Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009639.1 Hibiscus syriacus cultivar Beakdansim tig00117048_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: 15077257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 62
Found at i:5888435 original size:29 final size:29
Alignment explanation
Indices: 5888385--5888483 Score: 119
Period size: 29 Copynumber: 3.3 Consensus size: 29
5888375 GAAAAGATAG
*
5888385 AGAGAAAAATAGAAAGGAAAAAAAAGAAAAAT
1 AGAGAAAAATAG-AA--AAAAAAAAGAAAAAA
*
5888417 AGAGAAAAATAGAAAAAAAATAGAAAAAA
1 AGAGAAAAATAGAAAAAAAAAAGAAAAAA
* *
5888446 ATAGAAAAA-AGAGAAAAAAAGAGAAAAAA
1 AGAGAAAAATAGA-AAAAAAAAAGAAAAAA
5888475 AGAGAAAAA
1 AGAGAAAAA
5888484 GGAAAAGAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.05
29 44 0.72
31 2 0.03
32 12 0.20
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (29 bp):
AGAGAAAAATAGAAAAAAAAAAGAAAAAA
Found at i:5888494 original size:10 final size:9
Alignment explanation
Indices: 5888397--5888494 Score: 65
Period size: 10 Copynumber: 10.4 Consensus size: 9
5888387 AGAAAAATAG
5888397 AAAGGAAAA
1 AAAGGAAAA
*
5888406 AAAAGAAAA
1 AAAGGAAAA
*
5888415 ATAGAGAAAA
1 AAAG-GAAAA
* *
5888425 ATAGAAAAA
1 AAAGGAAAA
*
5888434 AAATAGAAAA
1 AAA-GGAAAA
*
5888444 AAA-TAGAAA
1 AAAGGA-AAA
5888453 AAAGAGAAAA
1 AAAG-GAAAA
5888463 AAAGAGAAAA
1 AAAG-GAAAA
*
5888473 AAA-GAGAA
1 AAAGGAAAA
5888481 AAAGGAAAA
1 AAAGGAAAA
5888490 GAAAG
1 -AAAG
5888495 AAATAAGAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 13
0.75 0.12 0.14
Matches are distributed among these distances:
8 8 0.11
9 26 0.37
10 36 0.51
11 1 0.01
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (9 bp):
AAAGGAAAA
Found at i:5888504 original size:16 final size:17
Alignment explanation
Indices: 5888374--5888508 Score: 55
Period size: 18 Copynumber: 7.6 Consensus size: 17
5888364 AAAAAGAGAT
5888374 AGAAAAGATAGAGAGAAAA
1 AGAAAAGA-A-AGAGAAAA
* *
5888393 ATAGAAAGGAA-A-AAAA
1 AGA-AAAGAAAGAGAAAA
*
5888409 AGAAAA-ATAGAGAAAAA
1 AGAAAAGAAAGAG-AAAA
* *
5888426 TAGAAAAAAAATAGAAAA
1 -AGAAAAGAAAGAGAAAA
* *
5888444 AAATAGAAAAAAGAGAAAAAA
1 AGA-A-AAGAAAGAG--AAAA
*
5888465 AGAGAAAAAAAGAGAAAA
1 AGA-AAAGAAAGAGAAAA
*
5888483 AGGAAAAGAAAGA-AATA
1 A-GAAAAGAAAGAGAAAA
5888500 AG-AAAGAAA
1 AGAAAAGAAA
5888509 ACCGATCAAA
Statistics
Matches: 92, Mismatches: 13, Indels: 26
0.70 0.10 0.20
Matches are distributed among these distances:
14 1 0.01
15 11 0.12
16 7 0.08
17 11 0.12
18 25 0.27
19 17 0.18
20 13 0.14
21 7 0.08
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (17 bp):
AGAAAAGAAAGAGAAAA
Found at i:5888505 original size:29 final size:26
Alignment explanation
Indices: 5888397--5888509 Score: 111
Period size: 28 Copynumber: 4.0 Consensus size: 26
5888387 AGAAAAATAG
*
5888397 AAAGGAAAAAAAAGAAAAATAGAGAAA
1 AAAGGAAAAAAAAGAAAAA-AAAGAAA
*
5888424 AATAGAAAAAAAATAGAAAAAAATAGAAA
1 AA-AGGAAAAAAA-AGAAAAAAA-AGAAA
5888453 AAA-GAGAAAAAAAGAGAAAAAAAGAGAA
1 AAAGGA-AAAAAAAGA-AAAAAAAGA-AA
*
5888481 AAAGGAAAAGAAAGAAATAAGAAAGAAA
1 AAAGGAAAAAAAAGAAA-AA-AAAGAAA
5888509 A
1 A
5888510 CCGATCAAAT
Statistics
Matches: 73, Mismatches: 4, Indels: 17
0.78 0.04 0.18
Matches are distributed among these distances:
27 11 0.15
28 41 0.56
29 21 0.29
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (26 bp):
AAAGGAAAAAAAAGAAAAAAAAGAAA
Found at i:5890514 original size:55 final size:55
Alignment explanation
Indices: 5890462--5890985 Score: 454
Period size: 55 Copynumber: 9.8 Consensus size: 55
5890452 CAATTTTTTT
* * * * *
5890462 AGAAACTAAGTATGATTTTCATAAGTTTGTTGACGATTTTGAAATGAGTTTTTAAA
1 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGTTTTT-AA
* ** * * *
5890518 AGAAACTAAGTCTGATTTATAGAAGTTTCTTGATTATTTTTAAATGAGCTTTCAA
1 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGTTTTTAA
* *
5890573 AGAAACTAAGTCTGATTTTTAGAAGTTTCCTGATGATTTT-AAATGAGTTTTTAA
1 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGTTTTTAA
*
5890627 AGAAACTAAGTCTGATTTTTAGAAGTTTCTCGACGATTTTCAAATGAG-TTTTAA
1 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGTTTTTAA
** * * *
5890681 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGATTATTTTTAAATGAGCTTTCAA
1 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGTTTTTAA
* * *
5890736 AGAGACTAAGTCTGATTTTCAAAAGTTTCTTGACGATTTTCAAATGAG-TTTT--
1 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGTTTTTAA
* * * ** *
5890788 ----A--AAGTCTGATTTTTAGAAGTTTCTTGATGATTTTTAAATAAACTTTCAA
1 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGTTTTTAA
* * ** * * *
5890837 AGAAATTAAGCCT-ACTTTTTAGGGGTTTCTTGATG-TTTTCAAATGA-ATTTGAA
1 AGAAACTAAGTCTGA-TTTTTAGAAGTTTCTTGACGATTTTCAAATGAGTTTTTAA
* * * * ** * * *
5890890 AGAATCTAAGCCTAATTTTCAGGGGTTTCTTGATG-TTTTCAAATGA-ATTTGAA
1 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGTTTTTAA
* * * * *
5890943 ATAAGCTAAGCCT-ATTTTTTAGGAGTTTCTTGATG-TTTTCAAA
1 AGAAACTAAGTCTGA-TTTTTAGAAGTTTCTTGACGATTTTCAAA
5890986 CCAATTTTCA
Statistics
Matches: 403, Mismatches: 51, Indels: 31
0.83 0.11 0.06
Matches are distributed among these distances:
46 35 0.09
47 3 0.01
48 1 0.00
52 1 0.00
53 91 0.23
54 113 0.28
55 116 0.29
56 43 0.11
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.42
Consensus pattern (55 bp):
AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGTTTTTAA
Found at i:5890637 original size:54 final size:54
Alignment explanation
Indices: 5890462--5891134 Score: 466
Period size: 53 Copynumber: 12.6 Consensus size: 54
5890452 CAATTTTTTT
* * * * *
5890462 AGAAACTAAGTATGATTTTCATAAGTTTGTTGACGATTTTGAAATGAGTTTTTAAA
1 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAG-TTTT-AA
* ** * *
5890518 AGAAACTAAGTCTGATTTATAGAAGTTTCTTGATTATTTTTAAATGAGCTTTCAA
1 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAG-TTTTAA
* *
5890573 AGAAACTAAGTCTGATTTTTAGAAGTTTCCTGATGATTTT-AAATGAGTTTTTAA
1 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAG-TTTTAA
*
5890627 AGAAACTAAGTCTGATTTTTAGAAGTTTCTCGACGATTTTCAAATGAGTTTTAA
1 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGTTTTAA
** * *
5890681 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGATTATTTTTAAATGAGCTTTCAA
1 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAG-TTTTAA
* * *
5890736 AGAGACTAAGTCTGATTTTCAAAAGTTTCTTGACGATTTTCAAATGAGTTTT--
1 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGTTTTAA
* * * * *
5890788 ----A--AAGTCTGATTTTTAGAAGTTTCTTGATGATTTTTAAATAAACTTTCAA
1 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAAT-GAGTTTTAA
* * ** * * *
5890837 AGAAATTAAGCCT-ACTTTTTAGGGGTTTCTTGATG-TTTTCAAATGAATTTGAA
1 AGAAACTAAGTCTGA-TTTTTAGAAGTTTCTTGACGATTTTCAAATGAGTTTTAA
* * * * ** * * *
5890890 AGAATCTAAGCCTAATTTTCAGGGGTTTCTTGATG-TTTTCAAATGAATTTGAA
1 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGTTTTAA
* * * * * ** *
5890943 ATAAGCTAAGCCT-ATTTTTTAGGAGTTTCTTGATG-TTTTCAAACCAATTTTCAA
1 AGAAACTAAGTCTGA-TTTTTAGAAGTTTCTTGACGATTTTCAAATGAGTTTT-AA
* * ** ** * * *
5890997 ATAAATTAAG-CATG-TTTCCAGGGGTTTCTTGATG-TTTTCAAATGAATTTGAA
1 AGAAACTAAGTC-TGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGTTTTAA
* * * * ** * * *
5891049 ATAAGCTAAG-CTTGGTTTTCAGGGGTTTCTTGATG-TTTTCAAATGAATTTGAA
1 AGAAACTAAGTC-TGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGTTTTAA
* * * **
5891102 AGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGA
1 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGA
