT
1 TTTTT
443007 GATGTGATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
8 2 0.05
9 14 0.38
10 18 0.49
11 3 0.08
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.72
Consensus pattern (10 bp):
TTTTTAATAT
Found at i:443006 original size:20 final size:19
Alignment explanation
Indices: 442953--443006 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
442943 TATTAAAATC
442953 ATTTTTAAT-TTTTTTATG
1 ATTTTTAATATTTTTTATG
*
442971 ATTTTTAATAATTTTTATAG
1 ATTTTTAATATTTTTTAT-G
*
442991 TTTTTTAATATTTTTT
1 ATTTTTAATATTTTTT
443007 GATGTGATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 9 0.29
19 7 0.23
20 15 0.48
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (19 bp):
ATTTTTAATATTTTTTATG
Found at i:444995 original size:28 final size:27
Alignment explanation
Indices: 444964--445037 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 27
444954 ATATTTATCT
*
444964 TATATTATTTTAATATTTAATATTTTTA
1 TATATTATTTTAATATTAAAT-TTTTTA
*
444992 TATATT-TTTTATTTATTAAATTTTTTA
1 TATATTATTTTA-ATATTAAATTTTTTA
* *
445019 TATAATCATCTTAATATTA
1 TAT-ATTATTTTAATATTA
445038 TTTTAGTGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 14 0.37
28 20 0.53
29 4 0.11
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (27 bp):
TATATTATTTTAATATTAAATTTTTTA
Found at i:445001 original size:27 final size:28
Alignment explanation
Indices: 444964--445022 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
444954 ATATTTATCT
*
444964 TATATTATTTTA-ATATTTAATATTTTTA
1 TATATTATTTTATATATTAAAT-TTTTTA
*
444992 TATATT-TTTTATTTATTAAATTTTTTA
1 TATATTATTTTATATATTAAATTTTTTA
445019 TATA
1 TATA
445023 ATCATCTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 15 0.54
28 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (28 bp):
TATATTATTTTATATATTAAATTTTTTA
Found at i:445267 original size:72 final size:74
Alignment explanation
Indices: 445166--445303 Score: 226
Period size: 72 Copynumber: 1.9 Consensus size: 74
445156 TAGTTAACAT
*
445166 TATTTTCTTACCAAATTAATATTTATATACTATTTTGTATTAATTTACCAAACTAAACTAAAAAT
1 TATTTTCTTACCAAATTAATATTTATATACTACTTTGTATTAATTTACCAAACTAAACTAAAAAT
445231 GTTACCAAA
66 GTTACCAAA
* * *
445240 TATTTT-TTAGCAAATTAAT-TTTATATACTACTTTGTATTAGTTTATCAAACTAAACTAAAAAT
1 TATTTTCTTACCAAATTAATATTTATATACTACTTTGTATTAATTTACCAAACTAAACTAAAAAT
445303 G
66 G
445304 CTACTAACTT
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
72 42 0.70
73 12 0.20
74 6 0.10
ACGTcount: A:0.41, C:0.12, G:0.04, T:0.43
Consensus pattern (74 bp):
TATTTTCTTACCAAATTAATATTTATATACTACTTTGTATTAATTTACCAAACTAAACTAAAAAT
GTTACCAAA
Found at i:446722 original size:19 final size:20
Alignment explanation
Indices: 446687--446725 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
446677 TTAATTTTTA
446687 TTTAAAAATATATATATATT
1 TTTAAAAATATATATATATT
446707 TTTAAAAATATA-ATATATT
1 TTTAAAAATATATATATATT
446726 AAATGCACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTAAAAATATATATATATT
Found at i:456592 original size:13 final size:13
Alignment explanation
Indices: 456569--456603 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
456559 TTTCTGCTAC
456569 TTTTTCATTTTCAT
1 TTTTTCATTTTC-T
456583 TTTTTC-TTTTCT
1 TTTTTCATTTTCT
456595 TTTTTCATT
1 TTTTTCATT
