Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008150.1 Hibiscus syriacus cultivar Beakdansim tig00110716_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3012591
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 14
Found at i:2654549 original size:15 final size:14
Alignment explanation
Indices: 2654413--2654549 Score: 91
Period size: 14 Copynumber: 9.7 Consensus size: 14
2654403 CCTTAACTAT
2654413 AAAACCCT-AACTAC
1 AAAACCCTAAAC-AC
** * *
2654427 AAAACTATAACCAG
1 AAAACCCTAAACAC
* *
2654441 AAAACCCTAAATAA
1 AAAACCCTAAACAC
**
2654455 AAAACCCTAAGTAC
1 AAAACCCTAAACAC
*
2654469 AAAACCCT-AACTAT
1 AAAACCCTAAAC-AC
*
2654483 AAAACCCTAAATAC
1 AAAACCCTAAACAC
*
2654497 AAAACCCTAAATAC
1 AAAACCCTAAACAC
2654511 AAAACCCT-AACTAC
1 AAAACCCTAAAC-AC
**
2654525 AAAATGCTAAACAC
1 AAAACCCTAAACAC
*
2654539 TAAAATCCTAA
1 -AAAACCCTAA
2654550 CTAACTAAAA
Statistics
Matches: 97, Mismatches: 20, Indels: 11
0.76 0.16 0.09
Matches are distributed among these distances:
13 3 0.03
14 78 0.80
15 16 0.16
ACGTcount: A:0.55, C:0.27, G:0.02, T:0.16
Consensus pattern (14 bp):
AAAACCCTAAACAC
Found at i:2654583 original size:17 final size:16
Alignment explanation
Indices: 2654540--2654583 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
2654530 GCTAAACACT
2654540 AAAATCCTAACTAACTA
1 AAAAT-CTAACTAACTA
* *
2654557 AAAATATAACTTACTAA
1 AAAATCTAACTAACT-A
2654574 AAAATCTAAC
1 AAAATCTAAC
2654584 CTTAAAACTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.57, C:0.18, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAATCTAACTAACTA
Found at i:2654604 original size:27 final size:27
Alignment explanation
Indices: 2654566--2654617 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2654556 AAAAATATAA
*
2654566 CTTACTAAAAAA-TCTAACCTTAAAACT
1 CTTACTAAAAAACCCTAA-CTTAAAACT
*
2654593 CTTACTATAAAACCCTAACTTAAAA
1 CTTACTAAAAAACCCTAACTTAAAA
2654618 AATATTCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (27 bp):
CTTACTAAAAAACCCTAACTTAAAACT
Found at i:2655292 original size:37 final size:37
Alignment explanation
Indices: 2655242--2655323 Score: 164
Period size: 37 Copynumber: 2.2 Consensus size: 37
2655232 GGAGCATTAG
2655242 ATTTTAAAGGTAAAACTGTTATTTGGCATTAAAATGA
1 ATTTTAAAGGTAAAACTGTTATTTGGCATTAAAATGA
2655279 ATTTTAAAGGTAAAACTGTTATTTGGCATTAAAATGA
1 ATTTTAAAGGTAAAACTGTTATTTGGCATTAAAATGA
2655316 ATTTTAAA
1 ATTTTAAA
2655324 TTCATTTGGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (37 bp):
ATTTTAAAGGTAAAACTGTTATTTGGCATTAAAATGA
Found at i:2661780 original size:56 final size:56
Alignment explanation
Indices: 2661720--2661839 Score: 152
Period size: 56 Copynumber: 2.1 Consensus size: 56
2661710 ACGTCAGACG
* * *
2661720 TGCTAAGTACCACATAACTGA-TAGTAACACCACCATCACATAAAAGATATCAAACA
1 TGCTAAATACCACACAACT-ACTAGTAACACCACCATCACATAAAAGACATCAAACA
** * **
2661776 TGCTAAATACCATGCAACTACTAGTAGCACCACCATCACATAAGTGACATCAAACA
1 TGCTAAATACCACACAACTACTAGTAACACCACCATCACATAAAAGACATCAAACA
2661832 TGCTAAAT
1 TGCTAAAT
2661840 GCTCTACCTC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
55 1 0.02
56 54 0.98
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.21
Consensus pattern (56 bp):
TGCTAAATACCACACAACTACTAGTAACACCACCATCACATAAAAGACATCAAACA
Found at i:2662584 original size:34 final size:33
Alignment explanation
Indices: 2662545--2662615 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 33
2662535 TTTTGTAAAG
* *
2662545 GGGAAATGTTCTAGCTTATCCCATGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTATCCCATG-AAAAACTA
*
2662579 GGGAAAGGTTCTAGTTTATCCCATGAAAAACTA
1 GGGAAAGGTTCTAGCTTATCCCATGAAAAACTA
2662612 GGGA
1 GGGA
2662616 GTTGTAAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 11 0.32
34 23 0.68
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTTATCCCATGAAAAACTA
Found at i:2663693 original size:20 final size:20
Alignment explanation
Indices: 2663638--2663698 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
2663628 AGGGTGTCAA
*
2663638 AGTGTATCCATACACGCTGC
1 AGTGTATCCATACACTCTGC
* *
2663658 AGTATATCCATGCACTCTGC
1 AGTGTATCCATACACTCTGC
*
2663678 AGTGTATCCATACACTATGC
1 AGTGTATCCATACACTCTGC
2663698 A
1 A
2663699 TCGATGCACC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (20 bp):
AGTGTATCCATACACTCTGC
Found at i:2663800 original size:15 final size:15
Alignment explanation
Indices: 2663777--2663806 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2663767 ATGCACCCTA
*
2663777 AGTGTACCGATGCAC
1 AGTGCACCGATGCAC
2663792 AGTGCACCGATGCAC
1 AGTGCACCGATGCAC
2663807 CCTGCAGTGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.17
Consensus pattern (15 bp):
AGTGCACCGATGCAC
Found at i:2663816 original size:20 final size:20
Alignment explanation
Indices: 2663791--2663829 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
2663781 TACCGATGCA
2663791 CAGTGCA-CCGATGCACCCTG
1 CAGTGCATCC-ATGCACCCTG
2663811 CAGTGCATCCATGCACCCT
1 CAGTGCATCCATGCACCCT
2663830 AGCTGAAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.21, C:0.41, G:0.21, T:0.18
Consensus pattern (20 bp):
CAGTGCATCCATGCACCCTG
Found at i:2666449 original size:21 final size:19
Alignment explanation
Indices: 2666406--2666463 Score: 82
Period size: 18 Copynumber: 3.0 Consensus size: 19
2666396 CAACAATTGG
2666406 TAACAATTGATATC-TTTT
1 TAACAATTGATATCTTTTT
2666424 TAACAATTGATATCATTTTGT
1 TAACAATTGATATC-TTTT-T
*
2666445 TAACAATTGGTATCTTTTT
1 TAACAATTGATATCTTTTT
2666464 CATTAAACAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 14 0.39
19 1 0.03
20 7 0.19
21 14 0.39
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.50
Consensus pattern (19 bp):
TAACAATTGATATCTTTTT
Found at i:2666741 original size:20 final size:20
Alignment explanation
Indices: 2666686--2666746 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
2666676 AGGGTGTCAA
* *
2666686 AGTGTATTCATACACCCTGC
1 AGTGTATCCATACACTCTGC
* * *
2666706 AGTGTATCTATGCACTCTGT
1 AGTGTATCCATACACTCTGC
*
2666726 AGTGTATCCATACACTGTGC
1 AGTGTATCCATACACTCTGC
2666746 A
1 A
2666747 TCGATGCACC
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (20 bp):
AGTGTATCCATACACTCTGC
Found at i:2666863 original size:20 final size:20
Alignment explanation
Indices: 2666842--2666917 Score: 125
Period size: 20 Copynumber: 3.8 Consensus size: 20
2666832 TGATGCACAG
* * *
2666842 TGCATCGATACACCCTACAG
1 TGCATCCATGCACCCTACAA
2666862 TGCATCCATGCACCCTACAA
1 TGCATCCATGCACCCTACAA
2666882 TGCATCCATGCACCCTACAA
1 TGCATCCATGCACCCTACAA
2666902 TGCATCCATGCACCCT
1 TGCATCCATGCACCCT
2666918 GGCTGCAACG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.28, C:0.39, G:0.12, T:0.21
Consensus pattern (20 bp):
TGCATCCATGCACCCTACAA
Found at i:2668229 original size:45 final size:46
Alignment explanation
Indices: 2668142--2668231 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 46
2668132 TGAAAAAGCC
* *
2668142 TGAGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCAG
1 TGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCAG
2668188 TGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 TGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
2668232 TTCGATGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 22 0.52
46 20 0.48
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.28
Consensus pattern (46 bp):
TGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCAG
Found at i:2676960 original size:46 final size:45
Alignment explanation
Indices: 2676904--2676993 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
2676894 TGAAAAAGCT
* *
2676904 TGAGTACATCGATGCATGGTCTTGTACATCGATGCATCAAATGCAC
1 TGAGTACATCGATGCATGGT-ATGTACATCGATGCATAAAATGCAC
* * *
2676950 TGAGTGCATCGATGCATGGTATGTGCATTGATGCATAAAATGCA
1 TGAGTACATCGATGCATGGTATGTACATCGATGCATAAAATGCA
2676994 TTCGATGTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 20 0.51
46 19 0.49
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (45 bp):
TGAGTACATCGATGCATGGTATGTACATCGATGCATAAAATGCAC
Found at i:2683351 original size:3 final size:3
Alignment explanation
Indices: 2683345--2683381 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2683335 AATAATAATA
2683345 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
2683382 AATGTTCTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:2687423 original size:14 final size:14
Alignment explanation
Indices: 2687404--2687431 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2687394 AAGTGAAAGA
2687404 ATAGTTATATAATT
1 ATAGTTATATAATT
2687418 ATAGTTATATAATT
1 ATAGTTATATAATT
2687432 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:2688666 original size:7 final size:7
Alignment explanation
Indices: 2688654--2688756 Score: 50
Period size: 7 Copynumber: 14.9 Consensus size: 7
2688644 TATGTGATAA
2688654 GGTTTAG
1 GGTTTAG
2688661 GGTTTAG
1 GGTTTAG
*
2688668 GATTTAG
1 GGTTTAG
**
2688675 AATTTA-
1 GGTTTAG
* *
2688681 TGTGATAG
1 GGT-TTAG
* *
2688689 GATTTAA
1 GGTTTAG
2688696 GGTTTAG
1 GGTTTAG
*
2688703 AGTTTAG
1 GGTTTAG
*
2688710 AGTTTAG
1 GGTTTAG
2688717 GGTTTA-
1 GGTTTAG
* *
2688723 TGTGTTAA
1 GGT-TTAG
2688731 GGTTTAG
1 GGTTTAG
*
2688738 GGTTTTG
1 GGTTTAG
*
2688745 TG-TTAG
1 GGTTTAG
2688751 GGTTTA
1 GGTTTA
2688757 AGTTATGCCA
Statistics
Matches: 71, Mismatches: 20, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
6 7 0.10
7 61 0.86
8 3 0.04