5891135 TGTTTTTAAA
Statistics
Matches: 528, Mismatches: 70, Indels: 41
0.83 0.11 0.06
Matches are distributed among these distances:
46 34 0.06
47 4 0.01
48 1 0.00
52 14 0.03
53 192 0.36
54 124 0.23
55 116 0.22
56 43 0.08
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (54 bp):
AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGTTTTAA
Found at i:5890655 original size:109 final size:107
Alignment explanation
Indices: 5890462--5890985 Score: 489
Period size: 109 Copynumber: 4.9 Consensus size: 107
5890452 CAATTTTTTT
* * * * * * *
5890462 AGAAACTAAGTATGATTTTCATAAGTTTGTTGACGATTTTGAAATGAGTTTTTAAAAGAAACTAA
1 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGATGATTTT-AAATGAG-CTTTCAAAGAAACTAA
* ** *
5890527 GTCTGATTTATAGAAGTTTCTTGATTATTTTTAAATGAGCTTTCAA
64 GTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAG-TTT-AA
* * *
5890573 AGAAACTAAGTCTGATTTTTAGAAGTTTCCTGATGATTTTAAATGAGTTTTTAAAGAAACTAAGT
1 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGATGATTTTAAATGAGCTTTCAAAGAAACTAAGT
*
5890638 CTGATTTTTAGAAGTTTCTCGACGATTTTCAAATGAGTTTTAA
66 CTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAG-TTTAA
* *
5890681 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGATTATTTTTAAATGAGCTTTCAAAGAGACTAAG
1 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGATGA-TTTTAAATGAGCTTTCAAAGAAACTAAG
* *
5890746 TCTGATTTTCAAAAGTTTCTTGACGATTTTCAAATGAGTTT--
65 TCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGTTTAA
* * * *
5890787 ---TA--AAGTCTGATTTTTAGAAGTTTCTTGATGATTTTTAAATAAACTTTCAAAGAAATTAAG
1 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGATGA-TTTTAAATGAGCTTTCAAAGAAACTAAG
* ** * *
5890847 CCT-ACTTTTTAGGGGTTTCTTGATG-TTTTCAAATGAATTTGAA
65 TCTGA-TTTTTAGAAGTTTCTTGACGATTTTCAAATGAGTTT-AA
* * * * ** * * * *
5890890 AGAATCTAAGCCTAATTTTCAGGGGTTTCTTGATG-TTTTCAAATGA-ATTTGAAATAAGCTAAG
1 AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGATGATTTT-AAATGAGCTTTCAAAGAAACTAAG
* * *
5890953 CCT-ATTTTTTAGGAGTTTCTTGATG-TTTTCAAA
65 TCTGA-TTTTTAGAAGTTTCTTGACGATTTTCAAA
5890986 CCAATTTTCA
Statistics
Matches: 353, Mismatches: 49, Indels: 27
0.82 0.11 0.06
Matches are distributed among these distances:
100 15 0.04
101 70 0.20
103 1 0.00
106 47 0.13
107 5 0.01
108 62 0.18
109 112 0.32
110 7 0.02
111 34 0.10
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.42
Consensus pattern (107 bp):
AGAAACTAAGTCTGATTTTTAGAAGTTTCTTGATGATTTTAAATGAGCTTTCAAAGAAACTAAGT
CTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGTTTAA
Found at i:5890865 original size:101 final size:100
Alignment explanation
Indices: 5890688--5890891 Score: 266
Period size: 101 Copynumber: 2.0 Consensus size: 100
5890678 TAAAGAAACT
* * * * *
5890688 AAGTCTGATTTTTAGAAGTTTCTTGATTATTTTTAAATGAGCTTTCAAAGAGACTAAGTCTGATT
1 AAGTCTGATTTTTAGAAGTTTCTTGATGATTTTTAAATAAACTTTCAAAGAAACTAAGCCTGATT
* *
5890753 TTCAAAAGTTTCTTGACGATTTTCAAATGAGTTTTA
66 TTCAAAAGTTTCTTGACG-TTTTCAAATGAATTTGA
*
5890789 AAGTCTGATTTTTAGAAGTTTCTTGATGATTTTTAAATAAACTTTCAAAGAAATTAAGCCT-ACT
1 AAGTCTGATTTTTAGAAGTTTCTTGATGATTTTTAAATAAACTTTCAAAGAAACTAAGCCTGA-T
* *** *
5890853 TTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGA
65 TTTCAAAAGTTTCTTGACGTTTTCAAATGAATTTGA
5890889 AAG
1 AAG
5890892 AATCTAAGCC
Statistics
Matches: 89, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
100 19 0.21
101 70 0.79
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.43
Consensus pattern (100 bp):
AAGTCTGATTTTTAGAAGTTTCTTGATGATTTTTAAATAAACTTTCAAAGAAACTAAGCCTGATT
TTCAAAAGTTTCTTGACGTTTTCAAATGAATTTGA
Found at i:5890914 original size:53 final size:53
Alignment explanation
Indices: 5890806--5891190 Score: 409
Period size: 53 Copynumber: 7.2 Consensus size: 53
5890796 ATTTTTAGAA
* * * * *
5890806 GTTTCTTGATGATTTTTAAATAAACTTTCAAAGAAAT-TAAGCCTACTTTTTAGGG
1 GTTTCTTGATG-TTTTCAAATGAA-TTTGAAAG-AATCTAAGCCTAATTTTCAGGG
5890861 GTTTCTTGATGTTTTCAAATGAATTTGAAAGAATCTAAGCCTAATTTTCAGGG
1 GTTTCTTGATGTTTTCAAATGAATTTGAAAGAATCTAAGCCTAATTTTCAGGG
* * * * *
5890914 GTTTCTTGATGTTTTCAAATGAATTTGAAATAAGCTAAGCCTATTTTTTAGGA
1 GTTTCTTGATGTTTTCAAATGAATTTGAAAGAATCTAAGCCTAATTTTCAGGG
** * * * * *
5890967 GTTTCTTGATGTTTTCAAACCAATTTTCAAATAAAT-TAAGCAT-GTTTCCAGGG
1 GTTTCTTGATGTTTTCAAATGAA-TTTGAAA-GAATCTAAGCCTAATTTTCAGGG
* * * **
5891020 GTTTCTTGATGTTTTCAAATGAATTTGAAATAAGCTAAGCTTGGTTTTCAGGG
1 GTTTCTTGATGTTTTCAAATGAATTTGAAAGAATCTAAGCCTAATTTTCAGGG
* *
5891073 GTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGCTAAGCCTAATTTTTAGGG
1 GTTTCTTGATGTTTTCAAATGAATTTGAAAGAATCTAAGCCTAATTTTCAGGG
* * * * * *
5891126 GTTTCTTGATGTTTTTAAATAAATTTTCAATGAAAT-TAAACCTTATTTTCAGGG
1 GTTTCTTGATGTTTTCAAATGAA-TTTGAAAG-AATCTAAGCCTAATTTTCAGGG
5891180 GTTTCTTGATG
1 GTTTCTTGATG
5891191 ACGATTTTCA
Statistics
Matches: 283, Mismatches: 40, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
51 2 0.01
52 15 0.05
53 197 0.70
54 54 0.19
55 15 0.05
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.42
Consensus pattern (53 bp):
GTTTCTTGATGTTTTCAAATGAATTTGAAAGAATCTAAGCCTAATTTTCAGGG
Found at i:5891041 original size:159 final size:159
Alignment explanation
Indices: 5890796--5891247 Score: 575
Period size: 159 Copynumber: 2.8 Consensus size: 159
5890786 TTAAAGTCTG
* * * * *
5890796 ATTTTTAGAAGTTTCTTGATGATTTTTAAATAAACTTTCAAAGAAATTAAGCCTACTTTTTAGGG
1 ATTTTTAGGAGTTTCTTGATG-TTTTTAAATAAATTTTCAAATAAATTAAGCATA-TTTTCAGGG
*
5890861 GTTTCTTGATGTTTTCAAATGAATTTGAAAGAATCTAAGCCTAATTTTCAGGGGTTTCTTGATGT
64 GTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGT
*
5890926 TTTCAAATGAATTTGAAATAAGCTAAGCCTA
129 TTTCAAATGAATTTGAAAGAAGCTAAGCCTA
* * ** * *
5890957 TTTTTTAGGAGTTTCTTGATGTTTTCAAACCAATTTTCAAATAAATTAAGCATGTTTCCAGGGGT
1 ATTTTTAGGAGTTTCTTGATGTTTTTAAATAAATTTTCAAATAAATTAAGCATATTTTCAGGGGT
* * **
5891022 TTCTTGATGTTTTCAAATGAATTTGAAATAAGCTAAGCTTGGTTTTCAGGGGTTTCTTGATGTTT
66 TTCTTGATGTTTTCAAATGAATTTGAAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGTTT
5891087 TCAAATGAATTTGAAAGAAGCTAAGCCTA
131 TCAAATGAATTTGAAAGAAGCTAAGCCTA
* * *
5891116 ATTTTTAGGGGTTTCTTGATGTTTTTAAATAAATTTTC-AATGAAATTAAACCTTATTTTCAGGG
1 ATTTTTAGGAGTTTCTTGATGTTTTTAAATAAATTTTCAAAT-AAATT-AAGCATATTTTCAGGG
* * * *
5891180 GTTTCTTGATGACGATTTTC-AATGAGTTTTTAAAAGGAAGCTAAGCCTAATTTTTAGGGGTTCC
64 GTTTCTTGAT---G-TTTTCAAATGA--ATTTGAAA-GAAGCTAAGCCTAATTTTCAGGGGTTTC
5891244 TTGA
122 TTGA
5891248 CAACTAAGAA
Statistics
Matches: 248, Mismatches: 34, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
158 3 0.01
159 135 0.54
160 48 0.19
161 19 0.08
163 6 0.02
164 5 0.02
165 6 0.02
166 26 0.10
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.42
Consensus pattern (159 bp):
ATTTTTAGGAGTTTCTTGATGTTTTTAAATAAATTTTCAAATAAATTAAGCATATTTTCAGGGGT
TTCTTGATGTTTTCAAATGAATTTGAAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGTTT
TCAAATGAATTTGAAAGAAGCTAAGCCTA
Found at i:5891378 original size:21 final size:21
Alignment explanation
Indices: 5891352--5891393 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5891342 CGGGTCATCT
*
5891352 ATAAGTCTTTCGAGCAAGATG
1 ATAAGTCCTTCGAGCAAGATG
* *
5891373 ATAAGTCCTTCGGGCAGGATG
1 ATAAGTCCTTCGAGCAAGATG
5891394 CTTTCAAATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.26
Consensus pattern (21 bp):
ATAAGTCCTTCGAGCAAGATG
Found at i:5891630 original size:254 final size:254
Alignment explanation
Indices: 5891178--5891636 Score: 792