456604 AAAAAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 7 0.35
13 7 0.35
14 6 0.30
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTCATTTTCT
Found at i:462752 original size:30 final size:30
Alignment explanation
Indices: 462694--462755 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
462684 GTGCTTGAAT
* *
462694 TTGACATTTTTTTTAATTTGGCATCTAAAC
1 TTGACATTTTTTTTAATTTGACACCTAAAC
*
462724 TTGACATTTTTTTTAATTTGATACCTAAAC
1 TTGACATTTTTTTTAATTTGACACCTAAAC
462754 TT
1 TT
462756 TTTTTTGTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.13, G:0.08, T:0.52
Consensus pattern (30 bp):
TTGACATTTTTTTTAATTTGACACCTAAAC
Found at i:463268 original size:31 final size:30
Alignment explanation
Indices: 463191--463270 Score: 79
Period size: 31 Copynumber: 2.6 Consensus size: 30
463181 GACCCCCAAA
* * *
463191 AAGTTTAAGTACTAACTTAAGAAAAATTGCC
1 AAGTTT-AGTACCAAATTAAGAAAAAGTGCC
* * *
463222 AAGTTTAGATGCCAAATTAGGAAAAAGTGTC
1 AAGTTTAG-TACCAAATTAAGAAAAAGTGCC
463253 AAGTTTGAGTACCAAATT
1 AAGTTT-AGTACCAAATT
463271 GAACCAAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
30 2 0.05
31 36 0.90
32 2 0.05
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.29
Consensus pattern (30 bp):
AAGTTTAGTACCAAATTAAGAAAAAGTGCC
Found at i:464511 original size:12 final size:12
Alignment explanation
Indices: 464494--464519 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
464484 ATAAACAGTA
464494 AAAAATTTAAAT
1 AAAAATTTAAAT
464506 AAAAATTTAAAT
1 AAAAATTTAAAT
464518 AA
1 AA
464520 TATAGTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAAATTTAAAT
Found at i:469270 original size:17 final size:17
Alignment explanation
Indices: 469248--469293 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
469238 TTTTATTTTG
469248 AATTTAAATTTGCA-TAT-
1 AATTTAAATTT--ATTATA
469265 AATTTAAATTTATTATA
1 AATTTAAATTTATTATA
469282 AATTTAAATTTA
1 AATTTAAATTTA
469294 AAATTAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.04
16 3 0.11
17 23 0.85
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
AATTTAAATTTATTATA
Found at i:470022 original size:21 final size:22
Alignment explanation
Indices: 469970--470027 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 22
469960 ATAAATATGT
469970 TATTAATAAT-ATTGATGATAA
1 TATTAATAATAATTGATGATAA
**
469991 TATCATAATAATAATTG-TTTTAA
1 TAT--TAATAATAATTGATGATAA
470014 TATTAATAATAATT
1 TATTAATAATAATT
470028 AGTAAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 14 0.44
23 14 0.44
24 4 0.12
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (22 bp):
TATTAATAATAATTGATGATAA
Found at i:470304 original size:16 final size:16
Alignment explanation
Indices: 470279--470310 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
470269 AAGTTTTGAA
*
470279 ATTTTTCCAGATCTGG
1 ATTTTACCAGATCTGG
470295 ATTTTACCAGATCTGG
1 ATTTTACCAGATCTGG
470311 GTTCGGGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (16 bp):
ATTTTACCAGATCTGG
Found at i:471160 original size:30 final size:29
Alignment explanation
Indices: 471097--471167 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
471087 GATTTCACCA
* * *
471097 AAAATACCA-TTTTACCCCCAAACTTTCC
1 AAAATTCCATTTTTAACCCCAAAATTTCC
471125 AAAATTCCATTTTTAACCCCAAAATTTCC
1 AAAATTCCATTTTTAACCCCAAAATTTCC
* *
471154 TGAAATTACATTTT