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.46
Consensus pattern (7 bp):
GGTTTAG
Found at i:2688700 original size:35 final size:35
Alignment explanation
Indices: 2688643--2688715 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
2688633 TCATAACTAA
*
2688643 TTATGTGATAAGGTTTAGGGTTTAG-GATTTAGAAT
1 TTATGTGATAAGGTTTAAGGTTTAGAG-TTTAGAAT
*
2688678 TTATGTGAT-AGGATTTAAGGTTTAGAGTTTAGAGT
1 TTATGTGATAAGG-TTTAAGGTTTAGAGTTTAGAAT
2688713 TTA
1 TTA
2688716 GGGTTTATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 3 0.09
35 30 0.88
36 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (35 bp):
TTATGTGATAAGGTTTAAGGTTTAGAGTTTAGAAT
Found at i:2688748 original size:20 final size:21
Alignment explanation
Indices: 2688711--2688756 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
2688701 AGAGTTTAGA
2688711 GTTTAGGGTTTATGTGTTAAG
1 GTTTAGGGTTTATGTGTTAAG
*
2688732 GTTTAGGGTTT-TGTGTTAGG
1 GTTTAGGGTTTATGTGTTAAG
2688752 GTTTA
1 GTTTA
2688757 AGTTATGCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (21 bp):
GTTTAGGGTTTATGTGTTAAG
Found at i:2690475 original size:26 final size:26
Alignment explanation
Indices: 2690435--2690521 Score: 129
Period size: 26 Copynumber: 3.3 Consensus size: 26
2690425 CCTAGTATTG
*
2690435 GTTTTGGTGTTTGGTTCTCTGTCCCTT
1 GTTTT-GTGCTTGGTTCTCTGTCCCTT
* * *
2690462 ATTTTTTGCTTGGTGCTCTGTCCCTT
1 GTTTTGTGCTTGGTTCTCTGTCCCTT
2690488 GTTTTGTGCTTGGTTCTCTGTCCCTT
1 GTTTTGTGCTTGGTTCTCTGTCCCTT
2690514 GTTTTGTG
1 GTTTTGTG
2690522 TGTCTGCAGA
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
26 49 0.92
27 4 0.08
ACGTcount: A:0.01, C:0.20, G:0.24, T:0.55
Consensus pattern (26 bp):
GTTTTGTGCTTGGTTCTCTGTCCCTT
Found at i:2690900 original size:17 final size:17
Alignment explanation
Indices: 2690878--2690914 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
2690868 ATTCGAGTTT
*
2690878 GAGTTCGAGCTTTAATC
1 GAGTTCGAGCTTGAATC
2690895 GAGTTCGAGCTTGAATC
1 GAGTTCGAGCTTGAATC
2690912 GAG
1 GAG
2690915 CTCAAAATCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (17 bp):
GAGTTCGAGCTTGAATC
Found at i:2690913 original size:11 final size:11
Alignment explanation
Indices: 2690899--2690962 Score: 65
Period size: 11 Copynumber: 5.6 Consensus size: 11
2690889 TTAATCGAGT
*
2690899 TCGAGCTTGAA
1 TCGAGCTTAAA
*
2690910 TCGAGCTCAAAA
1 TCGAGCT-TAAA
*
2690922 TCGAGCTTGAA
1 TCGAGCTTAAA
*
2690933 TCGAGCTCCAAA
1 TCGAGCT-TAAA
*
2690945 TCGAGCTTCAA
1 TCGAGCTTAAA
2690956 TCGAGCT
1 TCGAGCT
2690963 CGAGTCTCGA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 25 0.58
12 18 0.42
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (11 bp):
TCGAGCTTAAA
Found at i:2690925 original size:12 final size:11
Alignment explanation
Indices: 2690908--2690963 Score: 60
Period size: 12 Copynumber: 4.9 Consensus size: 11
2690898 TTCGAGCTTG
2690908 AATCGAGCTCAA
1 AATCGAGCTC-A
**
2690920 AATCGAGCTTG
1 AATCGAGCTCA
2690931 AATCGAGCTCCA
1 AATCGAGCT-CA
2690943 AATCGAGCTTC-
1 AATCGAGC-TCA
2690954 AATCGAGCTC
1 AATCGAGCTC
2690964 GAGTCTCGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
10 2 0.05
11 17 0.45
12 18 0.47
13 1 0.03
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (11 bp):
AATCGAGCTCA
Found at i:2690929 original size:23 final size:23
Alignment explanation
Indices: 2690899--2690963 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
2690889 TTAATCGAGT
2690899 TCGAGCTTGAATCGAGCTCAAAA
1 TCGAGCTTGAATCGAGCTCAAAA
*
2690922 TCGAGCTTGAATCGAGCTCCAAA
1 TCGAGCTTGAATCGAGCTCAAAA
*
2690945 TCGAGCTTCAATCGAGCTC
1 TCGAGCTTGAATCGAGCTC
2690964 GAGTCTCGAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (23 bp):
TCGAGCTTGAATCGAGCTCAAAA
Found at i:2699098 original size:17 final size:17
Alignment explanation
Indices: 2699056--2699102 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
2699046 GGTTCCATAA
2699056 AAGTTCTTATTTTGTTTT
1 AAGTT-TTATTTTGTTTT
*
2699074 CA-TCTTTATTTTGTTTT
1 AAGT-TTTATTTTGTTTT
2699091 AAGTTTTATTTT
1 AAGTTTTATTTT
2699103 AAACGTGCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 22 0.88
18 3 0.12
ACGTcount: A:0.17, C:0.06, G:0.09, T:0.68
Consensus pattern (17 bp):
AAGTTTTATTTTGTTTT
Found at i:2703450 original size:11 final size:11
Alignment explanation
Indices: 2703434--2703458 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2703424 AAAAATAGAA
2703434 AAAATAAAAAT
1 AAAATAAAAAT
2703445 AAAATAAAAAT
1 AAAATAAAAAT
2703456 AAA
1 AAA
2703459 TTCTTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:2705771 original size:19 final size:19
Alignment explanation
Indices: 2705747--2705788 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
2705737 AGTTGTCGGG
2705747 GCATTATAGAGTCCAAAAA
1 GCATTATAGAGTCCAAAAA
2705766 GCATTATAGAGTCCAAAAA
1 GCATTATAGAGTCCAAAAA
2705785 GCAT
1 GCAT
2705789 CCTACTAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.21
Consensus pattern (19 bp):
GCATTATAGAGTCCAAAAA
Found at i:2716545 original size:73 final size:74
Alignment explanation
Indices: 2716449--2716600 Score: 227
Period size: 73 Copynumber: 2.1 Consensus size: 74
2716439 AAAAAAGAAA
2716449 TAAATCCTAATTAAAATACTTAAAACTATTTAAACTAAAATAT-ATAAAACAAAGATAAGA-TAA
1 TAAATCCTAATTAAAATACTTAAAACTATTTAAACT-AAATATCATAAAACAAAGATAAGATTAA
*
2716512 AATATTATCC
65 AATAATATCC
* * * *
2716522 TAAATCCTAATTAAAATACTTAAAACTATTTAAACTAAATTTCCTAAAACAAATATAATATTTAA
1 TAAATCCTAATTAAAATACTTAAAACTATTTAAACTAAATATCATAAAACAAAGATAAGA-TTAA
2716587 AATAATATCC
65 AATAATATCC
2716597 TAAA
1 TAAA
2716601 ACATGAGTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
72 5 0.07
73 50 0.70
75 16 0.23
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.32
Consensus pattern (74 bp):
TAAATCCTAATTAAAATACTTAAAACTATTTAAACTAAATATCATAAAACAAAGATAAGATTAAA
ATAATATCC
Found at i:2720486 original size:5 final size:5
Alignment explanation
Indices: 2720476--2720548 Score: 51
Period size: 5 Copynumber: 14.2 Consensus size: 5
2720466 TAAGCATCTG
* * * **
2720476 ATAAA ATAAA ATAAA AT-AA ATAGA ATGAA ATAAA GTTTGCA A-AAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA --ATAAA ATAAA ATAAA
2720526 ATGAAA ATAAAA ATAAA ATAAA A
1 AT-AAA AT-AAA ATAAA ATAAA A
2720549 CGAAATGGGT
Statistics
Matches: 52, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
4 6 0.12
5 34 0.65
6 10 0.19
7 2 0.04
ACGTcount: A:0.71, C:0.01, G:0.07, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:2726048 original size:18 final size:17
Alignment explanation
Indices: 2726016--2726062 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
2726006 GATAAAGATG
*
2726016 AAAAGATAAAAATAATA
1 AAAAAATAAAAATAATA
* *
2726033 AAATAAATAAATATAATT
1 AAA-AAATAAAAATAATA
2726051 AAAAAATAAAAA
1 AAAAAATAAAAA
2726063 AGGGGGAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (17 bp):
AAAAAATAAAAATAATA
Found at i:2726985 original size:73 final size:74
Alignment explanation
Indices: 2726895--2727046 Score: 227
Period size: 73 Copynumber: 2.1 Consensus size: 74
2726885 AAAAAAGAAA
* *
2726895 TAAATTCTAATTAAAATACTTAAAACTATTTAAACTAAAATACCTAAAACAAAGAT-ATGA-TAA
1 TAAATCCTAATTAAAATAATTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAT-ATTAA
*
2726958 AATATTATCC
65 AATAATATCC
* *
2726968 TAAATCCTAATTAAAATAATTAAAACTATTTAAACTAAAATTCCTAAAACAAATATAATATTTAA
1 TAAATCCTAATTAAAATAATTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAATA-TTAA
2727033 AATAATATCC
65 AATAATATCC
2727043 TAAA
1 TAAA
2727047 AAATGAGTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
73 53 0.75
74 2 0.03
75 16 0.23
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.32
Consensus pattern (74 bp):
TAAATCCTAATTAAAATAATTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAATATTAAA
ATAATATCC
Found at i:2727408 original size:22 final size:20
Alignment explanation
Indices: 2727383--2727431 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 20
2727373 ATTATGACTC
* *
2727383 TTTTAATTTTTCTTACTTTATA
1 TTTTAATTTTTATCA-TTT-TA
*
2727405 TTTTTATTTTTATCATTTTA
1 TTTTAATTTTTATCATTTTA
2727425 TTTTAAT
1 TTTTAAT
2727432 AATTTATTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 8 0.35
21 3 0.13
22 12 0.52
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTAATTTTTATCATTTTA
Found at i:2727423 original size:14 final size:13
Alignment explanation
Indices: 2727399--2727451 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
2727389 TTTTTCTTAC
2727399 TTTATATTTTTATT
1 TTTATA-TTTTATT
2727413 TTTATCATTTTATT
1 TTTAT-ATTTTATT
* *
2727427 TTAATAATTTATT
1 TTTATATTTTATT
2727440 TCTTATAATTTT
1 T-TTAT-ATTTT
2727452 TCTACTTTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
13 8 0.25
14 19 0.59
15 5 0.16
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTATATTTTATT
Found at i:2730194 original size:21 final size:20
Alignment explanation
Indices: 2730150--2730196 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
2730140 AGGAAACATA
*
2730150 AAAAGACAAGAAAAAAAAGGG
1 AAAA-ACAAGAAAAAAAAGCG
*
2730171 AAAAACAATAAAAAAAATGCG
1 AAAAACAAGAAAAAAAA-GCG
2730192 AAAAA
1 AAAAA
2730197 AGTCAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.74, C:0.06, G:0.15, T:0.04
Consensus pattern (20 bp):
AAAAACAAGAAAAAAAAGCG
Found at i:2741922 original size:20 final size:19
Alignment explanation
Indices: 2741885--2741923 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2741875 GTTTAAAGTG