Period size: 254 Copynumber: 1.8 Consensus size: 254
5891168 TTATTTTCAG
* * * *
5891178 GGGTTTCTTGATGACGATTTTCAATGAGTTTTTAAAAGGAAGCTAAGCCTAATTTTTAGGGGTTC
1 GGGTTTCTTGATGACGATCTCCAAAGAGTTTTTAAAAGGAAGCTAAGACTAATTTTTAGGGGTTC
*
5891243 CTTGACAACTAAGAAATTAAGCTTGATTTTCAAGGGTTTCATGATGAGTAAGTCCTTCGGGCCAT
66 CTTGACAACTAAGAAACTAAGCTTGATTTTCAAGGGTTTCATGATGAGTAAGTCCTTCGGGCCAT
* *
5891308 CAGTAAGTCTTTCGAGCATGATGCTTAAATCCCTCGGGTCATCTATAAGTCTTTCGAGCAAGATG
131 CAGTAAGTCTTTCGAGCATGATGCTTAAATCCCTCGGGTCATCTATAAGTCTTTCAAGCAAAATG
5891373 ATAAGTCCTTCGGGCAGGATGCTTTCAAATGGGTTTTTAGAAACTAAGCCTGATTTTTA
196 ATAAGTCCTTCGGGCAGGATGCTTTCAAATGGGTTTTTAGAAACTAAGCCTGATTTTTA
** *
5891432 GGGTTTCTTGATGATTATCTCCAAAGAGTTTTTAAAAGGAAGCTAAGACTAATTTTTAGGGGTTT
1 GGGTTTCTTGATGACGATCTCCAAAGAGTTTTTAAAAGGAAGCTAAGACTAATTTTTAGGGGTTC
* *
5891497 CTTGACAACTAAGAAGCTAAGCTTGATTTTCAAGGGTTTCATGATGAGTAATTCCTTCGGGCCAT
66 CTTGACAACTAAGAAACTAAGCTTGATTTTCAAGGGTTTCATGATGAGTAAGTCCTTCGGGCCAT
* *
5891562 TAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCAAGCAAAATG
131 CAGTAAGTCTTTCGAGCATGATGCTTAAATCCCTCGGGTCATCTATAAGTCTTTCAAGCAAAATG
5891627 ATAAGTCCTT
196 ATAAGTCCTT
5891637 TAGACTATCC
Statistics
Matches: 191, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
254 191 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.35
Consensus pattern (254 bp):
GGGTTTCTTGATGACGATCTCCAAAGAGTTTTTAAAAGGAAGCTAAGACTAATTTTTAGGGGTTC
CTTGACAACTAAGAAACTAAGCTTGATTTTCAAGGGTTTCATGATGAGTAAGTCCTTCGGGCCAT
CAGTAAGTCTTTCGAGCATGATGCTTAAATCCCTCGGGTCATCTATAAGTCTTTCAAGCAAAATG
ATAAGTCCTTCGGGCAGGATGCTTTCAAATGGGTTTTTAGAAACTAAGCCTGATTTTTA
Found at i:5891777 original size:39 final size:38
Alignment explanation
Indices: 5891734--5891863 Score: 172
Period size: 39 Copynumber: 3.4 Consensus size: 38
5891724 GATGGATCAA
*
5891734 TATCTCACTTGAGATAGTTTCACTCGAAACAGAAGGTTT
1 TATCTCACTTGAGATAGTTTCACTCGAAACA-AAGATTT
* *
5891773 TATCTCACTTGAGATTGTTTCACCCGAAACAAAAGATTT
1 TATCTCACTTGAGATAGTTTCACTCGAAAC-AAAGATTT
* * *
5891812 TATCTCGCTTTAGATAGTTTCACTCAAAACAAA-ATTT
1 TATCTCACTTGAGATAGTTTCACTCGAAACAAAGATTT
*
5891849 TATCTCACTCGAGAT
1 TATCTCACTTGAGAT
5891864 TATTTTTCTT
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
37 16 0.20
38 3 0.04
39 59 0.75
40 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (38 bp):
TATCTCACTTGAGATAGTTTCACTCGAAACAAAGATTT
Found at i:5891924 original size:72 final size:73
Alignment explanation
Indices: 5891814--5892099 Score: 323
Period size: 72 Copynumber: 3.9 Consensus size: 73
5891804 AAAGATTTTA
* * *
5891814 TCTCGCTTTAGATAGTTTCACTCAAAACAAAATTTTATCTCACTCGAGATTATTTTTCTTAAAAC
1 TCTCGCTTGAGACAGTTTCACTCGAAACAAAATTTTATCTCACTCGAGATTATTTTTCTTAAAAC
5891879 AAA-TTCG
66 AAACTTCG
* * * * *
5891886 CCTAGCTTGAGACAGTTTCACTCGAAACAAAATTTTATCTCAC-CTGGGATTGTGTTTCTTAAAA
1 TCTCGCTTGAGACAGTTTCACTCGAAACAAAATTTTATCTCACTC-GAGATTATTTTTCTTAAAA
5891950 CAAACTTCG
65 CAAACTTCG
* * ** **
5891959 TCTCGCTTGTGACAGTTTCCACTTGAAACAAAATTTTA--TCACTTTAGATTGGTTTTCTTAAAA
1 TCTCGCTTGAGACAGTTT-CACTCGAAACAAAATTTTATCTCACTCGAGATTATTTTTCTTAAAA
*
5892022 CAAACTTTG
65 CAAACTTCG
* * *
5892031 TCTCGCTTGAGACAATTTTTACTCGAAACAATAAATTTTATCTCGCTCGAGATTA--TTTCTTAA
1 TCTCGCTTGAGAC-AGTTTCACTCGAAAC-A-AAATTTTATCTCACTCGAGATTATTTTTCTTAA
5892094 AACAAA
63 AACAAA
5892100 TTTCATTTGG
Statistics
Matches: 179, Mismatches: 26, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
71 1 0.01
72 105 0.59
73 24 0.13
74 40 0.22
76 9 0.05
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37
Consensus pattern (73 bp):
TCTCGCTTGAGACAGTTTCACTCGAAACAAAATTTTATCTCACTCGAGATTATTTTTCTTAAAAC
AAACTTCG
Found at i:5892113 original size:146 final size:145
Alignment explanation
Indices: 5891741--5892105 Score: 330
Period size: 146 Copynumber: 2.5 Consensus size: 145
5891731 CAATATCTCA
* * * * ** *
5891741 CTTGAGATAGTTTCACTCGAAACAGAAGGTTTTATCTCACTTGAGATTGT-TTCACCCGAAACAA
1 CTTGAGACAGTTTCACTCGAAACA-AA-ATTTTATCTCACCTGAGATTGTATT--TCTTAAA-AC
* * * ** *
5891805 AAGATTTTATCTCGCTT-TAGATAGTTT-CACTCAAAACAAAATTTTATCTCACTCGAGATTATT
61 AA-ACTTCATCTCGCTTGT-GACAGTTTCCACTTGAAACAAAATTTTA-CTCACTCGAGATTAGT
5891868 TTTCTTAAAACAAATTCGCCTAG
123 TTTCTTAAAACAAATTCGCCTAG
* *
5891891 CTTGAGACAGTTTCACTCGAAACAAAATTTTATCTCACCTGGGATTGTGTTTCTTAAAACAAACT
1 CTTGAGACAGTTTCACTCGAAACAAAATTTTATCTCACCTGAGATTGTATTTCTTAAAACAAACT
* ** *
5891956 TCGTCTCGCTTGTGACAGTTTCCACTTGAAACAAAATTTTA-TCACTTTAGATTGGTTTTCTTAA
66 TCATCTCGCTTGTGACAGTTTCCACTTGAAACAAAATTTTACTCACTCGAGATTAGTTTTCTTAA
* * *
5892020 AACAAACTTTGTCTCG
131 AACAAA-TTCGCCTAG
* * *
5892036 CTTGAGACAATTTTTACTCGAAACAATAAATTTTATCTC-GCTCGAGA-T-TATTTCTTAAAACA
1 CTTGAGAC-AGTTTCACTCGAAAC-A-AAATTTTATCTCACCT-GAGATTGTATTTCTTAAAACA
*
5892098 AATTTCAT
62 AACTTCAT
5892106 TTGGCTTGAA
Statistics
Matches: 179, Mismatches: 28, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
144 25 0.14
145 32 0.18
146 53 0.30
147 8 0.04
148 34 0.19
149 4 0.02
150 23 0.13
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (145 bp):
CTTGAGACAGTTTCACTCGAAACAAAATTTTATCTCACCTGAGATTGTATTTCTTAAAACAAACT
TCATCTCGCTTGTGACAGTTTCCACTTGAAACAAAATTTTACTCACTCGAGATTAGTTTTCTTAA
AACAAATTCGCCTAG
Found at i:5892275 original size:36 final size:36
Alignment explanation
Indices: 5892168--5892277 Score: 118
Period size: 36 Copynumber: 3.1 Consensus size: 36
5892158 AAACAAGAAA
* * *
5892168 TTTATCTCACTTGAGATTATTTT-TCTTAAAACAAAC
1 TTTATCTCACCTGAGA-TATTTTCTCTTCAAACAAAT
* * *
5892204 TTCATCTCA-CTAGAGACAATTTCTC-TCGAAACAAAT
1 TTTATCTCACCT-GAGATATTTTCTCTTC-AAACAAAT
5892240 TTTATCTCACCTGAGATATTTTCTCTTCAAACAAAT
1 TTTATCTCACCTGAGATATTTTCTCTTCAAACAAAT
5892276 TT
1 TT
5892278 CTTTTGATTC
Statistics
Matches: 60, Mismatches: 9, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
35 6 0.10
36 50 0.83
37 4 0.07
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.40
Consensus pattern (36 bp):
TTTATCTCACCTGAGATATTTTCTCTTCAAACAAAT
Found at i:5892878 original size:42 final size:41
Alignment explanation
Indices: 5892781--5892881 Score: 125
Period size: 42 Copynumber: 2.4 Consensus size: 41
5892771 TTAGCTTGTT
* * *
5892781 TCCATCGCATAAGGAGTTGGAACATCATCGACTTTTGCTCG
1 TCCATCACATAAGGAGTTGGAACATCATCGACTTTCGCTAG
5892822 TCCATCACATAAGGAGTTGGATTAGCATCATC-A-TTTCGCTAG
1 TCCATCACATAAGGAGTTGGA--A-CATCATCGACTTTCGCTAG
*
5892864 TCCATCACAAAAGGAGTT
1 TCCATCACATAAGGAGTT
5892882 AGATCAACAA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
41 20 0.38
42 24 0.45
43 2 0.04
44 7 0.13
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (41 bp):
TCCATCACATAAGGAGTTGGAACATCATCGACTTTCGCTAG
Found at i:5893006 original size:20 final size:19
Alignment explanation
Indices: 5892944--5893007 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 19
5892934 CCAGTGAAGA
5892944 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* * *
5892963 CATCCGATAAGGGAGAAGAA--
1 -GTTC-ATAA-TGAGAAGAACT
5892983 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
5893003 GTTCA
1 GTTCA
5893008 ACCTTAGCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 8 0.24
18 4 0.12
19 2 0.06
20 7 0.21
21 4 0.12
22 8 0.24
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.23
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:5893177 original size:199 final size:199
Alignment explanation
Indices: 5892822--5893211 Score: 559
Period size: 199 Copynumber: 2.0 Consensus size: 199