1 -AAAATTCCATTTT
471168 CACCATCGAG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
28 8 0.22
29 17 0.47
30 11 0.31
ACGTcount: A:0.37, C:0.27, G:0.01, T:0.35
Consensus pattern (29 bp):
AAAATTCCATTTTTAACCCCAAAATTTCC
Found at i:487530 original size:15 final size:15
Alignment explanation
Indices: 487496--487532 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
487486 TTTTAAATTT
*
487496 ATTTTATATAAAAAA
1 ATTTAATATAAAAAA
487511 A--TAATATAAAAAA
1 ATTTAATATAAAAAA
487524 ATTTAATAT
1 ATTTAATAT
487533 GGGCGGGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
13 12 0.63
15 7 0.37
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTTAATATAAAAAA
Found at i:489699 original size:17 final size:18
Alignment explanation
Indices: 489677--489711 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
489667 TATATTTAAT
*
489677 TTTTGGGTTAA-ATAAAA
1 TTTTGGGTAAACATAAAA
489694 TTTTGGGTAAACATAAAA
1 TTTTGGGTAAACATAAAA
489712 AATAGTCACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.43, C:0.03, G:0.17, T:0.37
Consensus pattern (18 bp):
TTTTGGGTAAACATAAAA
Found at i:490474 original size:31 final size:29
Alignment explanation
Indices: 490405--490478 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
490395 ACAAAATACT
**
490405 AACATAAGTGACTAAAACGTAACATTTCA
1 AACATAAGTGACTAAAACGTAACATGGCA
*
490434 AACATAAGTGACTAAAATGTAACATGAGGCA
1 AACATAAGTGACTAAAACGTAACAT--GGCA
*
490465 AACAAAAGTGACTA
1 AACATAAGTGACTA
490479 TTTTTGTAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.20
Consensus pattern (29 bp):
AACATAAGTGACTAAAACGTAACATGGCA
Found at i:499324 original size:24 final size:24
Alignment explanation
Indices: 499297--499342 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
499287 AAAAAAATTA
*
499297 TATTTTTTTTGATGCTTTTTTTTT
1 TATTTTTTTGGATGCTTTTTTTTT
*
499321 TATTTTTTTGGTTGCTTTTTTT
1 TATTTTTTTGGATGCTTTTTTT
499343 GCTGTTTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.07, C:0.04, G:0.11, T:0.78
Consensus pattern (24 bp):
TATTTTTTTGGATGCTTTTTTTTT
Found at i:499350 original size:24 final size:24
Alignment explanation
Indices: 499297--499350 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
499287 AAAAAAATTA
* **
499297 TATTTTTTTTGATGCTTTTTTTTT
1 TATTTTTTTGGATGCTTTTTTTGC
*
499321 TATTTTTTTGGTTGCTTTTTTTGC
1 TATTTTTTTGGATGCTTTTTTTGC
*
499345 TGTTTT
1 TATTTT
499351 GGTGTTGTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.06, C:0.06, G:0.13, T:0.76
Consensus pattern (24 bp):
TATTTTTTTGGATGCTTTTTTTGC
Found at i:499362 original size:59 final size:62
Alignment explanation
Indices: 499299--499436 Score: 148
Period size: 59 Copynumber: 2.3 Consensus size: 62
499289 AAAAATTATA
* * *
499299 TTTTTTTTGATGCT-TTTT-TTTTTAT-TTTTTTGGTTGC-TTTTTTTGCTGTTTTGGTGTTG
1 TTTTTTTTGATGCTATTTTATTTTT-TCTGTTTTGGTTGCATTTTTTTACTGTTTTGATGTTG
499358 -TTTTTTT-A--CTATTTTATTTTTTCTGTTTTGGTTGCTATTTTTTTACTGTTTTGATGTTG
1 TTTTTTTTGATGCTATTTTATTTTTTCTGTTTTGGTTGC-ATTTTTTTACTGTTTTGATGTTG
* *
499417 TTATTTTTGTTGCTACTTTT
1 TTTTTTTTGATGCTA-TTTT
499437 TATGTTTTGC
Statistics
Matches: 64, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
55 2 0.03
56 5 0.08
57 17 0.27
58 7 0.11
59 20 0.31
60 6 0.09
63 3 0.05
64 4 0.06
ACGTcount: A:0.07, C:0.07, G:0.15, T:0.71