*
2741885 GAATTATGAAATTGAAGGT
1 GAATTATGAAATTCAAGGT
*
2741904 GAATTCATGTAATTCAAGGT
1 GAATT-ATGAAATTCAAGGT
2741924 TAAATGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.33
Consensus pattern (19 bp):
GAATTATGAAATTCAAGGT
Found at i:2743505 original size:6 final size:6
Alignment explanation
Indices: 2743494--2743797 Score: 201
Period size: 6 Copynumber: 50.8 Consensus size: 6
2743484 AAACAATCTA
* *
2743494 CTTCTT CTTCTT CTTCTT CTTCTT TTTCTC CTTCTT CTTC-T CATTCTT
1 CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT C-TTCTT
* * * *
2743542 CTCCTT -TTCCTT CTCCTT CTTC-T CTTCTT CTTCTC CTTCTC CTTCTT
1 CTTCTT CTT-CTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT
* * * * * * *
2743589 CTCCCT CTCCTT C-TCATT CTCCTT CTTCTT CTTCTC CTCCTT CTTCTC
1 CTTCTT CTTCTT CTTC-TT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT
* * * * * *
2743637 CTTCTT CTTATC CTTCTC CTTCTG CTTCTT CTACTT CTCCTT CTTCTT
1 CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT
* * * * * *
2743685 C-TCATC CTTCTT CTCCTT CTCCTT CTTCTT CTTC-T CCTCATT ATTCTC
1 CTTC-TT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTC-TT CTTCTT
* * ** *
2743733 CTTC-T CATTCTT CTCCTT C-TCATT CTTCTT CTGCTT CCCCTT CTTCTC
1 CTTCTT C-TTCTT CTTCTT CTTC-TT CTTCTT CTTCTT CTTCTT CTTCTT
* *
2743781 CTCCTT ATTCTT CTTCT
1 CTTCTT CTTCTT CTTCT
2743798 AAAAAATATT
Statistics
Matches: 230, Mismatches: 53, Indels: 30
0.73 0.17 0.10
Matches are distributed among these distances:
5 17 0.07
6 200 0.87
7 13 0.06
ACGTcount: A:0.03, C:0.40, G:0.01, T:0.56
Consensus pattern (6 bp):
CTTCTT
Found at i:2743514 original size:15 final size:15
Alignment explanation
Indices: 2743494--2743797 Score: 201
Period size: 15 Copynumber: 20.3 Consensus size: 15
2743484 AAACAATCTA
2743494 CTTCTTCTTCTTCTT
1 CTTCTTCTTCTTCTT
* *
2743509 CTTCTTCTTTTTCTC
1 CTTCTTCTTCTTCTT
2743524 CTTCTTCTTC-TCATT
1 CTTCTTCTTCTTC-TT
*
2743539 CTTCTCCTT-TTCCTT
1 CTTCTTCTTCTT-CTT
*
2743554 CTCCTTCTTC-TCTT
1 CTTCTTCTTCTTCTT
* *
2743568 CTTCTTCTCCTTCTC
1 CTTCTTCTTCTTCTT
* * *
2743583 CTTCTTCTCCCTCTC
1 CTTCTTCTTCTTCTT
*
2743598 CTTC-TCATTCTCCTT
1 CTTCTTC-TTCTTCTT
* *
2743613 CTTCTTCTTCTCCTC
1 CTTCTTCTTCTTCTT
*
2743628 CTTCTTCTCCTTCTT
1 CTTCTTCTTCTTCTT
* * *
2743643 CTTATCCTTCTCCTT
1 CTTCTTCTTCTTCTT
* *
2743658 CTGCTTCTTCTACTT
1 CTTCTTCTTCTTCTT
*
2743673 CTCCTTCTTCTTC-T
1 CTTCTTCTTCTTCTT
* *
2743687 CATCCTTCTTCTCCTT
1 C-TTCTTCTTCTTCTT
*
2743703 CTCCTTCTTCTTCTT
1 CTTCTTCTTCTTCTT
* * *
2743718 C-TCCTCATTATTCTC
1 CTTCTTC-TTCTTCTT
*
2743733 CTTC-TCATTCTTCTC
1 CTTCTTC-TTCTTCTT
2743748 CTTC-TCATTCTTCTT
1 CTTCTTC-TTCTTCTT
* **
2743763 CTGCTTCCCCTTCTT
1 CTTCTTCTTCTTCTT
* * *
2743778 CTCCTCCTTATTCTT
1 CTTCTTCTTCTTCTT
2743793 CTTCT
1 CTTCT
2743798 AAAAAATATT
Statistics
Matches: 231, Mismatches: 46, Indels: 24
0.77 0.15 0.08
Matches are distributed among these distances:
14 20 0.09
15 202 0.87
16 9 0.04
ACGTcount: A:0.03, C:0.40, G:0.01, T:0.56
Consensus pattern (15 bp):
CTTCTTCTTCTTCTT
Found at i:2743777 original size:33 final size:33
Alignment explanation
Indices: 2743494--2743797 Score: 233
Period size: 33 Copynumber: 9.2 Consensus size: 33
2743484 AAACAATCTA
* * * *
2743494 CTTCTTCTTCTTCTTCTTCTTCTTTTTCTCCTT
1 CTTCTTCTCCTTCTCCTTCTTCTTCTTCTCATT
* * * *
2743527 CTTCTTCTCATTCTTCTCCTT-TTCCTTCTCCTT
1 CTTCTTCTCCTTCTCCTTCTTCTT-CTTCTCATT
* * **
2743560 CTTCTCTTCTTCTTCTCCTTCTCCTTCTTCTCCCT
1 C-T-TCTTCTCCTTCTCCTTCTTCTTCTTCTCATT
* * * *
2743595 CTCCTTCTCATTCTCCTTCTTCTTCTTCTCCTC
1 CTTCTTCTCCTTCTCCTTCTTCTTCTTCTCATT
* * * * *
2743628 CTTCTTCTCCTTCTTCTTATCCTTCTCCTTC-TG
1 CTTCTTCTCCTTCTCCTTCTTCTTCTTC-TCATT
* *
2743661 CTTCTTCTACTTCT-C--CTTCTTCTTCTCATC
1 CTTCTTCTCCTTCTCCTTCTTCTTCTTCTCATT
*
2743691 CTTCTTCTCCTTCTCCTTCTTCTTCTTCTC-CT
1 CTTCTTCTCCTTCTCCTTCTTCTTCTTCTCATT
* * *
2743723 CATTATTCTCCTTCTCATTCTTCTCCTTCTCATT
1 C-TTCTTCTCCTTCTCCTTCTTCTTCTTCTCATT
* * * * *
2743757 CTTCTTCTGCTTCCCCTTCTTCTCCTCCTTATT
1 CTTCTTCTCCTTCTCCTTCTTCTTCTTCTCATT
2743790 CTTCTTCT
1 CTTCTTCT
2743798 AAAAAATATT
Statistics
Matches: 219, Mismatches: 41, Indels: 22
0.78 0.15 0.08
Matches are distributed among these distances:
29 2 0.01
30 21 0.10
31 1 0.00
32 4 0.02
33 160 0.73
34 6 0.03
35 23 0.11
36 2 0.01
ACGTcount: A:0.03, C:0.40, G:0.01, T:0.56
Consensus pattern (33 bp):
CTTCTTCTCCTTCTCCTTCTTCTTCTTCTCATT
Found at i:2744091 original size:12 final size:12
Alignment explanation
Indices: 2744070--2744104 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2744060 TCGGCTCAGG
2744070 TCGTGGTCGTGA
1 TCGTGGTCGTGA
*
2744082 TCGTGATCGTGA
1 TCGTGGTCGTGA
*
2744094 TGGTGGTCGTG
1 TCGTGGTCGTG
2744105 GTAATATGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.14, G:0.43, T:0.34
Consensus pattern (12 bp):
TCGTGGTCGTGA
Found at i:2756251 original size:31 final size:31
Alignment explanation
Indices: 2756216--2756277 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
2756206 TTTGGTGAAT
2756216 TTCAATATGTCATTCTCACTAGGAACTCCCA
1 TTCAATATGTCATTCTCACTAGGAACTCCCA
*
2756247 TTCAATATGTCCTTCTCACTAGGAACTCCCA
1 TTCAATATGTCATTCTCACTAGGAACTCCCA
2756278 AACTCTTGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.31, G:0.10, T:0.32
Consensus pattern (31 bp):
TTCAATATGTCATTCTCACTAGGAACTCCCA
Found at i:2757669 original size:14 final size:14
Alignment explanation
Indices: 2757652--2757681 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2757642 TACCATTGTT
2757652 CTCATATAGATCTC
1 CTCATATAGATCTC
*
2757666 CTCATCTAGATCTC
1 CTCATATAGATCTC
2757680 CT
1 CT
2757682 TTCAAAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.33, G:0.07, T:0.37
Consensus pattern (14 bp):
CTCATATAGATCTC
Found at i:2760098 original size:22 final size:22
Alignment explanation
Indices: 2760070--2760123 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
2760060 ACATCATTAT
2760070 TATGCATTATTATAATAAAACG
1 TATGCATTATTATAATAAAACG
2760092 TATGCATTATTATAATAAAACG
1 TATGCATTATTATAATAAAACG
2760114 TATGCATTAT
1 TATGCATTAT
2760124 GGAAATGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGCATTATTATAATAAAACG
Found at i:2762698 original size:3 final size:3
Alignment explanation
Indices: 2762690--2762723 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
2762680 GGCTCGGCTC
2762690 GTG GTG GTG GTG GT- GTG GTG GTG GTG GTG GTG GT
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GT
2762724 AATACGTGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
GTG
Found at i:2763836 original size:21 final size:21
Alignment explanation
Indices: 2763810--2763857 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
2763800 ATCAAAGACC
2763810 TCCAATGAGGAAGAAGCTTCT
1 TCCAATGAGGAAGAAGCTTCT
2763831 TCCAATGAGGAAGAAGCTTCT
1 TCCAATGAGGAAGAAGCTTCT
2763852 TCCAAT
1 TCCAAT
2763858 AGCAATTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (21 bp):
TCCAATGAGGAAGAAGCTTCT
Found at i:2773640 original size:18 final size:18
Alignment explanation
Indices: 2773612--2773767 Score: 86
Period size: 18 Copynumber: 8.3 Consensus size: 18
2773602 TAATATAAAA
2773612 TTATA-TATAAACTATAT
1 TTATATTATAAACTATAT
2773629 TTATATTATAAACTATA-
1 TTATATTATAAACTATAT
*
2773646 TAATTATTATAAACTATAT
1 TTA-TATTATAAACTATAT
* ** *
2773665 ATATAAATTAT-ATTTATGT
1 -T-TATATTATAAACTATAT
* *
2773684 GCACTATATATATAAAATATGTAT
1 ---TTATAT-TATAAACTA--TAT
* *
2773708 ATAAAATTATAAACTATAT
1 -TTATATTATAAACTATAT
2773727 TTATATTATAAACTATA-
1 TTATATTATAAACTATAT
*
2773744 TTATTATTATAAGCTATAT
1 TTA-TATTATAAACTATAT
*
2773763 ATATA
1 TTATA
2773768 AATTATGTTT
Statistics
Matches: 107, Mismatches: 19, Indels: 25
0.71 0.13 0.17
Matches are distributed among these distances:
17 10 0.09
18 55 0.51
19 10 0.09
20 10 0.09
21 13 0.12
22 7 0.07
24 2 0.02
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.46
Consensus pattern (18 bp):
TTATATTATAAACTATAT
Found at i:2773671 original size:13 final size:13
Alignment explanation
Indices: 2773598--2773802 Score: 57
Period size: 13 Copynumber: 15.3 Consensus size: 13
2773588 AAATATAATA
*
2773598 TATATAATATAAAA
1 TATAT-ATATAAAC
2773612 T-TATATATAAAC
1 TATATATATAAAC
* *
2773624 TATAT-T-TATAT
1 TATATATATAAAC
*
2773635 TATAAACTATATAA-
1 TATATA-TATA-AAC
2773649 T-TAT-TATAAAC
1 TATATATATAAAC
*
2773660 TATATATATAAAT
1 TATATATATAAAC
* **
2773673 TATATTTATGTGCAC
1 TATA--TATATAAAC
*
2773688 TATATATATAAAA
1 TATATATATAAAC
* *
2773701 TATGTATATAAAA
1 TATATATATAAAC
* *
2773714 T-TATAAACTATA-
1 TATATATA-TAAAC
*
2773726 TTTATATTATAAAC
1 TATATA-TATAAAC
2773740 TATATTATTATTATAAGC
1 TATA-TA-TA-TA-AA-C
*
2773758 TATATATATAAAT
1 TATATATATAAAC
* * *
2773771 TATGTTTATGTGAAC
1 TA--TATATATAAAC
*
2773786 TATATGTATAAAC
1 TATATATATAAAC
2773799 TATA
1 TATA
2773803 AAAAGTATAT
Statistics
Matches: 140, Mismatches: 31, Indels: 41
0.66 0.15 0.19
Matches are distributed among these distances:
10 2 0.01
11 12 0.09
12 17 0.12
13 60 0.43
14 10 0.07
15 26 0.19
16 4 0.03
17 4 0.03
18 5 0.04
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (13 bp):
TATATATATAAAC
Found at i:2773677 original size:49 final size:49
Alignment explanation
Indices: 2773605--2773779 Score: 173
Period size: 49 Copynumber: 3.6 Consensus size: 49
2773595 ATATATATAA
*
2773605 TATAAAAT-TATATATAAACTATATTTATATTATAAACTATATAATTAT
1 TATAAACTATATATATAAACTATATTTATATTATAAACTATATAATTAT