5892812 CTTTTGCTCG
* *
5892822 TCCATCACATAAGGAGTTGGATTAGCATCATCATTTCGCTAGTCCATCACAAAAGGAGTTAGATC
1 TCCATCACATAAGGAGTTGGATCAGCATCATCATTTCACTAGTCCATCACAAAAGGAGTTAGATC
* * * *
5892887 AACAACACCTTAGCTCAATCATCGCATATGGAAATGGATCAACATTTCCAGTGAAGAGTTCATAA
66 AACAACACCTTAGATCAATCATCACAGAAGGAAATGGATCAACATTTCCAGTGAAGAGTTCATAA
* * *
5892952 TGAGAAGAACTCATCCGATAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCT
131 TGAGAAGAACTCATCCGACAAGGGAGAAAAAATTCATAATGAGAAGAACTTGTTCAACCTTAGCT
5893017 TGTT
196 TGTT
* * * * *
5893021 TCCATCGCATAAGGAGTTGGATCATCATCTTCATTTCACTCA-TCCATCACATAAGGAGTTGGAT
1 TCCATCACATAAGGAGTTGGATCAGCATCATCATTTCACT-AGTCCATCACAAAAGGAGTTAGAT
* * ** * *
5893085 CAGCATCACC-TAGGATCAATCATCACAGAAGGAGGTGGATCAACATTTCTAGTGGAGAGTTCAT
65 CAACAACACCTTA-GATCAATCATCACAGAAGGAAATGGATCAACATTTCCAGTGAAGAGTTCAT
*
5893149 AATGAGAAGAACTCATCCGACGAGGGAGAAAAAATTCATAATGAGAAGAACTTGTTCAACCTT
129 AATGAGAAGAACTCATCCGACAAGGGAGAAAAAATTCATAATGAGAAGAACTTGTTCAACCTT
5893212 GGTGATTTAA
Statistics
Matches: 168, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
198 2 0.01
199 165 0.98
200 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (199 bp):
TCCATCACATAAGGAGTTGGATCAGCATCATCATTTCACTAGTCCATCACAAAAGGAGTTAGATC
AACAACACCTTAGATCAATCATCACAGAAGGAAATGGATCAACATTTCCAGTGAAGAGTTCATAA
TGAGAAGAACTCATCCGACAAGGGAGAAAAAATTCATAATGAGAAGAACTTGTTCAACCTTAGCT
TGTT
Found at i:5894333 original size:30 final size:30
Alignment explanation
Indices: 5894262--5894338 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 30
5894252 GGTAGTGGCT
* * *
5894262 AAAATGTAAGTTCTAAAAGTTTAGTAGCTA
1 AAAATGTAATTTATAAAAGTTTAGGAGCTA
*
5894292 AAATAT-AAATTTATAAAAGTTTAGG-GACTA
1 AAA-ATGTAATTTATAAAAGTTTAGGAG-CTA
*
5894322 AAAATGTAATTTTTAAA
1 AAAATGTAATTTATAAA
5894339 TTTATATATT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
29 3 0.08
30 33 0.87
31 2 0.05
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTATAAAAGTTTAGGAGCTA
Found at i:5895499 original size:20 final size:21
Alignment explanation
Indices: 5895458--5895502 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5895448 TGGAGTATTC
*
5895458 AATGCTGAAATTTAATTATAG
1 AATGCTGAAATTTAAGTATAG
5895479 AATGCT-AAATTTTAAGT-TAG
1 AATGCTGAAA-TTTAAGTATAG
5895499 AATG
1 AATG
5895503 TTGGTTTGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.38
Consensus pattern (21 bp):
AATGCTGAAATTTAAGTATAG
Found at i:5897759 original size:24 final size:24
Alignment explanation
Indices: 5897727--5897774 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
5897717 AGTCTTCCTG
5897727 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
5897751 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
5897775 TATGTCATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:5898986 original size:31 final size:31
Alignment explanation
Indices: 5898951--5899009 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
5898941 ATTACCATTA
* * *
5898951 AACCAAGACACCTCATCCTTATTATCTTTCG
1 AACCAAGAAACCTCAACCTTATCATCTTTCG
5898982 AACCAAGAAACCTCAACCTTATCATCTT
1 AACCAAGAAACCTCAACCTTATCATCTT
5899010 CCTTGAGTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.34, C:0.32, G:0.05, T:0.29
Consensus pattern (31 bp):
AACCAAGAAACCTCAACCTTATCATCTTTCG
Found at i:5903403 original size:257 final size:258
Alignment explanation
Indices: 5902947--5903461 Score: 1023
Period size: 257 Copynumber: 2.0 Consensus size: 258
5902937 ATGCCACCCC
5902947 AGAGTTCATGGTTTGCTACCCCTTTTACTTTCACCGTGTTGCGGTGTTGTTATTAACTGATCTTG
1 AGAGTTCATGGTTTGCTACCCCTTTTACTTTCACCGTGTTGCGGTGTTGTTATTAACTGATCTTG
5903012 ATAAAGTTTTGTACATTTATTTCTATAATGTCCAACTTGTTTGCAATGATAACATTTCCCTTCCA
66 ATAAAGTTTTGTACATTTATTTCTATAATGTCCAACTTGTTTGCAATGATAACATTTCCCTTCCA
5903077 TGAGTCAGCATTGACTGTAATGATTCTTTCCACAAAACTCACATTCTGGTTTAGGACGAAATCTC
131 TGAGTCAGCATTGACTGTAATGATTCTTTCCACAAAACTCACATTCTGGTTTAGGACGAAATCTC
5903142 GAACCTTTAGTATCTGCTGAAGCTGCATGGGTCTTCTT-GACTTCCCTTCAGCAAATCCTTTT
196 GAACCTTTAGTATCTGCTGAAGCTGCATGGGTCTTCTTGGACTTCCCTTCAGCAAATCCTTTT
5903204 AGAGTTCATGGTTTGCTACCCCTTTTACTTTCACCGTGTTGCGGTGTTGTTATTAACTGATCTTG
1 AGAGTTCATGGTTTGCTACCCCTTTTACTTTCACCGTGTTGCGGTGTTGTTATTAACTGATCTTG
5903269 ATAAAGTTTTGTACATTTATTTCTATAATGTCCAACTTGTTTGCAATGATAACATTTCCCTTCCA
66 ATAAAGTTTTGTACATTTATTTCTATAATGTCCAACTTGTTTGCAATGATAACATTTCCCTTCCA
5903334 TGAGTCAGCATTGACTGTAATGATTCTTTCCACAAAACTCACATTCTGGTTTAGGACGAAATCTC
131 TGAGTCAGCATTGACTGTAATGATTCTTTCCACAAAACTCACATTCTGGTTTAGGACGAAATCTC
5903399 GAACCTTTAGTATCTGCTGAAGCTGCATGGGTCTTCTTGGACTTCCCTTCAGCAAATCCTTTT
196 GAACCTTTAGTATCTGCTGAAGCTGCATGGGTCTTCTTGGACTTCCCTTCAGCAAATCCTTTT
5903462 TTTCTCGTAG
Statistics
Matches: 257, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
257 233 0.91
258 24 0.09
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (258 bp):
AGAGTTCATGGTTTGCTACCCCTTTTACTTTCACCGTGTTGCGGTGTTGTTATTAACTGATCTTG
ATAAAGTTTTGTACATTTATTTCTATAATGTCCAACTTGTTTGCAATGATAACATTTCCCTTCCA
TGAGTCAGCATTGACTGTAATGATTCTTTCCACAAAACTCACATTCTGGTTTAGGACGAAATCTC
GAACCTTTAGTATCTGCTGAAGCTGCATGGGTCTTCTTGGACTTCCCTTCAGCAAATCCTTTT
Found at i:5905437 original size:24 final size:24
Alignment explanation
Indices: 5905405--5905451 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
5905395 AGTCTTCCTG
5905405 ATGATGTATAAAACATCTATGTAA
1 ATGATGTATAAAACATCTATGTAA
5905429 ATGATGTATAAAACATCTATGTA
1 ATGATGTATAAAACATCTATGTA
5905452 CTATGTCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.34
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAA
Found at i:5906705 original size:31 final size:31
Alignment explanation
Indices: 5906667--5906725 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
5906657 ATTACCATTA
* * *
5906667 AACCAAGACACCTCATCCTTATTATCTTTCC
1 AACCAAGAAACCTCAACCTTATCATCTTTCC
5906698 AACCAAGAAACCTCAACCTTATCATCTT
1 AACCAAGAAACCTCAACCTTATCATCTT
5906726 CCTTAAGTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.34, C:0.34, G:0.03, T:0.29
Consensus pattern (31 bp):
AACCAAGAAACCTCAACCTTATCATCTTTCC
Found at i:5909360 original size:24 final size:23
Alignment explanation
Indices: 5909332--5909376 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
5909322 TGATGCTATT
5909332 TGGATCA-ATTTATGGTCGTATTTA
1 TGGATCATATTT-TGGTC-TATTTA
*
5909356 TGGATGATATTTTGGTCTATT
1 TGGATCATATTTTGGTCTATT
5909377 CTAAGAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 4 0.21
24 11 0.58
25 4 0.21
ACGTcount: A:0.22, C:0.07, G:0.22, T:0.49
Consensus pattern (23 bp):
TGGATCATATTTTGGTCTATTTA
Found at i:5912905 original size:20 final size:20
Alignment explanation
Indices: 5912862--5912910 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
5912852 TGGAGTATTC
5912862 AATGTTGAAATTTAATTATGG
1 AATGTTGAAATTTAATTA-GG
*
5912883 AATGTTGAATTTTAAGTTA-G
1 AATGTTGAAATTTAA-TTAGG
5912903 AATGTTGA
1 AATGTTGA
5912911 TTTGAGGATC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 9 0.35
21 14 0.54
22 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (20 bp):
AATGTTGAAATTTAATTAGG
Found at i:5922208 original size:21 final size:20
Alignment explanation
Indices: 5922183--5922236 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
5922173 ACTCAGTTTT
5922183 CAAATTCGCAACGAGATTCTC
1 CAAATTCGCAACGAGATT-TC
* * * *
5922204 CAAATTTGCAATGCGATTTT
1 CAAATTCGCAACGAGATTTC
*
5922224 TAAATTCGCAACG
1 CAAATTCGCAACG
5922237 CGGATTTCGT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (20 bp):