Consensus pattern (62 bp):
TTTTTTTTGATGCTATTTTATTTTTTCTGTTTTGGTTGCATTTTTTTACTGTTTTGATGTTG
Found at i:499372 original size:22 final size:22
Alignment explanation
Indices: 499315--499372 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
499305 TTGATGCTTT
* *
499315 TTTTTTTA-TTTTTTTGGTTGC
1 TTTTTTTACTATTTTGGGTTGC
* *
499336 TTTTTTTGCTGTTTTGGTGTTG-
1 TTTTTTTACTATTTTGG-GTTGC
499358 TTTTTTTACTATTTT
1 TTTTTTTACTATTTT
499373 ATTTTTTCTG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 7 0.23
22 19 0.63
23 4 0.13
ACGTcount: A:0.05, C:0.05, G:0.16, T:0.74
Consensus pattern (22 bp):
TTTTTTTACTATTTTGGGTTGC
Found at i:499378 original size:37 final size:37
Alignment explanation
Indices: 499337--499409 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
499327 TTTGGTTGCT
* *
499337 TTTTTTGCTGTTTTGG-TGTTGTTTTTTTACTATTTTA
1 TTTTTT-CTGTTTTGGTTGCTATTTTTTTACTATTTTA
*
499374 TTTTTTCTGTTTTGGTTGCTATTTTTTTACTGTTTT
1 TTTTTTCTGTTTTGGTTGCTATTTTTTTACTATTTT
499410 GATGTTGTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 9 0.28
37 23 0.72
ACGTcount: A:0.07, C:0.07, G:0.15, T:0.71
Consensus pattern (37 bp):
TTTTTTCTGTTTTGGTTGCTATTTTTTTACTATTTTA
Found at i:499400 original size:23 final size:24
Alignment explanation
Indices: 499374--499424 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
499364 TACTATTTTA
499374 TTTTTT-CTGTTTTG-GTTGCTAT
1 TTTTTTACTGTTTTGAGTTGCTAT
*
499396 TTTTTTACTGTTTTGATGTTGTTAT
1 TTTTTTACTGTTTTGA-GTTGCTAT
499421 TTTT
1 TTTT
499425 GTTGCTACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 6 0.24
23 8 0.32
25 11 0.44
ACGTcount: A:0.08, C:0.06, G:0.16, T:0.71
Consensus pattern (24 bp):
TTTTTTACTGTTTTGAGTTGCTAT
Found at i:499618 original size:12 final size:12
Alignment explanation
Indices: 499601--499644 Score: 72
Period size: 12 Copynumber: 3.7 Consensus size: 12
499591 ACATAAAGAA
499601 TTTTTAATGTAT
1 TTTTTAATGTAT
499613 TTTTTAATGTAT
1 TTTTTAATGTAT
499625 TTTTTAATGT-T
1 TTTTTAATGTAT
499636 TGTTTTAAT
1 T-TTTTAAT
499645 ATTTTTAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 2 0.06
12 29 0.94
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.68
Consensus pattern (12 bp):
TTTTTAATGTAT
Found at i:499627 original size:22 final size:22
Alignment explanation
Indices: 499601--499650 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 22
499591 ACATAAAGAA
499601 TTTTTAATGTATT-TTTTAATGTAT
1 TTTTTAATGT-TTGTTTTAA--TAT
499625 TTTTTAATGTTTGTTTTAATAT
1 TTTTTAATGTTTGTTTTAATAT
499647 TTTT
1 TTTT
499651 AAGTTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.28
23 2 0.08
24 16 0.64
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.70
Consensus pattern (22 bp):
TTTTTAATGTTTGTTTTAATAT
Found at i:499667 original size:21 final size:21
Alignment explanation
Indices: 499625--499668 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
499615 TTTAATGTAT
* *
499625 TTTTTAATGTTTGTTTTAATA
1 TTTTTAATGTTTATTTGAATA
499646 TTTTTAA-GTTTATTTGATATA
1 TTTTTAATGTTTATTTGA-ATA
499667 TT
1 TT
499669 ATATATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (21 bp):
TTTTTAATGTTTATTTGAATA
Found at i:501621 original size:7 final size:7
Alignment explanation
Indices: 501604--501642 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