* * * * *
2773653 TATAAACTATATATATAAATTATATTTATGTGCACTATA-TATATAAAATAT
1 TATAAACTATATATATAAACTATATTTATAT-TA-TAAACTATAT-AATTAT
*
2773704 GTATATAA--A-AT-TATAAACTATATTTATATTATAAACTATATTATTAT
1 -TATA-AACTATATATATAAACTATATTTATATTATAAACTATATAATTAT
* * *
2773751 TATAAGCTATATATATAAATTATGTTTAT
1 TATAAACTATATATATAAACTATATTTAT
2773780 GTGAACTATA
Statistics
Matches: 101, Mismatches: 15, Indels: 21
0.74 0.11 0.15
Matches are distributed among these distances:
45 1 0.01
46 4 0.04
47 8 0.08
48 15 0.15
49 50 0.50
50 8 0.08
51 9 0.09
52 4 0.04
53 2 0.02
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.46
Consensus pattern (49 bp):
TATAAACTATATATATAAACTATATTTATATTATAAACTATATAATTAT
Found at i:2773729 original size:98 final size:98
Alignment explanation
Indices: 2773617--2773797 Score: 317
Period size: 98 Copynumber: 1.8 Consensus size: 98
2773607 TAAAATTATA
2773617 TATAAACTATATTTATATTATAAACTATATAATTATTATAAACTATATATATAAATTATATTTAT
1 TATAAACTATATTTATATTATAAACTATATAATTATTATAAACTATATATATAAATTATATTTAT
*
2773682 GTGCACTATATATATAAAATATGTATATAAAAT
66 GTGAACTATATATATAAAATATGTATATAAAAT
* * *
2773715 TATAAACTATATTTATATTATAAACTATATTATTATTATAAGCTATATATATAAATTATGTTTAT
1 TATAAACTATATTTATATTATAAACTATATAATTATTATAAACTATATATATAAATTATATTTAT
*
2773780 GTGAACTATATGTATAAA
66 GTGAACTATATATATAAA
2773798 CTATAAAAAG
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 78 1.00
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (98 bp):
TATAAACTATATTTATATTATAAACTATATAATTATTATAAACTATATATATAAATTATATTTAT
GTGAACTATATATATAAAATATGTATATAAAAT
Found at i:2773861 original size:57 final size:57
Alignment explanation
Indices: 2773799--2773909 Score: 168
Period size: 57 Copynumber: 1.9 Consensus size: 57
2773789 ATGTATAAAC
* * *
2773799 TATAAAAAGTATATAGTTTATAAACTATTATTTATATTAATATAGTATATATATATA
1 TATAAAAACTATATAATTTATAAACTATAATTTATATTAATATAGTATATATATATA
***
2773856 TATAAAAACTATATAATTTATATGTTATAATTTATATTAATATAGTATATATAT
1 TATAAAAACTATATAATTTATAAACTATAATTTATATTAATATAGTATATATAT
2773910 GTATGTATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (57 bp):
TATAAAAACTATATAATTTATAAACTATAATTTATATTAATATAGTATATATATATA
Found at i:2774226 original size:42 final size:42
Alignment explanation
Indices: 2774168--2774277 Score: 166
Period size: 42 Copynumber: 2.6 Consensus size: 42
2774158 ACAATAGTTA
* *
2774168 ATATATGTAACTTATAGCATGTGTATACATGCAATGTAAACT
1 ATATATGTAACTTATAGCATATGTATACATGCAATGTAAAAT
* *
2774210 ATATATGTAACTTATAGTATATGTATACATGTAATGTAAAAT
1 ATATATGTAACTTATAGCATATGTATACATGCAATGTAAAAT
* *
2774252 ATATATGTAACTTATAGTACATGTAT
1 ATATATGTAACTTATAGCATATGTAT
2774278 GTATAAACTA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (42 bp):
ATATATGTAACTTATAGCATATGTATACATGCAATGTAAAAT
Found at i:2774232 original size:16 final size:15
Alignment explanation
Indices: 2774211--2774276 Score: 52
Period size: 16 Copynumber: 4.5 Consensus size: 15
2774201 ATGTAAACTA
2774211 TATATGTAACTTATAG
1 TATATGTAAC-TATAG
2774227 TATATGTATAC-AT-G
1 TATATGTA-ACTATAG
*
2774241 TA-ATGTAA-AATA-
1 TATATGTAACTATAG
2774253 TATATGTAACTTATAG
1 TATATGTAAC-TATAG
*
2774269 TACATGTA
1 TATATGTA
2774277 TGTATAAACT
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
12 5 0.12
13 11 0.27
14 3 0.07
15 5 0.12
16 15 0.37
17 2 0.05
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (15 bp):
TATATGTAACTATAG
Found at i:2774236 original size:24 final size:23
Alignment explanation
Indices: 2774209--2774277 Score: 60
Period size: 24 Copynumber: 3.1 Consensus size: 23
2774199 CAATGTAAAC
2774209 TATATATGTAACTTATAGTATATG
1 TATATATGTAACTTATAGTA-ATG
*
2774233 TATACATGTAA-TGTA-A--AA--
1 TATATATGTAACT-TATAGTAATG
2774251 TATATATGTAACTTATAGTACATG
1 TATATATGTAACTTATAGTA-ATG
2774275 TAT
1 TAT
2774278 GTATAAACTA
Statistics
Matches: 35, Mismatches: 2, Indels: 16
0.66 0.04 0.30
Matches are distributed among these distances:
18 12 0.34
19 2 0.06
20 1 0.03
21 2 0.06
22 1 0.03
23 2 0.06
24 15 0.43
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.42
Consensus pattern (23 bp):
TATATATGTAACTTATAGTAATG
Found at i:2774305 original size:2 final size:2
Alignment explanation
Indices: 2774298--2774335 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
2774288 TGTATAGTAA
2774298 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
2774336 AAGTAAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2774423 original size:7 final size:7
Alignment explanation
Indices: 2774413--2774465 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
2774403 TATATAAAAA
2774413 AAACCCT
1 AAACCCT
**
2774420 AAACGTT
1 AAACCCT
*
2774427 AAACCCG
1 AAACCCT
* *
2774434 AGACCTT
1 AAACCCT
*
2774441 AAACTCT
1 AAACCCT
2774448 AAACCCT
1 AAACCCT
2774455 AAACCCT
1 AAACCCT
2774462 AAAC
1 AAAC
2774466 TTTAAATCTT
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.43, C:0.34, G:0.06, T:0.17
Consensus pattern (7 bp):
AAACCCT
Found at i:2774432 original size:14 final size:14
Alignment explanation
Indices: 2774413--2774488 Score: 73
Period size: 14 Copynumber: 5.5 Consensus size: 14
2774403 TATATAAAAA
*
2774413 AAACCCTAAACGTT
1 AAACCCTAAACCTT
* *
2774427 AAACCCGAGACCTT
1 AAACCCTAAACCTT
* *
2774441 AAACTCTAAACCCT
1 AAACCCTAAACCTT
*
2774455 AAACCCTAAACTTT
1 AAACCCTAAACCTT
* *
2774469 AAATCTTAAACCTT
1 AAACCCTAAACCTT
2774483 -AACCCT
1 AAACCCT
2774489 TTCCTATGTA
Statistics
Matches: 47, Mismatches: 15, Indels: 1
0.75 0.24 0.02
Matches are distributed among these distances:
13 4 0.09
14 43 0.91
ACGTcount: A:0.41, C:0.32, G:0.04, T:0.24
Consensus pattern (14 bp):
AAACCCTAAACCTT
Found at i:2774471 original size:21 final size:21
Alignment explanation
Indices: 2774413--2774480 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
2774403 TATATAAAAA
* *
2774413 AAACCCTAAACGTTAAACCCG
1 AAACCCTAAACTTTAAACCCT
* * *
2774434 AGACCTTAAACTCTAAACCCT
1 AAACCCTAAACTTTAAACCCT
* *
2774455 AAACCCTAAACTTTAAATCTT
1 AAACCCTAAACTTTAAACCCT
2774476 AAACC
1 AAACC
2774481 TTAACCCTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.43, C:0.31, G:0.04, T:0.22
Consensus pattern (21 bp):
AAACCCTAAACTTTAAACCCT
Found at i:2774523 original size:18 final size:18
Alignment explanation
Indices: 2774500--2774534 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2774490 TCCTATGTAA
2774500 TTTACATATGAACTATAG
1 TTTACATATGAACTATAG
*
2774518 TTTACATATTAACTATA
1 TTTACATATGAACTATA
2774535 TATATAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (18 bp):
TTTACATATGAACTATAG
Found at i:2774623 original size:2 final size:2
Alignment explanation
Indices: 2774608--2774894 Score: 124
Period size: 2 Copynumber: 146.0 Consensus size: 2
2774598 AAAACAAAAT
* *
2774608 TA TA -A TA TA T- TA TA TA TA -A TA TA -A GTT TA TA TA TA AA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA
* * * * *
2774648 TA TA TA TA AA CTA TG TA TA TA AA CTA TA TA TG TA TA AA CTA TA
1 TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA
* * * * *
2774691 AA AA GTA TA TA GTT TA TA -A AA TA TA -A TT 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
* * * *
2774733 TG TA TA TA TA TA TA TA TA TA TA AA CTA TA TA TG TA TA AA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA
* * * *
2774777 TA -A AA TA TA TA GTT TA TA AA T- TA TA -A TT TA TA T- TA -A TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
2774815 TA GTA TA TA TA -A T- TA TG TA TA -A CTA -A TA TA -A GTA -A TC
1 TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA
*
2774852 TA TA GA -A 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
2774893 TA
1 TA
2774895 GTTTATAGAA
Statistics
Matches: 213, Mismatches: 41, Indels: 62
0.67 0.13 0.20
Matches are distributed among these distances:
1 18 0.08
2 182 0.85
3 13 0.06
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:2774624 original size:7 final size:7
Alignment explanation
Indices: 2774608--2774894 Score: 55
Period size: 7 Copynumber: 39.6 Consensus size: 7
2774598 AAAACAAAAT
2774608 TATAATA
1 TATAATA
*
2774615 TATTATA
1 TATAATA
2774622 TATAATA
1 TATAATA
* *
2774629 TA-AGTT
1 TATAATA
2774635 TAT-ATA
1 TATAATA
2774641 TA-AACTA
1 TATAA-TA
2774648 TAT-ATA
1 TATAATA
2774654 TA-AACTA
1 TATAA-TA
*
2774661 TGT-ATA
1 TATAATA
2774667 TA-AACTA
1 TATAA-TA
*
2774674 TAT-ATG
1 TATAATA
2774680 TATAAACTA
1 TAT-AA-TA
*
2774689 TAAAAAGTA
1 T-ATAA-TA
* *
2774698 TATAGTT
1 TATAATA
*
2774705 TATAAAA
1 TATAATA
*
2774712 TATAATT
1 TATAATA
2774719 TATATATA
1 TATA-ATA
*
2774727 TATATATG
1 TATA-ATA
2774735 TATATATA
1 TATA-ATA
2774743 TATATATA
1 TATA-ATA
2774751 TATAA-A
1 TATAATA
*
2774757 CTATATATG
1 -TATA-ATA
2774766 TATAAACTA
1 TAT-AA-TA
2774775 TATAAAATA
1 TAT--AATA
* *
2774784 TATAGTT
1 TATAATA
2774791 TATAA-A
1 TATAATA
*
2774797 TTATAATT
1 -TATAATA
*
2774805 TATATTAA
1 TATAAT-A
*
2774813 TATAGTA
1 TATAATA
2774820 TAT-ATA
1 TATAATA
* *
2774826 -ATTATG
1 TATAATA
2774832 TATAACTAA
1 TATAA-T-A
2774841 TATAAGTA
1 TATAA-TA
*
2774849 -AT-CTA
1 TATAATA
*
2774854 TAGAATA
1 TATAATA
2774861 TAT-ATA
1 TATAATA
2774867 TATATATA
1 TATA-ATA
2774875 TATATATA
1 TATA-ATA
2774883 TATATATA
1 TATA-ATA
2774891 TATA
1 TATA
2774895 GTTTATAGAA
Statistics
Matches: 206, Mismatches: 42, Indels: 63
0.66 0.14 0.20
Matches are distributed among these distances:
5 4 0.02
6 33 0.16
7 76 0.37
8 66 0.32
9 23 0.11