CAAATTCGCAACGAGATTTC
Found at i:5924693 original size:23 final size:23
Alignment explanation
Indices: 5924667--5924719 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
5924657 GAAACTGTCG
*
5924667 CGTAGAATTGTCCCGAAGGACCA
1 CGTAGAATTGTCCCGAAAGACCA
* *
5924690 CGTAGAATTGTCCTGAAAGACCG
1 CGTAGAATTGTCCCGAAAGACCA
5924713 CGTAGAA
1 CGTAGAA
5924720 CCCTCGACTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (23 bp):
CGTAGAATTGTCCCGAAAGACCA
Found at i:5924902 original size:30 final size:30
Alignment explanation
Indices: 5924822--5924905 Score: 91
Period size: 30 Copynumber: 2.8 Consensus size: 30
5924812 AAGTATCTAT
* *
5924822 TATTCACATATATCACATT-ACGTAGAACA
1 TATTCACATATATCATATTCACATAGAACA
* **
5924851 TTTTCACATATAATGGT-TTCACATAGAACA
1 TATTCACATAT-ATCATATTCACATAGAACA
*
5924881 TATTCATATATATCATATTCACATA
1 TATTCACATATATCATATTCACATA
5924906 TTAATAAAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
29 15 0.35
30 28 0.65
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.37
Consensus pattern (30 bp):
TATTCACATATATCATATTCACATAGAACA
Found at i:5924906 original size:15 final size:15
Alignment explanation
Indices: 5924822--5924906 Score: 57
Period size: 15 Copynumber: 5.7 Consensus size: 15
5924812 AAGTATCTAT
5924822 TATTCACATATATCA
1 TATTCACATATATCA
* * * *
5924837 CATT-ACGTAGAACA
1 TATTCACATATATCA
* **
5924851 TTTTCACATATAATGG
1 TATTCACATAT-ATCA
* *
5924867 T-TTCACATAGAACA
1 TATTCACATATATCA
*
5924881 TATTCATATATATCA
1 TATTCACATATATCA
5924896 TATTCACATAT
1 TATTCACATAT
5924907 TAATAAAATC
Statistics
Matches: 48, Mismatches: 19, Indels: 6
0.66 0.26 0.08
Matches are distributed among these distances:
14 11 0.23
15 35 0.73
16 2 0.04
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.38
Consensus pattern (15 bp):
TATTCACATATATCA
Found at i:5925431 original size:21 final size:20
Alignment explanation
Indices: 5925389--5925438 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
5925379 CTCACTCTTG
5925389 GTATCGATACCTCCACATCA
1 GTATCGATACCTCCACATCA
*
5925409 GTATCGATACTACTTCA-ATCA
1 GTATCGATAC--CTCCACATCA
5925430 GTATCGATA
1 GTATCGATA
5925439 TTGTTCATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.37
21 13 0.48
22 4 0.15
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (20 bp):
GTATCGATACCTCCACATCA
Found at i:5925824 original size:25 final size:28
Alignment explanation
Indices: 5925782--5925834 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 28
5925772 TCCAATTACT
5925782 AACCATATTTCATCAATTC-CC-TTAAA
1 AACCATATTTCATCAATTCACCATTAAA
5925808 AACC-TATTTCA-CTAATTCACCATTAAA
1 AACCATATTTCATC-AATTCACCATTAAA
5925835 TCCTCAATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 1 0.04
25 12 0.50
26 6 0.25
27 5 0.21
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.34
Consensus pattern (28 bp):
AACCATATTTCATCAATTCACCATTAAA
Found at i:5932935 original size:23 final size:23
Alignment explanation
Indices: 5932905--5932965 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
5932895 CCATCTAGAC
5932905 GTATCGATACACATTCAAAGAGG
1 GTATCGATACACATTCAAAGAGG
**
5932928 GTATCGATACGTATTCAAAGAGG
1 GTATCGATACACATTCAAAGAGG
**
5932951 CCATCGATACACATT
1 GTATCGATACACATT
5932966 GAAGCAATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (23 bp):
GTATCGATACACATTCAAAGAGG
Found at i:5933014 original size:21 final size:21
Alignment explanation
Indices: 5932990--5933068 Score: 140
Period size: 21 Copynumber: 3.8 Consensus size: 21
5932980 ACCTAGCAAG
* *
5932990 GGGGTATCGAAACCTCTTTAT
1 GGGGTATCGATACCTGTTTAT
5933011 GGGGTATCGATACCTGTTTAT
1 GGGGTATCGATACCTGTTTAT
5933032 GGGGTATCGATACCTGTTTAT
1 GGGGTATCGATACCTGTTTAT
5933053 GGGGTATCGATACCTG
1 GGGGTATCGATACCTG
5933069 ATGCACAGAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.20, C:0.16, G:0.29, T:0.34
Consensus pattern (21 bp):
GGGGTATCGATACCTGTTTAT
Found at i:5933025 original size:42 final size:42
Alignment explanation
Indices: 5932978--5933068 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
5932968 AGCAATATTA
5932978 ATACCTAG-CAAGGGGGTATCGAAACCTCTTTATGGGGTATCG
1 ATACCT-GTCAAGGGGGTATCGAAACCTCTTTATGGGGTATCG
** * * *
5933020 ATACCTGTTTATGGGGTATCGATACCTGTTTATGGGGTATCG
1 ATACCTGTCAAGGGGGTATCGAAACCTCTTTATGGGGTATCG
5933062 ATACCTG
1 ATACCTG
5933069 ATGCACAGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 1 0.02
42 42 0.98
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (42 bp):
ATACCTGTCAAGGGGGTATCGAAACCTCTTTATGGGGTATCG
Found at i:5951994 original size:30 final size:30
Alignment explanation
Indices: 5951955--5952039 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 30
5951945 AAGTATCTCT
* *
5951955 TATTTACATATATCACATTCACGTAGAACA
1 TATTCACATATATCACATTCACATAGAACA
* * * ***
5951985 TTTTCACATAGAACGGTTTCACATAGAACA
1 TATTCACATATATCACATTCACATAGAACA
* *
5952015 TATTCATATATATCATATTCACATA
1 TATTCACATATATCACATTCACATA
5952040 TTAATAAAAT
Statistics
Matches: 40, Mismatches: 15, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.35
Consensus pattern (30 bp):
TATTCACATATATCACATTCACATAGAACA
Found at i:5951996 original size:15 final size:15
Alignment explanation
Indices: 5951971--5952039 Score: 68
Period size: 15 Copynumber: 4.6 Consensus size: 15
5951961 CATATATCAC
*
5951971 ATTCACGTAGAACAT
1 ATTCACATAGAACAT
* *
5951986 TTTCACATAGAACGGT
1 ATTCACATAGAAC-AT
5952002 -TTCACATAGAACAT
1 ATTCACATAGAACAT
* * *
5952016 ATTCATATATATCAT
1 ATTCACATAGAACAT
5952031 ATTCACATA
1 ATTCACATA
5952040 TTAATAAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
14 1 0.02
15 42 0.95
16 1 0.02
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (15 bp):
ATTCACATAGAACAT
Found at i:5952040 original size:15 final size:15
Alignment explanation
Indices: 5951955--5952040 Score: 57
Period size: 15 Copynumber: 5.7 Consensus size: 15
5951945 AAGTATCTCT
* *
5951955 TATTTACATATATCA
1 TATTCACATATAACA
* * *
5951970 CATTCACGTAGAACA
1 TATTCACATATAACA
* * *
5951985 TTTTCACATAGAACGG
1 TATTCACATATAAC-A
*
5952001 T-TTCACATAGAACA
1 TATTCACATATAACA
* *
5952015 TATTCATATATATCA
1 TATTCACATATAACA
5952030 TATTCACATAT
1 TATTCACATAT
5952041 TAATAAAATC
Statistics
Matches: 55, Mismatches: 14, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
14 1 0.02
15 53 0.96
16 1 0.02
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.36
Consensus pattern (15 bp):
TATTCACATATAACA
Found at i:5952566 original size:21 final size:20
Alignment explanation
Indices: 5952502--5952573 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
5952492 TCTTCCATTA
5952502 CAGTATCGATACCT-TAC-T
1 CAGTATCGATACCTCTACAT
*
5952520 CTTGGTATCGATACCTCTACAT
1 C--AGTATCGATACCTCTACAT
*
5952542 CAGTATCGATA-CTACTTCAAT
1 CAGTATCGATACCT-CTAC-AT
5952563 CAGTATCGATA
1 CAGTATCGATA
5952574 ATGTTCATCC
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
18 1 0.02
19 2 0.04
20 24 0.53
21 16 0.36
22 2 0.04
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.33
Consensus pattern (20 bp):
CAGTATCGATACCTCTACAT
Found at i:5955654 original size:60 final size:59
Alignment explanation
Indices: 5955550--5955676 Score: 159
Period size: 60 Copynumber: 2.1 Consensus size: 59
5955540 TAAAGCACAC
* ** *
5955550 AAATGATCCTCAACTATAGGATATTGCTTCTTTAAGTCTTTTGACTATTAAATGTAACA
1 AAATGGTCCTCAACTATAGGATATTGCTTCTTTAAGTCCCTTGACTATTAAAAGTAACA
* *
5955609 AAATGGTCCTCCAACTATAGAGA-ATTGCTT-TGTTGAGTCCCTTGACTATTAAAAGTTACA