501594 AAGATTTAGG
*
501604 GTTTGAA
1 GTTTGGA
*
501611 GTTTGGT
1 GTTTGGA
501618 GTTTGG-
1 GTTTGGA
501624 GTTTGGA
1 GTTTGGA
501631 GTTTGGA
1 GTTTGGA
501638 GTTTG
1 GTTTG
501643 AAATTCAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.10, C:0.00, G:0.41, T:0.49
Consensus pattern (7 bp):
GTTTGGA
Found at i:501627 original size:20 final size:20
Alignment explanation
Indices: 501602--501642 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
501592 TTAAGATTTA
*
501602 GGGTTTGAAGTTTGGTGTTT
1 GGGTTTGAAGTTTGGAGTTT
*
501622 GGGTTTGGAGTTTGGAGTTT
1 GGGTTTGAAGTTTGGAGTTT
501642 G
1 G
501643 AAATTCAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
GGGTTTGAAGTTTGGAGTTT
Found at i:501629 original size:13 final size:14
Alignment explanation
Indices: 501604--501642 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
501594 AAGATTTAGG
* *
501604 GTTTGAAGTTTGGT
1 GTTTGGAGTTTGGA
501618 GTTTGG-GTTTGGA
1 GTTTGGAGTTTGGA
501631 GTTTGGAGTTTG
1 GTTTGGAGTTTG
501643 AAATTCAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.10, C:0.00, G:0.41, T:0.49
Consensus pattern (14 bp):
GTTTGGAGTTTGGA
Found at i:502087 original size:63 final size:61
Alignment explanation
Indices: 502020--502139 Score: 150
Period size: 63 Copynumber: 1.9 Consensus size: 61
502010 TAATCTAACC
* * * * * * *
502020 TTTCAAAAGTTATAGAATTTTTAATTAAACCCTTTAATTCTTTTTGAAAATTCTCATTAATTT
1 TTTCAAAAATTATAAAACTTTGAATTAAACCCCTTAA-T-GTTTTAAAAATTCTCATTAATTT
*
502083 TTTCAAAAATTTTAAAACTTTGAATTAAACCCCTTAATGTTTTAAAAATTCTCATTA
1 TTTCAAAAATTATAAAACTTTGAATTAAACCCCTTAATGTTTTAAAAATTCTCATTA
502140 GACTCGAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
61 17 0.35
62 1 0.02
63 31 0.63
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.46
Consensus pattern (61 bp):
TTTCAAAAATTATAAAACTTTGAATTAAACCCCTTAATGTTTTAAAAATTCTCATTAATTT
Found at i:506674 original size:12 final size:12
Alignment explanation
Indices: 506657--506682 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
506647 CATTGAGGAG
506657 TAATTCGATAGA
1 TAATTCGATAGA
506669 TAATTCGATAGA
1 TAATTCGATAGA
506681 TA
1 TA
506683 TAAGCATTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (12 bp):
TAATTCGATAGA
Found at i:510607 original size:18 final size:17
Alignment explanation
Indices: 510586--510619 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
510576 TATATATATA
*
510586 TAATTTTGATTATAATTT
1 TAATTTTAATT-TAATTT
510604 TAATTTTAATTTAATT
1 TAATTTTAATTTAATT
510620 GTGCACGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TAATTTTAATTTAATTT
Found at i:511990 original size:23 final size:25
Alignment explanation
Indices: 511953--512002 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
511943 ATATTTTTAG
511953 AATAATCAGAGTTTAACT-GGAAAA
1 AATAATCAGAGTTTAACTAGGAAAA
* *
511977 AATAA-CAGTGTTTACCTAGGAAAA
1 AATAATCAGAGTTTAACTAGGAAAA
512001 AA
1 AA
512003 ATACGAGGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.50, C:0.10, G:0.16, T:0.24
Consensus pattern (25 bp):
AATAATCAGAGTTTAACTAGGAAAA
Found at i:515389 original size:13 final size:13
Alignment explanation
Indices: 515373--515397 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
515363 AAAACATCCA
515373 TTTTCAACAACTG
1 TTTTCAACAACTG