10 4 0.02
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (7 bp):
TATAATA
Found at i:2774651 original size:13 final size:13
Alignment explanation
Indices: 2774635--2774778 Score: 92
Period size: 13 Copynumber: 11.3 Consensus size: 13
2774625 AATATAAGTT
2774635 TATATATAAACTA
1 TATATATAAACTA
2774648 TATATATAAACTA
1 TATATATAAACTA
*
2774661 TGTATATAAACTA
1 TATATATAAACTA
2774674 TATATGTATAAACTA
1 TATA--TATAAACTA
2774689 TA-A-A-AAGTA-TA
1 TATATATAA--ACTA
*
2774700 TAGTTTATAAA--A
1 TA-TATATAAACTA
**
2774712 TATA-ATTTA-TA
1 TATATATAAACTA
* *
2774723 TATATATATA-TG
1 TATATATAAACTA
*
2774735 TATATATATA-TA
1 TATATATAAACTA
2774747 TATATATAAACTA
1 TATATATAAACTA
2774760 TATATGTATAAACTA
1 TATA--TATAAACTA
2774775 TATA
1 TATA
2774779 AAATATATAG
Statistics
Matches: 108, Mismatches: 10, Indels: 24
0.76 0.07 0.17
Matches are distributed among these distances:
10 5 0.05
11 11 0.10
12 29 0.27
13 35 0.32
14 2 0.02
15 26 0.24
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:2774701 original size:71 final size:69
Alignment explanation
Indices: 2774626--2774761 Score: 175
Period size: 71 Copynumber: 1.9 Consensus size: 69
2774616 ATTATATATA
*
2774626 ATATAAGTTTAT-ATATAAACTATATATATAAACTATGTATATAAACTATATATGTATAAACTAT
1 ATAT-AGTTTATAATATAAACTATATATATAAA-TATGTATATAAA-TATATATATATAAACTAT
2774690 AAAAAGT
63 AAAAAGT
** * *
2774697 ATATAGTTTATAAAATATAATTTATATATATATATATGTATATATATATATATATATAAACTATA
1 ATATAGTTTAT--AATATAAACTATATATATAAATATGTATATAAATATATATATATAAACTATA
2774762 TATGTATAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
70 7 0.12
71 22 0.39
72 11 0.19
73 17 0.30
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (69 bp):
ATATAGTTTATAATATAAACTATATATATAAATATGTATATAAATATATATATATAAACTATAAA
AAGT
Found at i:2774992 original size:7 final size:7
Alignment explanation
Indices: 2774980--2775013 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
2774970 AACACCGAAC
2774980 CTTAAAT
1 CTTAAAT
*
2774987 CTTAAAC
1 CTTAAAT
2774994 CTTAAAT
1 CTTAAAT
2775001 CTTAAAT
1 CTTAAAT
2775008 CTTAAA
1 CTTAAA
2775014 CCCTAGACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (7 bp):
CTTAAAT
Found at i:2774994 original size:14 final size:14
Alignment explanation
Indices: 2774977--2775013 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2774967 CTAAACACCG
2774977 AACCTTAAATCTTA
1 AACCTTAAATCTTA
2774991 AACCTTAAATCTTA
1 AACCTTAAATCTTA
*
2775005 AATCTTAAA
1 AACCTTAAA
2775014 CCCTAGACAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (14 bp):
AACCTTAAATCTTA
Found at i:2775133 original size:55 final size:57
Alignment explanation
Indices: 2775074--2775209 Score: 188
Period size: 57 Copynumber: 2.4 Consensus size: 57
2775064 TGTATACATG
* *
2775074 TAAACTATATATGTAACTTATAGTATATGTATGTATA-AA-CTATTTATA-GCATATA
1 TAAACTATATATGTAACCTATAGTATATGTATATATACAATCTATTTATATG-ATATA
* * * *
2775129 TAAACTATATATATATCCTATAATATATGTATATATACAATCTATTTATATGTTATA
1 TAAACTATATATGTAACCTATAGTATATGTATATATACAATCTATTTATATGATATA
2775186 TAAACTATATATGTAACCTATAGT
1 TAAACTATATATGTAACCTATAGT
2775210 TTATAAGCAA
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
55 32 0.46
56 2 0.03
57 34 0.49
58 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.43
Consensus pattern (57 bp):
TAAACTATATATGTAACCTATAGTATATGTATATATACAATCTATTTATATGATATA
Found at i:2775173 original size:24 final size:21
Alignment explanation
Indices: 2775146--2775194 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 21
2775136 TATATATATC
2775146 CTATAATATATGTATATATACAA
1 CTATAATATATGT-TATATA-AA
*
2775169 TCTAT-TTATATGTTATATAAA
1 -CTATAATATATGTTATATAAA
2775190 CTATA
1 CTATA
2775195 TATGTAACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 2 0.09
22 6 0.26
23 7 0.30
24 4 0.17
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (21 bp):
CTATAATATATGTTATATAAA
Found at i:2775494 original size:22 final size:22
Alignment explanation
Indices: 2775460--2775508 Score: 62
Period size: 25 Copynumber: 2.1 Consensus size: 22
2775450 TATAAACTAT
*
2775460 ATTATATTAATATAAGTTATTATTA
1 ATTATAAT-ATATAA-TTATT-TTA
2775485 ATTATAATATATAATTATTTTA
1 ATTATAATATATAATTATTTTA
2775507 AT
1 AT
2775509 ATTAATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 5 0.22
23 5 0.22
24 6 0.26
25 7 0.30
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
ATTATAATATATAATTATTTTA
Found at i:2775496 original size:30 final size:28
Alignment explanation
Indices: 2775448--2775519 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
2775438 TTAATTACAA
* * *
2775448 ATTATAAACTATATTATATTAATATAAGTT
1 ATTATTAATTATAATATA-TAAT-TAAGTT
**
2775478 ATTATTAATTATAATATATAATTATTTT
1 ATTATTAATTATAATATATAATTAAGTT
*
2775506 AATATTAATTATAA
1 ATTATTAATTATAA
2775520 ATACCATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
28 17 0.47
29 4 0.11
30 15 0.42
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (28 bp):
ATTATTAATTATAATATATAATTAAGTT
Found at i:2775514 original size:22 final size:23
Alignment explanation
Indices: 2775459--2775519 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 23
2775449 TTATAAACTA
*
2775459 TATT-ATATTAATATA-AGTTAT
1 TATTAATATTAATATATAATTAT
2775480 TATTAAT-TATAATATATAATTAT
1 TATTAATAT-TAATATATAATTAT
2775503 T-TTAATATTAAT-TATAA
1 TATTAATATTAATATATAA
2775520 ATACCATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
21 10 0.29
22 18 0.51
23 7 0.20
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TATTAATATTAATATATAATTAT
Found at i:2777193 original size:3 final size:3
Alignment explanation
Indices: 2777185--2777225 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2777175 ACTTGAACCT
2777185 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2777226 GTTGTTGTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2777820 original size:20 final size:20
Alignment explanation
Indices: 2777786--2777830 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2777776 ATTCTATTTT
* **
2777786 ATATTGTTTGCTTCTGTTTG
1 ATATTGTGTGCTTCTACTTG
*
2777806 ATATTGTGTGTTTCTACTTG
1 ATATTGTGTGCTTCTACTTG
2777826 ATATT
1 ATATT
2777831 TGTAAGGGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.09, G:0.18, T:0.58
Consensus pattern (20 bp):
ATATTGTGTGCTTCTACTTG
Found at i:2777973 original size:23 final size:23
Alignment explanation
Indices: 2777923--2777976 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
2777913 TTTAATGCAG
* *
2777923 GATGCTTGCTGAATTGATGCAAT
1 GATGCTTGATGAATTGATACAAT
* * *
2777946 AATGCTTGATGAATTGGTACATT
1 GATGCTTGATGAATTGATACAAT
2777969 GATGCTTG
1 GATGCTTG
2777977 CCGGTTGCTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (23 bp):
GATGCTTGATGAATTGATACAAT
Found at i:2778663 original size:15 final size:15
Alignment explanation
Indices: 2778599--2778664 Score: 66
Period size: 15 Copynumber: 4.4 Consensus size: 15
2778589 AATATTCAAC
2778599 TATTATCAATTTAAT
1 TATTATCAATTTAAT
*
2778614 TATTAATCATGTTTAA-
1 TATT-ATCA-ATTTAAT
*
2778630 TATTAAC-A-TTAAGT
1 TATTATCAATTTAA-T
2778644 TATTATCAATTTAAT
1 TATTATCAATTTAAT
2778659 TATTAT
1 TATTAT
2778665 TTTATTGCCA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
12 4 0.10
14 6 0.15
15 14 0.34
16 12 0.29
17 5 0.12
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (15 bp):
TATTATCAATTTAAT
Found at i:2778773 original size:14 final size:14
Alignment explanation
Indices: 2778754--2778800 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
2778744 ATTTTTTCTT
2778754 TATATAAATTAAAC
1 TATATAAATTAAAC
2778768 TATAT-AATT----
1 TATATAAATTAAAC
2778777 TATATAAATTAAAC
1 TATATAAATTAAAC
*
2778791 TATATTAATT
1 TATATAAATT
2778801 TTCCTTTTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:2778778 original size:23 final size:24
Alignment explanation
Indices: 2778752--2778801 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
2778742 TTATTTTTTC
2778752 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
2778775 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
2778799 TTT
1 TTT
2778802 TCCTTTTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:2779102 original size:15 final size:16
Alignment explanation
Indices: 2779062--2779107 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
2779052 TATTTACATG
* *
2779062 TCAGGTTAAAAACAGG
1 TCAGGTTGAAAACAGA
*
2779078 TCAAGTTGAAAACA-A
1 TCAGGTTGAAAACAGA
2779093 TCAGGTTGAAAACAG
1 TCAGGTTGAAAACAG
2779108 GTCGGGTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.46, C:0.13, G:0.22, T:0.20
Consensus pattern (16 bp):
TCAGGTTGAAAACAGA
Found at i:2781931 original size:40 final size:42
Alignment explanation
Indices: 2781869--2781956 Score: 101
Period size: 40 Copynumber: 2.1 Consensus size: 42
2781859 TTTAAACATA
* *
2781869 TAGCGGCGTTTACATTCTAAACG-C-C-ACAAAATAGTAACTT
1 TAGCGGCGTTTACATACAAAACGCCGCGACAAAATAGT-ACTT
** *
2781909 TAGCGGCGTTTTTATACAAAACGCCGCGACAAAGTAGTACTT
1 TAGCGGCGTTTACATACAAAACGCCGCGACAAAATAGTACTT
2781951 TAGCGG
1 TAGCGG
2781957 TGAAAGTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
40 19 0.47
41 1 0.03
42 11 0.28
43 9 0.22
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (42 bp):
TAGCGGCGTTTACATACAAAACGCCGCGACAAAATAGTACTT
Found at i:2782079 original size:41 final size:41
Alignment explanation
Indices: 2781963--2782347 Score: 360
Period size: 41 Copynumber: 9.4 Consensus size: 41
2781953 GCGGTGAAAG