1 AAATGGTCCT-CAACTATAG-GATATTGCTTCT-TTAAGTCCCTTGACTATTAAAAGTAACA
5955669 AAATGGTC
1 AAATGGTC
5955677 ACCCGGCTAT
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
59 10 0.17
60 47 0.80
61 2 0.03
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (59 bp):
AAATGGTCCTCAACTATAGGATATTGCTTCTTTAAGTCCCTTGACTATTAAAAGTAACA
Found at i:5955836 original size:3 final size:3
Alignment explanation
Indices: 5955825--5955931 Score: 178
Period size: 3 Copynumber: 35.0 Consensus size: 3
5955815 TTCTATTTTT
*
5955825 TTA TCTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5955871 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
*
5955917 TTA TTA TTG TTA TTA
1 TTA TTA TTA TTA TTA
5955932 ATATAAATTA
Statistics
Matches: 98, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
3 92 0.94
4 6 0.06
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:5956911 original size:10 final size:10
Alignment explanation
Indices: 5956896--5956933 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
5956886 TGGAGAGAAT
5956896 TTTCTCTCTC
1 TTTCTCTCTC
5956906 TTTCTC-C-C
1 TTTCTCTCTC
*
5956914 CTTCTCTCTC
1 TTTCTCTCTC
5956924 TTTCTCTCTC
1 TTTCTCTCTC
5956934 GCAGGCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
8 6 0.25
9 2 0.08
10 16 0.67
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (10 bp):
TTTCTCTCTC
Found at i:5957730 original size:29 final size:30
Alignment explanation
Indices: 5957698--5957775 Score: 72
Period size: 30 Copynumber: 2.6 Consensus size: 30
5957688 TAAAATTATG
* ** *
5957698 TTTTATTATTTTAGTCCC-CAAGATTTTGT
1 TTTTATTATTTTAGTCCCTAAAGATTCCGC
*
5957727 TTTTACATT-TTTTA-TCCCTAAAGCTTCCGC
1 TTTT--ATTATTTTAGTCCCTAAAGATTCCGC
5957757 TTTTATTATTTTAGTCCCT
1 TTTTATTATTTTAGTCCCT
5957776 TAACTTTTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
28 3 0.08
29 13 0.33
30 20 0.51
31 3 0.08
ACGTcount: A:0.19, C:0.19, G:0.08, T:0.54
Consensus pattern (30 bp):
TTTTATTATTTTAGTCCCTAAAGATTCCGC
Found at i:5957807 original size:29 final size:30
Alignment explanation
Indices: 5957766--5957847 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 30
5957756 CTTTTATTAT
* *
5957766 TTTAGTCCCTTAACTTTTTGTTTGTACT-A
1 TTTAGTCCTTTAACTTTATGTTTGTACTCA
* * *
5957795 TTTAGTCCTTTAAGTTTATGTTTTTACTCT
1 TTTAGTCCTTTAACTTTATGTTTGTACTCA
* * *
5957825 TTTGGTCCTTTAGCGTTATGTTT
1 TTTAGTCCTTTAACTTTATGTTT
5957848 TCCTCCTTTT
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 24 0.56
30 19 0.44
ACGTcount: A:0.15, C:0.15, G:0.13, T:0.57
Consensus pattern (30 bp):
TTTAGTCCTTTAACTTTATGTTTGTACTCA
Found at i:5958196 original size:17 final size:18
Alignment explanation
Indices: 5958168--5958201 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5958158 GAAATAAATC
*
5958168 AATTTAATTTTACTAATT
1 AATTTAATTTTAATAATT
5958186 AATTT-ATTTTAATAAT
1 AATTTAATTTTAATAAT
5958202 GCAATGTGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTTAATTTTAATAATT
Found at i:5959723 original size:32 final size:32
Alignment explanation
Indices: 5959679--5959740 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
5959669 TCTTATTTAT
5959679 ACTAACTAATTTCTTTTCTTTTGTTTGTGTAC
1 ACTAACTAATTTCTTTTCTTTTGTTTGTGTAC
*
5959711 ACTAACTTATTTCTTTTCTTTTGTTTGTGT
1 ACTAACTAATTTCTTTTCTTTTGTTTGTGT
5959741 CATTTTGTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.16, C:0.15, G:0.10, T:0.60
Consensus pattern (32 bp):
ACTAACTAATTTCTTTTCTTTTGTTTGTGTAC
Found at i:5960261 original size:6 final size:6
Alignment explanation
Indices: 5960250--5960296 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
5960240 GATCAACATT
*
5960250 TTTGCA TTTGCA TTTGCA TCTTTGCA TTTTGCA TCTGCA TTT-CA TTT
1 TTTGCA TTTGCA TTTGCA --TTTGCA -TTTGCA TTTGCA TTTGCA TTT
5960297 TAAGCATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
5 5 0.14
6 19 0.53
7 6 0.17
8 6 0.17
ACGTcount: A:0.15, C:0.19, G:0.13, T:0.53
Consensus pattern (6 bp):
TTTGCA
Found at i:5960273 original size:14 final size:15
Alignment explanation
Indices: 5960256--5960285 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5960246 CATTTTTGCA
5960256 TTTGCA-TTTGCATC
1 TTTGCATTTTGCATC
5960270 TTTGCATTTTGCATC
1 TTTGCATTTTGCATC
5960285 T
1 T
5960286 GCATTTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.13, C:0.20, G:0.13, T:0.53
Consensus pattern (15 bp):
TTTGCATTTTGCATC
Found at i:5960282 original size:21 final size:20
Alignment explanation
Indices: 5960250--5960289 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
5960240 GATCAACATT
*
5960250 TTTGCATTTGCATTTGCATC
1 TTTGCATTTGCATCTGCATC
5960270 TTTGCATTTTGCATCTGCAT
1 TTTGCA-TTTGCATCTGCAT
5960290 TTCATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.15, C:0.20, G:0.15, T:0.50
Consensus pattern (20 bp):
TTTGCATTTGCATCTGCATC
Found at i:5961600 original size:15 final size:14
Alignment explanation
Indices: 5961574--5961648 Score: 73
Period size: 15 Copynumber: 5.2 Consensus size: 14
5961564 GGACAAGAAA
*
5961574 AAACAAACAAAAA-
1 AAACAAAGAAAAAG
5961587 AAGAGCAAAGAAAAAG
1 AA-A-CAAAGAAAAAG
5961603 AAAACAAAGAGAAAAG
1 -AAACAAAGA-AAAAG
5961619 AAACAAAGAAAAA-
1 AAACAAAGAAAAAG
* *
5961632 AACCAAAGCAAAAG
1 AAACAAAGAAAAAG
5961646 AAA
1 AAA
5961649 AAACAAATAG
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
13 13 0.25
14 7 0.13
15 24 0.46
16 6 0.12
17 2 0.04
ACGTcount: A:0.76, C:0.11, G:0.13, T:0.00
Consensus pattern (14 bp):
AAACAAAGAAAAAG
Found at i:5961633 original size:45 final size:47
Alignment explanation
Indices: 5961571--5961677 Score: 132
Period size: 45 Copynumber: 2.3 Consensus size: 47
5961561 AAGGGACAAG
* * *
5961571 AAAAAACAAACAAAAAAAGAGCAAAG-AAAA-AGAAAACAAAGAG-AA
1 AAAAAACAAAGAAAAAAA-ACCAAAGCAAAAGAAAAAACAAAGAGCAA
* *
5961616 AAGAAACAAAG-AAAAAAACCAAAGCAAAAGAAAAAACAAATAGCAA
1 AAAAAACAAAGAAAAAAAACCAAAGCAAAAGAAAAAACAAAGAGCAA
5961662 AAAAAACAAAGAAAAA
1 AAAAAACAAAGAAAAA
5961678 TCAAAGTAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
43 6 0.12
44 10 0.19
45 20 0.38
46 12 0.23
47 4 0.08
ACGTcount: A:0.78, C:0.10, G:0.11, T:0.01
Consensus pattern (47 bp):
AAAAAACAAAGAAAAAAAACCAAAGCAAAAGAAAAAACAAAGAGCAA
Found at i:5961649 original size:18 final size:19
Alignment explanation
Indices: 5961623--5961667 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
5961613 GAAAAGAAAC
*
5961623 AAAGAAAAAAACCAA-AGCA
1 AAAG-AAAAAACAAATAGCA
5961642 AAAGAAAAAACAAATAGCA
1 AAAGAAAAAACAAATAGCA
5961661 AAA-AAAA
1 AAAGAAAA
5961668 CAAAGAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.78, C:0.11, G:0.09, T:0.02
Consensus pattern (19 bp):
AAAGAAAAAACAAATAGCA
Found at i:5961682 original size:11 final size:11
Alignment explanation
Indices: 5961581--5961728 Score: 78
Period size: 11 Copynumber: 13.4 Consensus size: 11
5961571 AAAAAACAAA
5961581 CAAA-AAAAGAG
1 CAAAGAAAA-AG
5961592 CAAAGAAAAAG
1 CAAAGAAAAAG
* * *
5961603 AAAACAAAGAG
1 CAAAGAAAAAG
*
5961614 -AAA-AGAAA-
1 CAAAGAAAAAG
*
5961622 CAAAGAAAAAAAC
1 CAAAG--AAAAAG
*
5961635 CAAAGCAAAAG
1 CAAAGAAAAAG
* *
5961646 AAAAAACAAATAG
1 CAAAGA-AAA-AG
5961659 CAAA-AAAAA-
1 CAAAGAAAAAG
*
5961668 CAAAGAAAAAT
1 CAAAGAAAAAG
5961679 CAAAGTAAAATAG
1 CAAAG-AAAA-AG
5961692 CAAAAGAAAAAG
1 C-AAAGAAAAAG
5961704 CAAAGAAAAAG
1 CAAAGAAAAAG
5961715 --AAGACAAAAG
1 CAAAGA-AAAAG
5961725 CAAA
1 CAAA
5961729 AAGACAAAGA
Statistics
Matches: 108, Mismatches: 13, Indels: 31