515386 TTTTCAACAACT
1 TTTTCAACAACT
515398 CGGCTCGAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.40
Consensus pattern (13 bp):
TTTTCAACAACTG
Found at i:521063 original size:24 final size:24
Alignment explanation
Indices: 521030--521078 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
521020 GAGGATGACC
*
521030 CAGAACTAGCAA-TTGCTTTGATAG
1 CAGAACTAGCAACTTG-TTTCATAG
*
521054 CAGAATTAGCAACTTGTTTCATAG
1 CAGAACTAGCAACTTGTTTCATAG
521078 C
1 C
521079 CATATCTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (24 bp):
CAGAACTAGCAACTTGTTTCATAG
Found at i:521509 original size:17 final size:18
Alignment explanation
Indices: 521487--521521 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
521477 GACACCTGTG
*
521487 TATTTTTTTAA-ATATGA
1 TATTTTATTAATATATGA
521504 TATTTTATTAATATATGA
1 TATTTTATTAATATATGA
521522 AAATACGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (18 bp):
TATTTTATTAATATATGA
Found at i:521784 original size:60 final size:59
Alignment explanation
Indices: 521553--521983 Score: 292
Period size: 60 Copynumber: 7.3 Consensus size: 59
521543 AAAATTTGGG
** * * * * * *
521553 GTGTTGGCCATCGCATGGCCGACACCCCCTGTT-TCAAAAAAAAAATTTCAAAATTTTTTG
1 GTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTCGAAAAAAAAA-TTC-TATTTTTTTA
*** * *
521613 GTGCAAGCTATCAAATGGCCGACATCCC-CTTTTCTCG-AAAAAAAATTAC-A-TTTTTTG
1 GTGTTGGCCATCAAATGGCCGACA-CCCTCTTTTCTCGAAAAAAAAATT-CTATTTTTTTA
*** * ** * * *
521670 GTGTTGGCCATTGCATGGCTGACACATTCTGTTTC-AGAAAAAAAAATTCAATTTTTTTT
1 GTGTTGGCCATCAAATGGCCGACACCCTCT-TTTCTCGAAAAAAAAATTCTATTTTTTTA
* ** * * * *
521729 GTGTTAGTTATCAAATGGCTGATACCCCTTTTTTCTCGAGAAAAAAAATT-TA-TTTTTTG
1 GTGTTGGCCATCAAATGGCCGACA-CCCTCTTTTCTCGA-AAAAAAAATTCTATTTTTTTA
521788 GATGTTGGCCATCAAATGGCCGACACCCTCTTTTCTCGAATAAAAAAATT-TAGAATTTTTTTA
1 G-TGTTGGCCATCAAATGGCCGACACCCTCTTTTCTCGAA-AAAAAAATTCT---ATTTTTTTA
** * * *
521851 GTGTTGGCCATCAAATGGCAAACACCCGCTTTTCTC-AAAAAAAAATTGTATTTTTTTC
1 GTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTCGAAAAAAAAATTCTATTTTTTTA
* * * * * **
521909 GTATTGGCAATCAAATAGCCGACACCCTTTTTTCTCG--AAAAAAATTGTATTTTTTGG
1 GTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTCGAAAAAAAAATTCTATTTTTTTA
*
521966 GTGTTGACCATCAAATGG
1 GTGTTGGCCATCAAATGG
521984 AAGACACCAA
Statistics
Matches: 295, Mismatches: 57, Indels: 41
0.75 0.15 0.10
Matches are distributed among these distances:
56 1 0.00
57 59 0.20
58 54 0.18
59 59 0.20
60 64 0.22
61 18 0.06
62 33 0.11
63 7 0.02
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (59 bp):
GTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTCGAAAAAAAAATTCTATTTTTTTA
Found at i:521922 original size:58 final size:59
Alignment explanation
Indices: 521622--521983 Score: 301
Period size: 59 Copynumber: 6.2 Consensus size: 59
521612 GGTGCAAGCT
** *
521622 ATCAAATGGCCGACATCCC-CTTTTCTCG-AAAAAAAATTACA-TTTTTTGGTGTTGGCC
1 ATCAAATGGCCGACA-CCCTCTTTTCTCGAAAAAAAAATTGTATTTTTTTAGTGTTGGCC
*** * ** * ** * * **
521679 ATTGCATGGCTGACACATTCTGTTTC-AGAAAAAAAAATTCAATTTTTTTTGTGTTAGTT
1 ATCAAATGGCCGACACCCTCT-TTTCTCGAAAAAAAAATTGTATTTTTTTAGTGTTGGCC
* * * *
521738 ATCAAATGGCTGATACCCCTTTTTTCTCGAGAAAAAAAATT-TA-TTTTTTGGATGTTGGCC
1 ATCAAATGGCCGACA-CCCTCTTTTCTCGA-AAAAAAAATTGTATTTTTTTAG-TGTTGGCC
*