* * ***
2781963 TTTTATAAAAACGCCGCTATAGACTCATACGTTAGTGGCGT
1 TTTTATATAAACGCCGCTAAAGACTCATGTTTTAGTGGCGT
* * * *** *
2782004 TTTT-TTTAAACGCCGCTATAGAATCATACGTTAGTGGCAT
1 TTTTATATAAACGCCGCTAAAGACTCATGTTTTAGTGGCGT
* * *
2782044 TTTTATACAAACGTCTCTAAAGACTCATGTTTTAGTGGCGT
1 TTTTATATAAACGCCGCTAAAGACTCATGTTTTAGTGGCGT
* ** **
2782085 TTTTATATAAACGCCGCTAAAGACTCGTACTTTAGTGATGT
1 TTTTATATAAACGCCGCTAAAGACTCATGTTTTAGTGGCGT
* * *
2782126 TTTTATATAAACGCCGCTATAGACTCTTGTTTTAGTGGTGT
1 TTTTATATAAACGCCGCTAAAGACTCATGTTTTAGTGGCGT
* * * ** *
2782167 TTCTATATAAATGCCG-TAAAAGACTCGTACTTTAGCGGCGT
1 TTTTATATAAACGCCGCT-AAAGACTCATGTTTTAGTGGCGT
* * * *
2782208 TTTTATACAAACGCCGCTGAAGACTGATGTTTTAGTAGCGT
1 TTTTATATAAACGCCGCTAAAGACTCATGTTTTAGTGGCGT
* * *
2782249 TTTTATATAAACGCCGCTATAGACTCTTGTTTTAGTGGCATT
1 TTTTATATAAACGCCGCTAAAGACTCATGTTTTAGTGGC-GT
* * *
2782291 TTCTTATAAAAATGCCGCTAAAGACTCATGTTTCAGTGGCGT
1 TT-TTATATAAACGCCGCTAAAGACTCATGTTTTAGTGGCGT
**
2782333 TTTTATGCAAACGCC
1 TTTTATATAAACGCC
2782348 ACAAGTTTAC
Statistics
Matches: 278, Mismatches: 61, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
40 37 0.13
41 202 0.73
42 7 0.03
43 32 0.12
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (41 bp):
TTTTATATAAACGCCGCTAAAGACTCATGTTTTAGTGGCGT
Found at i:2783307 original size:41 final size:40
Alignment explanation
Indices: 2783223--2783307 Score: 118
Period size: 41 Copynumber: 2.1 Consensus size: 40
2783213 TAGATAAGGT
* * *
2783223 GGGGAAGTTCCTTTACGTTTGTGTCTTATTGCCCGCCGGG
1 GGGGAAGTTCCTTTACATTTGTGTCTTATTGCCCACCGCG
2783263 GGGGAGAGTTCCTTTACATTTGTGTCTTATTGCCACACC-CG
1 GGGGA-AGTTCCTTTACATTTGTGTCTTATTGCC-CACCGCG
2783304 GGGG
1 GGGG
2783308 GGTTGTGTGG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
40 5 0.12
41 32 0.80
42 3 0.08
ACGTcount: A:0.13, C:0.22, G:0.32, T:0.33
Consensus pattern (40 bp):
GGGGAAGTTCCTTTACATTTGTGTCTTATTGCCCACCGCG
Found at i:2786998 original size:42 final size:42
Alignment explanation
Indices: 2786937--2787214 Score: 314
Period size: 42 Copynumber: 6.7 Consensus size: 42
2786927 ATATAAACGT
* * *
2786937 CGCTATAGATCTCGACCTTTTGTGGCGTTTGTTCTAAAAATGC
1 CGCTATAGATAT-GACCTTTTGCGGCGTTTGTTCCAAAAATGC
* *
2786980 CGCTATATATATGACCTTTTGC-G-G--TGTTCCATAAATGC
1 CGCTATAGATATGACCTTTTGCGGCGTTTGTTCCAAAAATGC
* * *
2787018 CGCTATAGACATGACC-TTTGCGGCGTTTGTTCCAAAAACGT
1 CGCTATAGATATGACCTTTTGCGGCGTTTGTTCCAAAAATGC
* * * *
2787059 CGCTATAGTTATGACCTTTTACGGTGTTTATTCCAAAAATGC
1 CGCTATAGATATGACCTTTTGCGGCGTTTGTTCCAAAAATGC
* *
2787101 CGCTATAGATATGACCTTTTGTGGCGTTTGTTCCAAAAACGC
1 CGCTATAGATATGACCTTTTGCGGCGTTTGTTCCAAAAATGC
* * ** * *
2787143 CGTTATAGATCTCGATATTTTGCGGCGTTTATTCCAAAAATGA
1 CGCTATAGATAT-GACCTTTTGCGGCGTTTGTTCCAAAAATGC
*
2787186 CGCTATAGATATGACCTTCTGCGGCGTTT
1 CGCTATAGATATGACCTTTTGCGGCGTTT
2787215 CTGCGGCGTT
Statistics
Matches: 193, Mismatches: 36, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
37 5 0.03
38 27 0.14
39 1 0.01
40 1 0.01
41 26 0.13
42 89 0.46
43 44 0.23
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (42 bp):
CGCTATAGATATGACCTTTTGCGGCGTTTGTTCCAAAAATGC
Found at i:2787193 original size:85 final size:83
Alignment explanation
Indices: 2786937--2787214 Score: 330
Period size: 85 Copynumber: 3.3 Consensus size: 83
2786927 ATATAAACGT
* * * * *
2786937 CGCTATAGATCTCGACCTTTTGTGGCGTTTGTTCTAAAAATGCCGCTATATATATGACCTTTTGC
1 CGCTATAGATAT-GACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATATGACCTTTTGC
* *
2787002 -GG--TGTTCCATAAATGC
65 GGGTTTATTCCAAAAATGC
* * * *
2787018 CGCTATAGACATGACC-TTTGCGGCGTTTGTTCCAAAAACGTCGCTATAGTTATGACCTTTTACG
1 CGCTATAGATATGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATATGACCTTTTGCG
2787082 GTGTTTATTCCAAAAATGC
66 G-GTTTATTCCAAAAATGC
* * * **
2787101 CGCTATAGATATGACCTTTTGTGGCGTTTGTTCCAAAAACGCCGTTATAGATCTCGATATTTTGC
1 CGCTATAGATATGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATAT-GACCTTTTGC
*
2787166 GGCGTTTATTCCAAAAATGA
65 GG-GTTTATTCCAAAAATGC
*
2787186 CGCTATAGATATGACCTTCTGCGGCGTTT
1 CGCTATAGATATGACCTTTTGCGGCGTTT
2787215 CTGCGGCGTT
Statistics
Matches: 167, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
79 40 0.24
80 5 0.03
81 11 0.07
83 27 0.16
84 32 0.19
85 52 0.31
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (83 bp):
CGCTATAGATATGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATATGACCTTTTGCG
GGTTTATTCCAAAAATGC
Found at i:2787244 original size:54 final size:54
Alignment explanation
Indices: 2787163--2787269 Score: 146
Period size: 54 Copynumber: 2.0 Consensus size: 54
2787153 CTCGATATTT
*
2787163 TGCGGCGTTTATTCCAAAAATGACGCTATAG-A-TATGACCTTCTGCGGCGTTTC
1 TGCGGCGTTTATTCCAAAAATGACGCTATAGCACT-CGACCTTCTGCGGCGTTTC
* * *
2787216 TGCGGCGTTTGTATCCAAAAATGCCGCTATAGCACTCGACCTTTTGCGGCGTTT
1 TGCGGCGTTTAT-TCCAAAAATGACGCTATAGCACTCGACCTTCTGCGGCGTTT
2787270 TTCCTATCGC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
53 11 0.23
54 18 0.38
55 17 0.36
56 1 0.02
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (54 bp):
TGCGGCGTTTATTCCAAAAATGACGCTATAGCACTCGACCTTCTGCGGCGTTTC
Found at i:2788056 original size:93 final size:92
Alignment explanation
Indices: 2787843--2788162 Score: 365
Period size: 93 Copynumber: 3.4 Consensus size: 92
2787833 TCGTTTTATG
* * * *
2787843 TATATATAAAAGGGGGATAATTATTGTAATTATCAAACTCTATTAAAATATATTTATTTATCTGA
1 TATATTTAAAAGAGAGATAATTATTTTAATTATCAAACTCTATTAAAATATA--TATTTATCTGA
* * * *
2787908 TAAAATCGAATTTGAT-TTGAAATATATTTA
64 TAGAATCTAATCTG-TGTTGAAATA-GTTTA
* * * * *
2787938 TCTATTTAAGAGGGAGATAATTATTTTAATTAACAAACTCTATTAAAATATATATTTATCTTATA
1 TATATTTAAAAGAGAGATAATTATTTTAATTATCAAACTCTATTAAAATATATATTTATCTGATA
* *
2788003 GAACCTAATCTGTGTTGAAATACGTGTA
66 GAATCTAATCTGTGTTGAAATA-GTTTA
* * *
2788031 TATATTTAAAAGAGAGATAATTATTTTAATTATCAAACTCAATTAGAATATATATTTATATGATA
1 TATATTTAAAAGAGAGATAATTATTTTAATTATCAAACTCTATTAAAATATATATTTATCTGATA
* **
2788096 GAATTTAATCTAAGTTGAAATAGATTTA
66 GAATCTAATCTGTGTTGAAATAG-TTTA
*
2788124 TATATTTAAAA-AGAGATAATTATTTTTAATTATTAAACT
1 TATATTTAAAAGAGAGATAATTA-TTTTAATTATCAAACT
2788163 TTTTCAAATT
Statistics
Matches: 194, Mismatches: 28, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
92 13 0.07
93 135 0.70
95 46 0.24
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (92 bp):
TATATTTAAAAGAGAGATAATTATTTTAATTATCAAACTCTATTAAAATATATATTTATCTGATA
GAATCTAATCTGTGTTGAAATAGTTTA
Found at i:2789575 original size:2 final size:2
Alignment explanation
Indices: 2789568--2789598 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2789558 CTTACAAAAC
2789568 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2789599 CGCACATCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2790992 original size:3 final size:3
Alignment explanation
Indices: 2790979--2791030 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
2790969 TTATTAGCAT
* *
2790979 TAA TAA GAA TAA T-A TAT TAA TAA TAA TAA TAA TAA TAA TAA TCAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
2791024 T-A TAA TA
1 TAA TAA TA
2791031 TTTATTTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 35 0.83
4 3 0.07
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2790996 original size:23 final size:23
Alignment explanation
Indices: 2790970--2791015 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2790960 AATTGTAAAT
* *
2790970 TATTAGCATTAATAAGAATAATA
1 TATTAACAATAATAAGAATAATA
* *
2790993 TATTAATAATAATAATAATAATA
1 TATTAACAATAATAAGAATAATA
2791016 ATAATCAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (23 bp):
TATTAACAATAATAAGAATAATA
Found at i:2791275 original size:56 final size:56
Alignment explanation
Indices: 2791206--2791360 Score: 156
Period size: 56 Copynumber: 2.8 Consensus size: 56
2791196 AATCTTCAAG
* * * *
2791206 AAACATGTCCGCTCTCTATTCTTTTAGAGAGTATAGGACTCGAAAAAATCTTCTG-
1 AAACAGGTTCGCTCTCTATTCTTTCAGGGAGTATAGGACTCGAAAAAATCTTCTGC
* * *
2791261 AACACGGGTTCGCTCCCTATTGC-TTCAGGGAGTATA-GATCTCG-AAGAATCTTCTGC
1 AA-ACAGGTTCGCTCTCTATT-CTTTCAGGGAGTATAGGA-CTCGAAAAAATCTTCTGC
* * *
2791317 AAACAGGTTCACTCTCTCTTTCTTTCAGGGAGTATAGAACTCGA
1 AAACAGGTTCGCTCTCT-ATTCTTTCAGGGAGTATAGGACTCGA
2791361 GCATCTTCTT
Statistics
Matches: 80, Mismatches: 12, Indels: 14
0.75 0.11 0.13
Matches are distributed among these distances:
55 28 0.35
56 50 0.62
57 2 0.03
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (56 bp):
AAACAGGTTCGCTCTCTATTCTTTCAGGGAGTATAGGACTCGAAAAAATCTTCTGC
Found at i:2791424 original size:54 final size:54
Alignment explanation
Indices: 2791264--2791476 Score: 264
Period size: 54 Copynumber: 3.9 Consensus size: 54
2791254 TCTTCTGAAC
* * * * * * * *
2791264 ACGGGTTCGCTCCCTATTGCTTCAGGGAGTATAGATCTCGAAGAATCTTCTGCAA
1 ACGGGTTCACTCCCTCTTTCTTTAGGGAGTATAGAACTCGAA-CATCTTCTTCCA
* * * *
2791319 ACAGGTTCACTCTCTCTTTCTTTCAGGGAGTATAGAACTCGAGCATCTTCTTCCT
1 ACGGGTTCACTCCCTCTTTCTTT-AGGGAGTATAGAACTCGAACATCTTCTTCCA
* *
2791374 ACGGGTTCACTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCCC
1 ACGGGTTCACTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCCA
* *
2791428 ACGGGTTCGCCCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTC
1 ACGGGTTCACTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTC
2791477 AAACAATCGT
Statistics
Matches: 137, Mismatches: 20, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
54 74 0.54
55 46 0.34
56 17 0.12