0.71 0.09 0.20
Matches are distributed among these distances:
9 14 0.13
10 14 0.13
11 39 0.36
12 21 0.19
13 16 0.15
14 4 0.04
ACGTcount: A:0.74, C:0.10, G:0.14, T:0.03
Consensus pattern (11 bp):
CAAAGAAAAAG
Found at i:5962842 original size:4 final size:4
Alignment explanation
Indices: 5962825--5962878 Score: 53
Period size: 4 Copynumber: 14.0 Consensus size: 4
5962815 GATCGAGAAA
*
5962825 ACAT ACAT -CAAT ACAT ACAT -CAAC ACAT ACAT ACAT AC-- ACAT ACAT
1 ACAT ACAT AC-AT ACAT ACAT AC-AT ACAT ACAT ACAT ACAT ACAT ACAT
5962871 ACAT ACAT
1 ACAT ACAT
5962879 GATACATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
2 2 0.05
3 2 0.05
4 36 0.86
5 2 0.05
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (4 bp):
ACAT
Found at i:5962842 original size:12 final size:12
Alignment explanation
Indices: 5962825--5962870 Score: 65
Period size: 12 Copynumber: 3.7 Consensus size: 12
5962815 GATCGAGAAA
*
5962825 ACATACATCAAT
1 ACATACATCAAC
5962837 ACATACATCAAC
1 ACATACATCAAC
5962849 ACATACATACATAC
1 ACATACAT-CA-AC
5962863 ACATACAT
1 ACATACAT
5962871 ACATACATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 19 0.61
13 2 0.06
14 10 0.32
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (12 bp):
ACATACATCAAC
Found at i:5963390 original size:36 final size:36
Alignment explanation
Indices: 5963350--5963505 Score: 165
Period size: 36 Copynumber: 4.3 Consensus size: 36
5963340 ACAAAGTTGA
** *
5963350 TCTCACTTGAGATCGTTTTCTCAAAAACAAAATTTG
1 TCTCACTTGAGATCAATTTCTCAAAAACAAATTTTG
5963386 TCTCACTTGAGA-CAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGATCAATTTCTC-AAAAACAAATTTTG
* *
5963422 TCTCACTCGAGAT-AATTTCTTGAAAAACAAATTTTG
1 TCTCACTTGAGATCAATTTC-TCAAAAACAAATTTTG
* * * * *
5963458 TCTCACTTAAGA-AAATTTATCTTAAAACAAATTTCG
1 TCTCACTTGAGATCAATTTCTC-AAAAACAAATTTTG
*
5963494 TCTCGCTTGAGA
1 TCTCACTTGAGA
5963506 CATTTTTCCT
Statistics
Matches: 102, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
35 8 0.08
36 93 0.91
37 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (36 bp):
TCTCACTTGAGATCAATTTCTCAAAAACAAATTTTG
Found at i:5963698 original size:107 final size:105
Alignment explanation
Indices: 5963271--5963786 Score: 439
Period size: 107 Copynumber: 4.9 Consensus size: 105
5963261 AATCTTTTGA
* * *
5963271 AAAACAAATCTT-GTCTCGCTTGAGACATTTTTCCTTTGAAATACAAATTTCGAATTTGTTTAAC
1 AAAACAAAT-TTCGTCTCGCTTGAGACATTTTTCCTTTGAAATACAAATTTTGAATTTGATTCAC
* * *
5963335 ATT-AAACAAAGTTGATCTCACTTGAGATCG-T-TTTC--TC
65 -TTGAAACAAAATTAATCTCACTTGAGATTGTTATTTCTTTC
* * * * * **
5963372 AAAAACAAAATTT-GTCTCACTTGAGACA-ATTT-CTCT-AAAAACAAATTTTGTCTCACTCGAG
1 -AAAAC-AAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAAATACAAATTTTG----AAT-TTG
** * ** * *** *
5963433 ATAATTTCTTGAAAAACAAATTTTGTCTCACTTAAGAAAATT-TATC-TT-
59 AT--TCACTTG--AAACAAAATTAATCTCACTTGAGATTGTTATTTCTTTC
* *
5963481 AAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGCTTCACT
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAAATACAAATTTTGAATTTGATTCACT
*
5963546 TGAAACAAAATTAATCTCACTTGAGATTTTTATTTCTTTC
66 TGAAACAAAATTAATCTCACTTGAGATTGTTATTTCTTTC
* * *
5963586 AAAACACATTTCGTCTCGCTTGAGACATTTTTTCCTTTGATATAAAAATTTTGAATTTGATTCAC
1 AAAACAAATTTCGTCTCGCTTGAGACA-TTTTTCCTTTGAAATACAAATTTTGAATTTGATTCAC
*
5963651 TTGAAACGAAAATTAATCTCACTTGAGATTGTTATTTTTTTC
65 TTGAAAC-AAAATTAATCTCACTTGAGATTGTTATTTCTTTC
* * * *
5963693 AAAACAAATTTCATCTCGTTTGAGACATTTTTCCTTTGAGAATACAAATTTCGAATTTGTTTTCA
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGA-AATACAAATTTTGAATTTG-ATTCA
* **
5963758 CATT-AAACAAAGTTGGTCTCACTTGAGAT
64 C-TTGAAACAAAATTAATCTCACTTGAGAT
5963787 CGTTTTCTCG
Statistics
Matches: 335, Mismatches: 54, Indels: 45
0.77 0.12 0.10
Matches are distributed among these distances:
99 12 0.04
100 3 0.01
101 3 0.01
102 43 0.13
103 9 0.03
104 9 0.03
105 28 0.08
106 57 0.17
107 98 0.29
108 48 0.14
109 9 0.03
110 4 0.01
111 12 0.04
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (105 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAAATACAAATTTTGAATTTGATTCACT
TGAAACAAAATTAATCTCACTTGAGATTGTTATTTCTTTC
Found at i:5963837 original size:36 final size:36
Alignment explanation
Indices: 5963762--5963920 Score: 167
Period size: 36 Copynumber: 4.4 Consensus size: 36
5963752 TTTTCACATT
* * ** *
5963762 AAACAAAGTTGGTCTCACTTGAGATCGTTTTCTC-GA
1 AAACAAATTTTGTCTCACTTGAGA-CAATTTCTCTAA
* *
5963798 AAACAAACTTTGTCTCACTTGAGGCAATTTCTCTAA
1 AAACAAATTTTGTCTCACTTGAGACAATTTCTCTAA
* *
5963834 AAACAATTTTTGTCTCATTTGAGACAATTTCTCTAA
1 AAACAAATTTTGTCTCACTTGAGACAATTTCTCTAA
* * ** *
5963870 AAATAATTTTTGTCTCGTTTGAGACAATTTCACTAA
1 AAACAAATTTTGTCTCACTTGAGACAATTTCTCTAA
*
5963906 AAACAAATGTTGTCT
1 AAACAAATTTTGTCT
5963921 TAGTGGAGAC
Statistics
Matches: 106, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
35 7 0.07
36 99 0.93
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.37
Consensus pattern (36 bp):
AAACAAATTTTGTCTCACTTGAGACAATTTCTCTAA
Found at i:5963930 original size:36 final size:36
Alignment explanation
Indices: 5963797--5963935 Score: 136
Period size: 36 Copynumber: 3.9 Consensus size: 36
5963787 CGTTTTCTCG
** * * *
5963797 AAAACAAACTTTGTCTCACTTGAGGCAATTTCTCTA
1 AAAACAATTTTTGTCTTAGTTGAGACAATTTCTCTA
* *
5963833 AAAACAATTTTTGTCTCATTTGAGACAATTTCTCTA
1 AAAACAATTTTTGTCTTAGTTGAGACAATTTCTCTA
* * *
5963869 AAAATAATTTTTGTC-TCGTTTGAGACAATTTCACTA
1 AAAACAATTTTTGTCTTAG-TTGAGACAATTTCTCTA
* * * *
5963905 AAAACAAATGTTGTCTTAGTGGAGACCATTT
1 AAAACAATTTTTGTCTTAGTTGAGACAATTT
5963936 TCCAAATTAT
Statistics
Matches: 86, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
36 84 0.98
37 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (36 bp):
AAAACAATTTTTGTCTTAGTTGAGACAATTTCTCTA
Found at i:5964330 original size:31 final size:31
Alignment explanation
Indices: 5964292--5964352 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
5964282 TCGTAAAAAA
* * *
5964292 ATCTTTGAGTTTGTTTCTTTTAAAAAAAATC
1 ATCTTTGAGTCTATTTCTATTAAAAAAAATC
*
5964323 ATCTTTGAGTCTATTTCTATTAAAACAAAT
1 ATCTTTGAGTCTATTTCTATTAAAAAAAAT
5964353 TTTGCCTCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.46
Consensus pattern (31 bp):
ATCTTTGAGTCTATTTCTATTAAAAAAAATC
Found at i:5964680 original size:32 final size:31
Alignment explanation
Indices: 5964620--5964680 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 31
5964610 CCTTGAGGCA
5964620 GTTTCTCTAGAAATACAAAATCTTTGAGTTT
1 GTTTCTCTAGAAATACAAAATCTTTGAGTTT
*
5964651 GTTTCTCTTGAAATA-AAACTATCTTTGAGT
1 GTTTCTCTAGAAATACAAA--ATCTTTGAGT
5964681 CGTTTTCCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 3 0.11
31 14 0.52
32 10 0.37
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (31 bp):
GTTTCTCTAGAAATACAAAATCTTTGAGTTT
Found at i:5964975 original size:32 final size:33
Alignment explanation
Indices: 5964904--5964975 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
5964894 TCCCTTGAAA
*
5964904 CAAAACAAACAAAATCTTTGAGTATGTTTTTCT
1 CAAAACAAACAAAATCTTTGAGTATGTTTCTCT
** * *
5964937 TGAAACAAA-AACATCTTTGAGTTTGTTTCTCT
1 CAAAACAAACAAAATCTTTGAGTATGTTTCTCT
5964969 CAAAACA
1 CAAAACA
5964976 CCGATCTTTG
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
32 25 0.78
33 7 0.22
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.35
Consensus pattern (33 bp):
CAAAACAAACAAAATCTTTGAGTATGTTTCTCT
Found at i:5965182 original size:28 final size:28
Alignment explanation