521798 ATCAAATGGCCGACACCCTCTTTTCTCGAATAAAAAAATTTAGAATTTTTTTAGTGTTGGCC
1 ATCAAATGGCCGACACCCTCTTTTCTCGAA-AAAAAAA-TT-GTATTTTTTTAGTGTTGGCC
** * * * *
521860 ATCAAATGGCAAACACCCGCTTTTCTC-AAAAAAAAATTGTATTTTTTTCGTATTGGCA
1 ATCAAATGGCCGACACCCTCTTTTCTCGAAAAAAAAATTGTATTTTTTTAGTGTTGGCC
* * ** *
521918 ATCAAATAGCCGACACCCTTTTTTCTCG--AAAAAAATTGTATTTTTTGGGTGTTGACC
1 ATCAAATGGCCGACACCCTCTTTTCTCGAAAAAAAAATTGTATTTTTTTAGTGTTGGCC
521975 ATCAAATGG
1 ATCAAATGG
521984 AAGACACCAA
Statistics
Matches: 242, Mismatches: 49, Indels: 28
0.76 0.15 0.09
Matches are distributed among these distances:
56 1 0.00
57 46 0.19
58 54 0.22
59 56 0.23
60 33 0.14
61 12 0.05
62 33 0.14
63 7 0.03
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (59 bp):
ATCAAATGGCCGACACCCTCTTTTCTCGAAAAAAAAATTGTATTTTTTTAGTGTTGGCC
Found at i:522104 original size:56 final size:59
Alignment explanation
Indices: 522017--522177 Score: 177
Period size: 56 Copynumber: 2.8 Consensus size: 59
522007 TTTTTTCTCC
* * * *
522017 AGAATAAGAG-GTGTCGGCCATTTGATGGCCAACACCCAAAAAATGCAA-CTTTT-TTG
1 AGAAAAAGAGAGTGTCGGCCATTTGATAGCCAACACCAAAAAAATGAAATCTTTTCTTG
* * * * *
522073 AGAAAAGGGGA-TGTCGGCCATTTGATAGCCAACACGAAAAAATTTTGAAATTTTTTCTTG
1 AGAAAAAGAGAGTGTCGGCCATTTGATAGCCAACACCAAAAAA--ATGAAATCTTTTCTTG
* *
522133 AGAAAAAGAGAGTGTCGACCATTTGATAGCTAACACCAAAAAAAT
1 AGAAAAAGAGAGTGTCGGCCATTTGATAGCCAACACCAAAAAAAT
522178 TTAAATTTTT
Statistics
Matches: 84, Mismatches: 15, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
56 35 0.42
58 4 0.05
59 5 0.06
60 12 0.14
61 28 0.33
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (59 bp):
AGAAAAAGAGAGTGTCGGCCATTTGATAGCCAACACCAAAAAAATGAAATCTTTTCTTG
Found at i:522189 original size:61 final size:60
Alignment explanation
Indices: 521987--522188 Score: 216
Period size: 61 Copynumber: 3.4 Consensus size: 60
521977 CAAATGGAAG
** * *
521987 ACACCAAAAAAATTTTAAATTTTTTTCTCCAGAATAAGAG-GTGTCGGCCATTTGATGGCCA
1 ACACCAAAAAAA-TTTAAA-TTTTTTCTTGAGAAAAAGAGAGTGTCGGCCATTTGATAGCCA
* ** * * *
522048 ACACCCAAAAAA-TGCAA-CTTTT-TTGAGAAAAGGGGA-TGTCGGCCATTTGATAGCCA
1 ACACCAAAAAAATTTAAATTTTTTCTTGAGAAAAAGAGAGTGTCGGCCATTTGATAGCCA
* * * *
522104 ACACGAAAAAATTTTGAAATTTTTTCTTGAGAAAAAGAGAGTGTCGACCATTTGATAGCTA
1 ACACCAAAAAAATTT-AAATTTTTTCTTGAGAAAAAGAGAGTGTCGGCCATTTGATAGCCA
522165 ACACCAAAAAAATTTAAATTTTTT
1 ACACCAAAAAAATTTAAATTTTTT
522189 TTTCTGAAAC
Statistics
Matches: 113, Mismatches: 22, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
56 36 0.32
57 5 0.04
58 2 0.02
59 7 0.06
60 21 0.19
61 42 0.37
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (60 bp):
ACACCAAAAAAATTTAAATTTTTTCTTGAGAAAAAGAGAGTGTCGGCCATTTGATAGCCA
Found at i:523571 original size:23 final size:23
Alignment explanation
Indices: 523524--523587 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
523514 TTCTATACGC
*
523524 GCAAGTGATAGTGGCACTACAAT
1 GCAAGTGACAGTGGCACTACAAT
*
523547 GCAAGTGACAGTGGCAC-ACTCAT
1 GCAAGTGACAGTGGCACTAC-AAT
* *
523570 GCAAATGACAGTGACACT
1 GCAAGTGACAGTGGCACT
523588 TTAGTGTGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 2 0.06
23 33 0.94
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (23 bp):
GCAAGTGACAGTGGCACTACAAT
Found at i:534934 original size:24 final size:24
Alignment explanation