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.32
Consensus pattern (54 bp):
ACGGGTTCACTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCCA
Found at i:2791572 original size:55 final size:55
Alignment explanation
Indices: 2791454--2791695 Score: 373
Period size: 55 Copynumber: 4.4 Consensus size: 55
2791444 TTTCTTTAGG
2791454 GAGTAT-AGAACTCGAAC-ATCTTCAAACAATCGTGCCTGCTCCCTATTCCTTCA-A
1 GAGTATAAG-ACTCGAACAATCTTC-AACAATCGTGCCTGCTCCCTATTCCTTCAGA
**
2791508 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTTTGCTCCCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGCCTGCTCCCTATTCCTTCAGA
* * * * *
2791563 GAGTGTAAGACTCGAACAATCTTCAACAATTGTGTCTGATCCTTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGCCTGCTCCCTATTCCTTCAGA
*
2791618 GAGTATAAGACTCGAACAATCTTCAACAATCGTGCCTGCTCCTTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGCCTGCTCCCTATTCCTTCAGA
2791673 GAGTATAAGACTCGAACAATCTT
1 GAGTATAAGACTCGAACAATCTT
2791696 GATGCTTTAA
Statistics
Matches: 174, Mismatches: 11, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
54 41 0.24
55 133 0.76
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (55 bp):
GAGTATAAGACTCGAACAATCTTCAACAATCGTGCCTGCTCCCTATTCCTTCAGA
Found at i:2792756 original size:21 final size:22
Alignment explanation
Indices: 2792730--2792778 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
2792720 CTGAACCCTC
*
2792730 CTTTTTG-CTTCATT-TTTTCT
1 CTTTTTGTATTCATTCTTTTCT
2792750 CATTTTTGTATTCATTCTTTTCT
1 C-TTTTTGTATTCATTCTTTTCT
2792773 CTTTTT
1 CTTTTT
2792779 CTCTTTTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 1 0.04
21 6 0.24
22 11 0.44
23 7 0.28
ACGTcount: A:0.08, C:0.18, G:0.04, T:0.69
Consensus pattern (22 bp):
CTTTTTGTATTCATTCTTTTCT
Found at i:2797464 original size:96 final size:96
Alignment explanation
Indices: 2797297--2797489 Score: 307
Period size: 96 Copynumber: 2.0 Consensus size: 96
2797287 CATTCTTACA
* * * *
2797297 TCCAATGTGAAGTGGTCTTCATGTCTTTATGAAGGGCTTTATCGTCCTTGGTATGACTGTATCTA
1 TCCAATGCGAAGCGATCTTCATGTCTCTATGAAGGGCTTTATCGTCCTTGGTATGACTGTATCTA
*
2797362 TCTCTTGAGTCAACATCTTGGCCTTTGCACC
66 TATCTTGAGTCAACATCTTGGCCTTTGCACC
*
2797393 TCCAATGCGAAGCGATCTTCATGTCTCTATGAAGGG-TCTTCTCGTCCTTGGTATGACTGTATCT
1 TCCAATGCGAAGCGATCTTCATGTCTCTATGAAGGGCT-TTATCGTCCTTGGTATGACTGTATCT
*
2797457 ATATCTTGAGTCAACATCTTGGCCTTTTCACC
65 ATATCTTGAGTCAACATCTTGGCCTTTGCACC
2797489 T
1 T
2797490 TTAAAGGAAT
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
95 1 0.01
96 88 0.99
ACGTcount: A:0.19, C:0.23, G:0.20, T:0.38
Consensus pattern (96 bp):
TCCAATGCGAAGCGATCTTCATGTCTCTATGAAGGGCTTTATCGTCCTTGGTATGACTGTATCTA
TATCTTGAGTCAACATCTTGGCCTTTGCACC
Found at i:2799612 original size:26 final size:26
Alignment explanation
Indices: 2799578--2799639 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
2799568 TGCACATACC
*
2799578 ATGCTTCGATGCACTCAGCGCATTTG
1 ATGCATCGATGCACTCAGCGCATTTG
*
2799604 ATGCATCGATGCACTCAGTGCATTTG
1 ATGCATCGATGCACTCAGCGCATTTG
2799630 ATGCATCGAT
1 ATGCATCGAT
2799640 CCACAAACCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.31
Consensus pattern (26 bp):
ATGCATCGATGCACTCAGCGCATTTG
Found at i:2803244 original size:30 final size:30
Alignment explanation
Indices: 2803208--2803270 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
2803198 ACATTAGCTA
2803208 TTTTCATCCTTTTGGATGTAAATGTTTTGT
1 TTTTCATCCTTTTGGATGTAAATGTTTTGT
2803238 TTTTCATCCTTTTGGATGTAAATGTTTTGT
1 TTTTCATCCTTTTGGATGTAAATGTTTTGT
2803268 TTT
1 TTT
2803271 AAACAACGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.16, C:0.10, G:0.16, T:0.59
Consensus pattern (30 bp):
TTTTCATCCTTTTGGATGTAAATGTTTTGT
Found at i:2806037 original size:14 final size:13
Alignment explanation
Indices: 2806004--2806041 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
2805994 ATCGAAAATC
2806004 TAAATTTAATTTT
1 TAAATTTAATTTT
2806017 TAAATTTAATGTTT
1 TAAATTTAAT-TTT
*
2806031 TAGATTTAATT
1 TAAATTTAATT
2806042 ATGTTGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (13 bp):
TAAATTTAATTTT
Found at i:2807691 original size:2 final size:2
Alignment explanation
Indices: 2807684--2807710 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2807674 TAGCAGCTTA
2807684 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2807711 ATCAATTGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2808254 original size:19 final size:19
Alignment explanation
Indices: 2808230--2808281 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
2808220 AATGCATTTT
*
2808230 ATGCATCGATGCACATACC
1 ATGCATCGATGCACAAACC
2808249 ATGCATCGATGCACAAACC
1 ATGCATCGATGCACAAACC
2808268 ATGCATCGATGCAC
1 ATGCATCGATGCAC
2808282 TCTGGCTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.33, C:0.31, G:0.17, T:0.19
Consensus pattern (19 bp):
ATGCATCGATGCACAAACC
Found at i:2808305 original size:83 final size:84
Alignment explanation
Indices: 2808165--2808318 Score: 206
Period size: 83 Copynumber: 1.8 Consensus size: 84
2808155 TTTCAAAGTG
* * *
2808165 ATGCACCGATGCACCAATCCATGCAACGATGCACCATGGATTAAATTGAACATCGAATGCATTTT
1 ATGCACCGATGCACCAAACCATGCAACGATGCACCATGGACTAAATTGAACATCGAATACATTTT
2808230 ATGCATCGATGCACATACC
66 ATGCATCGATGCACATACC
* * **
2808249 ATGCATCGATGCA-CAAACCATGCATCGATGCACTC-TGG-CTATTTTGAAACATCGAATACATT
1 ATGCACCGATGCACCAAACCATGCAACGATGCAC-CATGGACTAAATTG-AACATCGAATACATT
2808311 TTATGCAT
64 TTATGCAT
2808319 TGATACACTC
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
82 5 0.08
83 43 0.70
84 13 0.21
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (84 bp):
ATGCACCGATGCACCAAACCATGCAACGATGCACCATGGACTAAATTGAACATCGAATACATTTT
ATGCATCGATGCACATACC
Found at i:2810668 original size:3 final size:3
Alignment explanation
Indices: 2810645--2810702 Score: 66
Period size: 3 Copynumber: 19.7 Consensus size: 3
2810635 TTATTCGTAT
* * *
2810645 TAA TAA GAA TAA T-A TAT TAA TAA TAA TAA TCA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2810692 TCAA T-A TAA TA
1 T-AA TAA TAA TA
2810703 TATATTTTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
2 4 0.09
3 39 0.85
4 3 0.07
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2814097 original size:64 final size:64
Alignment explanation
Indices: 2814026--2814184 Score: 207
Period size: 65 Copynumber: 2.5 Consensus size: 64
2814016 GAATAAATTG
* *
2814026 AACATCG-ATGCATTTTATGCATCGATGCACATA-CCATGCATCGATGCACTCAGG-TTTTTATG
1 AACATCGAATGCATTTTATGCATCGATGCACA-AGACATGCATCGATGCACTCAGGATGTTT-TG
2814088 AA
64 -A
* **
2814090 AACATCGAATGTATTTTATGCATCGACACACAAGACATGCATCGATGCACTCAGGATGTTTTGA
1 AACATCGAATGCATTTTATGCATCGATGCACAAGACATGCATCGATGCACTCAGGATGTTTTGA
* *
2814154 AACATCGAATGCACTTCATGCATCGATGCAC
1 AACATCGAATGCATTTTATGCATCGATGCAC
2814185 TCTTAGTGCA
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
64 35 0.43
65 43 0.52
66 4 0.05
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTTATGCATCGATGCACAAGACATGCATCGATGCACTCAGGATGTTTTGA
Found at i:2814200 original size:64 final size:64
Alignment explanation
Indices: 2814026--2814200 Score: 173
Period size: 64 Copynumber: 2.7 Consensus size: 64
2814016 GAATAAATTG
* *
2814026 AACATCG-ATGCATTTTATGCATCGATGCACATACCA-TGCATCGATGCACTCAGGTTTTTATGA
1 AACATCGAATGCATTTTATGCATCGATGCAC-T-CAAGTGCATCGATGCACTCAGGTGTTTATGA
2814089 A
64 A
* *
2814090 AACATCGAATGTATTTTATGCATCGA--CACACAAGACATGCATCGATGCACTCAGGATGTTT-T
1 AACATCGAATGCATTTTATGCATCGATGCACTCAAG---TGCATCGATGCACTCAGG-TGTTTAT
2814152 G-A
62 GAA
* * * *
2814154 AACATCGAATGCACTTCATGCATCGATGCACTCTTAGTGCACCGATG
1 AACATCGAATGCATTTTATGCATCGATGCACTC-AAGTGCATCGATG
2814201 TACTAAGCGT
Statistics
Matches: 92, Mismatches: 10, Indels: 18
0.77 0.08 0.15
Matches are distributed among these distances:
61 2 0.02
63 3 0.03
64 40 0.43
65 37 0.40
66 8 0.09
67 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTTATGCATCGATGCACTCAAGTGCATCGATGCACTCAGGTGTTTATGAA
Found at i:2814428 original size:17 final size:18
Alignment explanation
Indices: 2814406--2814443 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2814396 TTGATAACAA
2814406 CAAGAAATAACA-AGAAT
1 CAAGAAATAACATAGAAT
* *
2814423 CAAGAATTAAGATAGAAT
1 CAAGAAATAACATAGAAT
2814441 CAA
1 CAA
2814444 AGAGAAAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.61, C:0.11, G:0.13, T:0.16
Consensus pattern (18 bp):
CAAGAAATAACATAGAAT
Found at i:2820222 original size:12 final size:12
Alignment explanation
Indices: 2820205--2820229 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2820195 AAGAGTTGAT
2820205 AAGTTGAATTTG
1 AAGTTGAATTTG
2820217 AAGTTGAATTTG
1 AAGTTGAATTTG
2820229 A
1 A
2820230 TTTGTCATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (12 bp):
AAGTTGAATTTG
Found at i:2823443 original size:23 final size:22
Alignment explanation
Indices: 2823372--2823453 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 22
2823362 ACACTGAACA
*
2823372 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCA--CCATTGAAT
* * *
2823396 GTGCATCGATACACCA-TAAAG
1 GTGCATCGATGCACCATTGAAT
*
2823417 GTGCACCGATGCACTCATTGAAT
1 GTGCATCGATGCAC-CATTGAAT
2823440 GTGCATCGATGCAC
1 GTGCATCGATGCAC
2823454 AAGGCCATGC
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
21 15 0.32
22 4 0.09
23 16 0.34
24 12 0.26
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACCATTGAAT
Found at i:2823859 original size:21 final size:21