Indices: 534860--534924 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
534850 TTCTATAATC
534860 TTCTACTTTATTTGTTTCAATTAAA
1 TTCTA-TTTATTTGTTTCAATTAAA
* *
534885 TTCTATTTATTTATTTTAATTAAA
1 TTCTATTTATTTGTTTCAATTAAA
*
534909 TTCTGTTTATTTGTTT
1 TTCTATTTATTTGTTT
534925 GAGTCAAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
24 31 0.86
25 5 0.14
ACGTcount: A:0.25, C:0.08, G:0.05, T:0.63
Consensus pattern (24 bp):
TTCTATTTATTTGTTTCAATTAAA
Found at i:537804 original size:17 final size:17
Alignment explanation
Indices: 537784--537840 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 17
537774 AATAATTTTA
537784 ATATTATTTTAATATTT
1 ATATTATTTTAATATTT
* *
537801 ATATTAATATAATA-TT
1 ATATTATTTTAATATTT
*
537817 ATA-TA-TTTAATATAT
1 ATATTATTTTAATATTT
537832 AT-TTATTTT
1 ATATTATTTT
537841 TATAATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
14 6 0.18
15 7 0.21
16 8 0.24
17 12 0.36
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATATTATTTTAATATTT
Found at i:537836 original size:11 final size:11
Alignment explanation
Indices: 537780--537836 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
537770 ATGTAATAAT
537780 TTTAATAT-TA
1 TTTAATATATA
*
537790 TTTTAATATTTA
1 -TTTAATATATA
537802 TATTAATATA-A
1 T-TTAATATATA
*
537813 --TATTATATA
1 TTTAATATATA
537822 TTTAATATATA
1 TTTAATATATA
537833 TTTA
1 TTTA
537837 TTTTTATAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
8 6 0.16
9 1 0.03
11 22 0.58
12 9 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTAATATATA
Found at i:537837 original size:19 final size:20
Alignment explanation
Indices: 537795--537850 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
537785 TATTATTTTA
537795 ATATT-TATA-TTAATATA-
1 ATATTATATATTTAATATAT
537812 ATATTATATATTTAATATAT
1 ATATTATATATTTAATATAT
*
537832 AT-TTAT-TTTTATAATATAT
1 ATATTATATATT-TAATATAT
537851 TCCAATTACA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
17 5 0.15
18 7 0.21
19 20 0.59
20 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATTATATATTTAATATAT
Found at i:540900 original size:22 final size:21
Alignment explanation
Indices: 540859--540900 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
540849 ATATTTTATT
540859 TAAATTTAATTATAAAATATG
1 TAAATTTAATTATAAAATATG
540880 TAAATATTAA-TATAAATATAT
1 TAAAT-TTAATTATAAA-ATAT
540901 ATTTTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATG
Found at i:541960 original size:51 final size:51
Alignment explanation
Indices: 541905--542064 Score: 272
Period size: 51 Copynumber: 3.2 Consensus size: 51
541895 CATTACGTGT
* *
541905 TTCATTCTCTGTTATTTGGTTGTTTTTAATTGTTTAAAGCAGCCACAACCA
1 TTCATTCTCTGTTATTTGATTGTTTTTAATTGTTTAAAGCAGCCACAATCA
*
541956 TTCATTCTCTGTTATTTGATTTTTTTTAATTG--T-AAGCAGCCACAATCA
1 TTCATTCTCTGTTATTTGATTGTTTTTAATTGTTTAAAGCAGCCACAATCA
542004 TTCATTCTCTGTTATTTGATTGTTTTTAATTGTTTAAAGCAGCCACAATCA
1 TTCATTCTCTGTTATTTGATTGTTTTTAATTGTTTAAAGCAGCCACAATCA
542055 TTCATTCTCT
1 TTCATTCTCT
542065 TTTAATTGTT
Statistics
Matches: 102, Mismatches: 4, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
48 45 0.44
49 1 0.01
50 1 0.01
51 55 0.54
ACGTcount: A:0.24, C:0.17, G:0.11, T:0.47
Consensus pattern (51 bp):
TTCATTCTCTGTTATTTGATTGTTTTTAATTGTTTAAAGCAGCCACAATCA
Done.