Alignment explanation
Indices: 2823835--2823882 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
2823825 AAAAACAAAC
2823835 AATTTTTCAACATTGTCTTTG
1 AATTTTTCAACATTGTCTTTG
2823856 AATTTTTCAACATTGTCTTTG
1 AATTTTTCAACATTGTCTTTG
2823877 AATTTT
1 AATTTT
2823883 CGAAATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.54
Consensus pattern (21 bp):
AATTTTTCAACATTGTCTTTG
Found at i:2825812 original size:17 final size:17
Alignment explanation
Indices: 2825790--2825828 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
2825780 ATTTAACAAA
2825790 AAGGGGGAGAATATAGT
1 AAGGGGGAGAATATAGT
2825807 AAGGGGGAGAATATAGT
1 AAGGGGGAGAATATAGT
2825824 AAGGG
1 AAGGG
2825829 AAGTAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.44, T:0.15
Consensus pattern (17 bp):
AAGGGGGAGAATATAGT
Found at i:2826330 original size:45 final size:46
Alignment explanation
Indices: 2826218--2826341 Score: 180
Period size: 46 Copynumber: 2.7 Consensus size: 46
2826208 GAATAAATTG
* *
2826218 AACATCGAATGCATTTTATACATCGATGCACTCAGGTTTTTATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACTCAGGTATTTATGAA
2826264 AACATCGAATGCATTTTATGCATCGATGCACTCAGGCTATTT-TG-A
1 AACATCGAATGCATTTTATGCATCGATGCACTCAGG-TATTTATGAA
* * *
2826309 AACATCGAATGCACTTCATGCATCGGTGCACTC
1 AACATCGAATGCATTTTATGCATCGATGCACTC
2826342 TTAGTGCACC
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
45 31 0.43
46 37 0.51
47 4 0.06
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (46 bp):
AACATCGAATGCATTTTATGCATCGATGCACTCAGGTATTTATGAA
Found at i:2829782 original size:2 final size:2
Alignment explanation
Indices: 2829777--2829832 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
2829767 TCATTACTGC
2829777 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
2829819 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
2829833 TAGGATAAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2839075 original size:130 final size:130
Alignment explanation
Indices: 2838934--2839181 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
2838924 TATTTATATA
*
2838934 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * *
2838999 TTAGCACATGATCATGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
2839064 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * *
2839129 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
2839182 GAAGAAAATT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:2839212 original size:130 final size:129
Alignment explanation
Indices: 2838948--2839212 Score: 309
Period size: 130 Copynumber: 2.0 Consensus size: 129
2838938 ATTTGGTCCT
* *
2838948 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * *** * * **** *
2839013 TGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
2839078 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
2839143 TGATATGTGTTATTGGTGACACATGTCACCTCCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
2839207 -A
128 CA
2839208 AAATT
1 AAATT
2839213 TGGGTCTTGG
Statistics
Matches: 113, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
130 100 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.35
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:2839670 original size:16 final size:18
Alignment explanation
Indices: 2839649--2839682 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
2839639 ATTTCTTATT
2839649 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
2839665 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
2839683 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:2839828 original size:21 final size:21
Alignment explanation
Indices: 2839804--2839846 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2839794 TATTACCTTA
2839804 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
2839825 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
2839846 A
1 A
2839847 TGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:2839864 original size:35 final size:35
Alignment explanation
Indices: 2839815--2839900 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 35
2839805 ATTGAAGTAT
** * * *
2839815 TTTAGAATTTAATTGAAGTATTTTAGAATTTATGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
2839850 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
2839885 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
2839901 TGACTGTTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.37, C:0.01, G:0.20, T:0.42
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:2840430 original size:12 final size:13
Alignment explanation
Indices: 2840413--2840442 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
2840403 TATATACCAC
2840413 ATATGAAAAAAA-
1 ATATGAAAAAAAT
2840425 ATATGAAAAAAAT
1 ATATGAAAAAAAT
2840438 ATATG
1 ATATG
2840443 TATTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (13 bp):
ATATGAAAAAAAT
Found at i:2848809 original size:21 final size:21
Alignment explanation
Indices: 2848785--2848841 Score: 51
Period size: 23 Copynumber: 2.6 Consensus size: 21
2848775 CCCTTGAATA
2848785 TGCATCGATACACCATGAAGG
1 TGCATCGATACACCATGAAGG
* * * *
2848806 TGCACCGATGCATTCCTTGAATG
1 TGCATCGATACA--CCATGAAGG
*
2848829 TGCATCAATACAC
1 TGCATCGATACAC
2848842 TCTGCTGTGT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
21 11 0.41
23 16 0.59
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (21 bp):
TGCATCGATACACCATGAAGG
Found at i:2848824 original size:44 final size:43
Alignment explanation
Indices: 2848741--2848841 Score: 132
Period size: 44 Copynumber: 2.3 Consensus size: 43
2848731 TTTGTGCATA
* *
2848741 ATGCATCGATACACTAGAGAGTGTACCGATGCATCCCTTGAAT
1 ATGCATCGATACACCAGAGAGTGCACCGATGCATCCCTTGAAT
*
2848784 ATGCATCGATACACCATGA-AGGTGCACCGATGCATTCCTTGAAT
1 ATGCATCGATACACCA-GAGA-GTGCACCGATGCATCCCTTGAAT
* *
2848828 GTGCATCAATACAC
1 ATGCATCGATACAC
2848842 TCTGCTGTGT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
43 16 0.31
44 35 0.69
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (43 bp):
ATGCATCGATACACCAGAGAGTGCACCGATGCATCCCTTGAAT
Found at i:2848831 original size:23 final size:22
Alignment explanation
Indices: 2848765--2848832 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
2848755 TAGAGAGTGT
*
2848765 ACCGATGCATCCCTTGAATATGC
1 ACCGATGCAT-CCTTGAATGTGC
* * * *
2848788 ATCGATACA-CCATGAAGGTGC
1 ACCGATGCATCCTTGAATGTGC
2848809 ACCGATGCATTCCTTGAATGTGC
1 ACCGATGCA-TCCTTGAATGTGC
2848832 A
1 A
2848833 TCAATACACT
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
21 16 0.47
23 18 0.53
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (22 bp):
ACCGATGCATCCTTGAATGTGC
Found at i:2850821 original size:45 final size:45
Alignment explanation
Indices: 2850771--2850926 Score: 215
Period size: 45 Copynumber: 3.5 Consensus size: 45
2850761 TTGATGTTTT
*
2850771 TGGATTGTTTTGGATGATTGAATTTGTTATGTTGGTTGTTTAAAC
1 TGGATTGTTTTGGATGACTGAATTTGTTATGTTGGTTGTTTAAAC
**
2850816 TGGATT-TTTTTTATGACTGAATTTGTTATGTTGGTTGTTTAAAC
1 TGGATTGTTTTGGATGACTGAATTTGTTATGTTGGTTGTTTAAAC
* ** *
2850860 TGGATTTTTTTTTATGACTGAATTTTTTATGTTGGTTGTTTAAAC
1 TGGATTGTTTTGGATGACTGAATTTGTTATGTTGGTTGTTTAAAC
* * *
2850905 TTGAATGTTTTGGATGATTGAA
1 TGGATTGTTTTGGATGACTGAA
2850927 CTTAATATAT
Statistics
Matches: 100, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
44 41 0.41
45 59 0.59
ACGTcount: A:0.21, C:0.03, G:0.22, T:0.53
Consensus pattern (45 bp):
TGGATTGTTTTGGATGACTGAATTTGTTATGTTGGTTGTTTAAAC
Found at i:2850838 original size:44 final size:45
Alignment explanation
Indices: 2850784--2850905 Score: 219
Period size: 45 Copynumber: 2.7 Consensus size: 45
2850774 ATTGTTTTGG
*
2850784 ATGATTGAATTTGTTATGTTGGTTGTTTAAACTGGA-TTTTTTTT
1 ATGACTGAATTTGTTATGTTGGTTGTTTAAACTGGATTTTTTTTT
2850828 ATGACTGAATTTGTTATGTTGGTTGTTTAAACTGGATTTTTTTTT
1 ATGACTGAATTTGTTATGTTGGTTGTTTAAACTGGATTTTTTTTT
*
2850873 ATGACTGAATTTTTTATGTTGGTTGTTTAAACT
1 ATGACTGAATTTGTTATGTTGGTTGTTTAAACT
2850906 TGAATGTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
44 35 0.47
45 40 0.53
ACGTcount: A:0.21, C:0.04, G:0.20, T:0.55
Consensus pattern (45 bp):
ATGACTGAATTTGTTATGTTGGTTGTTTAAACTGGATTTTTTTTT
Found at i:2850938 original size:2 final size:2
Alignment explanation
Indices: 2850931--2850972 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2850921 ATTGAACTTA
2850931 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
2850973 TTGGTTTGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2855646 original size:25 final size:23
Alignment explanation
Indices: 2855617--2855677 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 23
2855607 AATGTTAAAC
* *
2855617 ATTTTAGGTAGCGTCCAATATTAAT
1 ATTTTAGGTAGCGT--AAAAGTAAT
* *
2855642 ATTTTCGGTAGAG-AAAAGTAAT
1 ATTTTAGGTAGCGTAAAAGTAAT
2855664 ATTTTAGGTAGCGT
1 ATTTTAGGTAGCGT
2855678 TTTACCGGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
22 18 0.62
25 11 0.38
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (23 bp):
ATTTTAGGTAGCGTAAAAGTAAT
Found at i:2857037 original size:17 final size:16
Alignment explanation
Indices: 2857011--2857045 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
2857001 ATTAATAGTA
2857011 TATTAAATAATAATTTT
1 TATTAAATAAT-ATTTT
*
2857028 TATTATATAATATTTT
1 TATTAAATAATATTTT
2857044 TA
1 TA
2857046 CAAATATCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTAAATAATATTTT
Done.