Indices: 5965112--5965191 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 28
5965102 AACACATCAC
*
5965112 CTTTGAGTTTGTTT-TTCTTGAAACAAAT
1 CTTTGAGTCTGTTTCTT-TTGAAACAAAT
* *
5965140 CTTTGAGTCTTTTTCTTTTGAAACAAGT
1 CTTTGAGTCTGTTTCTTTTGAAACAAAT
* **
5965168 CTTTGAGTCAGTTTCCCTTGAAAC
1 CTTTGAGTCTGTTTCTTTTGAAAC
5965192 TATTATCCCT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 42 0.95
29 2 0.05
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.46
Consensus pattern (28 bp):
CTTTGAGTCTGTTTCTTTTGAAACAAAT
Found at i:5965535 original size:134 final size:133
Alignment explanation
Indices: 5965199--5965554 Score: 471
Period size: 134 Copynumber: 2.7 Consensus size: 133
5965189 AACTATTATC
* * *
5965199 CCTAAAGATGGCC-AGAACTCTTCATCAAGTATGAGCCGTGTCATCCACCGAACAGACCTCCTCA
1 CCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCC-CCGACCAGACCTCCTCA
* * * * ** *
5965263 TCATGTAGGAGCCATGTCAACCATAGATAATCAGTCGTCCTCATCAAGTAGGAACCGTGTTATCG
65 TCACGTAGGAGCCATGTC-ACCCTAGATAACCAGTCGTCCTCATCAAGTAAGAACCAAGTTATCA
*
5965328 TCCTT
129 CCCTT
** * *
5965333 CCTAAAGATGGCCAAGAACTCTTCATTGCGTATGAGCAGTGTCATCCCCCGACTAGACCTCCTTA
1 CCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCAT-CCCCGACCAGACCTCCTCA
* *
5965398 TCACATAGGAGCCATGTCACCCTAGATAACCAGTCGTCCTCATCACGTAAGAACCAAGTTATCAC
65 TCACGTAGGAGCCATGTCACCCTAGATAACCAGTCGTCCTCATCAAGTAAGAACCAAGTTATCAC
5965463 CCTT
130 CCTT
* **
5965467 CCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACCAAATTTCCTCA
1 CCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCC-CGACCAGACCTCCTCA
* *
5965532 TCACGTAGGAACCGTGTCACCCT
65 TCACGTAGGAGCCATGTCACCCT
5965555 TAGACGACCC
Statistics
Matches: 192, Mismatches: 27, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
133 3 0.02
134 130 0.68
135 57 0.30
136 2 0.01
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.24
Consensus pattern (133 bp):
CCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCGACCAGACCTCCTCAT
CACGTAGGAGCCATGTCACCCTAGATAACCAGTCGTCCTCATCAAGTAAGAACCAAGTTATCACC
CTT
Found at i:5965592 original size:43 final size:39
Alignment explanation
Indices: 5965482--5965597 Score: 108
Period size: 43 Copynumber: 2.8 Consensus size: 39
5965472 AGATGGCCAA
5965482 GAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACC
1 GAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACC
* * * * * *
5965521 AAATTTCCTCATCACGTAGGAACCGTGTCA-CCCTTAGACGACCC
1 GAA-CTCTTCATCACGTATGAGCAGTGTCATCCC-T---CGA-CC
*
5965565 GAACTCTTCATCACGTATGAGCAGTGTCGTCCC
1 GAACTCTTCATCACGTATGAGCAGTGTCATCCC
5965598 CAACAATCAA
Statistics
Matches: 57, Mismatches: 13, Indels: 9
0.72 0.16 0.11
Matches are distributed among these distances:
39 5 0.09
40 22 0.39
43 23 0.40
44 7 0.12
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.25
Consensus pattern (39 bp):
GAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACC
Found at i:5965756 original size:3 final size:3
Alignment explanation
Indices: 5965743--5965800 Score: 89
Period size: 3 Copynumber: 18.7 Consensus size: 3
5965733 TTTCTATTTT
*
5965743 TTA TCTA TTA TTA TTA TTA TTA TCA TTA TTA TTTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
5965790 TTA TTA TTA TT
1 TTA TTA TTA TT
5965801 GTTAATAATA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
3 45 0.88
4 6 0.12
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:5966785 original size:10 final size:10
Alignment explanation
Indices: 5966770--5966807 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
5966760 TGGAGAGAAT
5966770 TTTCTCTCTC
1 TTTCTCTCTC
5966780 TTTCTC-C-C
1 TTTCTCTCTC
*
5966788 CTTCTCTCTC
1 TTTCTCTCTC
5966798 TTTCTCTCTC
1 TTTCTCTCTC
5966808 GCAGGCAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
8 6 0.25
9 2 0.08
10 16 0.67
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (10 bp):
TTTCTCTCTC
Found at i:5967660 original size:29 final size:30
Alignment explanation
Indices: 5967619--5967689 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
5967609 CTTTTATTAT
*
5967619 TTTAGTCCCTTAAATTTTTGTTTGTACT-A
1 TTTAGTCCTTTAAATTTTTGTTTGTACTCA
* * *
5967648 TTTAGTCCTTTAAGTTTTTGTTTTTACTCT
1 TTTAGTCCTTTAAATTTTTGTTTGTACTCA
*
5967678 TTTGGTCCTTTA
1 TTTAGTCCTTTA
5967690 GCTTTCTGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 25 0.69
30 11 0.31
ACGTcount: A:0.15, C:0.14, G:0.11, T:0.59
Consensus pattern (30 bp):
TTTAGTCCTTTAAATTTTTGTTTGTACTCA
Found at i:5967688 original size:30 final size:30
Alignment explanation
Indices: 5967573--5967725 Score: 89
Period size: 30 Copynumber: 5.1 Consensus size: 30
5967563 GTCCCCAAGA
* * * *
5967573 TTTTGTTTTTACATTTTTTGGTCCCTAAAGC
1 TTTTGTTTTTAC-TCTTTTGGTCCTTTAAGT
** * * * * * *
5967604 TTCCGCTTTTATTATTTTAGTCCCTTAAAT
1 TTTTGTTTTTACTCTTTTGGTCCTTTAAGT
* * *
5967634 TTTTGTTTGTACT-ATTTAGTCCTTTAAGT
1 TTTTGTTTTTACTCTTTTGGTCCTTTAAGT
5967663 TTTTGTTTTTACTCTTTTGGTCCTTT-AGCT
1 TTTTGTTTTTACTCTTTTGGTCCTTTAAG-T
* *
5967693 TTCTG-TTTTCCTCCTTTTGGTCCTTGTAA-T
1 TTTTGTTTTTACT-CTTTTGGTCCTT-TAAGT
5967723 TTT
1 TTT
5967726 ATTTACTTAT
Statistics
Matches: 94, Mismatches: 23, Indels: 11
0.73 0.18 0.09
Matches are distributed among these distances:
29 33 0.35
30 51 0.54
31 9 0.10
32 1 0.01
ACGTcount: A:0.13, C:0.17, G:0.12, T:0.58
Consensus pattern (30 bp):
TTTTGTTTTTACTCTTTTGGTCCTTTAAGT
Found at i:5968049 original size:17 final size:18
Alignment explanation
Indices: 5968021--5968054 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5968011 GAAATAAATC
*
5968021 AATTTAATTTTACTAATT
1 AATTTAATTTTAATAATT
5968039 AATTT-ATTTTAATAAT
1 AATTTAATTTTAATAAT
5968055 GCAATGTGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTTAATTTTAATAATT
Found at i:5974789 original size:37 final size:37
Alignment explanation
Indices: 5974748--5974821 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
5974738 ACTAAACGTG
* * *
5974748 TAATTTACCCTAAAATCAATTGAAATGTGATATCTTT
1 TAATTTACACTAAAATCAATCGAAACGTGATATCTTT
* *
5974785 TAATTTACACTAAATTCAATCGAAACGTGATCTCTTT
1 TAATTTACACTAAAATCAATCGAAACGTGATATCTTT
5974822 CTTTTTATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.39
Consensus pattern (37 bp):
TAATTTACACTAAAATCAATCGAAACGTGATATCTTT
Found at i:5975997 original size:59 final size:59
Alignment explanation
Indices: 5975905--5976034 Score: 244
Period size: 59 Copynumber: 2.2 Consensus size: 59
5975895 ATGCATTTAA
5975905 ATAGTTGGGTGGCCTGATTGATAAGAATTTAAAAATGATGGTCAAAATAAAAATG-AGCT
1 ATAGTTGGGTGGCCTGATTGATAAGAATTTAAAAATGATGGTCAAAATAAAAA-GAAGCT
5975964 ATAGTTGGGTGGCCTGATTGATAAGAATTTAAAAATGATGGTCAAAATAAAAAGAAGCT
1 ATAGTTGGGTGGCCTGATTGATAAGAATTTAAAAATGATGGTCAAAATAAAAAGAAGCT
5976023 ATAGTTGGGTGG
1 ATAGTTGGGTGG
5976035 TCTTTAGTAT
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
58 1 0.01
59 69 0.99
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.28
Consensus pattern (59 bp):
ATAGTTGGGTGGCCTGATTGATAAGAATTTAAAAATGATGGTCAAAATAAAAAGAAGCT
Found at i:5977109 original size:23 final size:23
Alignment explanation
Indices: 5977083--5977132 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
5977073 ACTTTAAACG
* *
5977083 AACACCTTCACGAACGTTAAAAA
1 AACACATTCACAAACGTTAAAAA
* * *
5977106 AACATATTCACAAATGTTAAATA
1 AACACATTCACAAACGTTAAAAA
5977129 AACA
1 AACA
5977133 TGTTTGCGGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.52, C:0.20, G:0.06, T:0.22
Consensus pattern (23 bp):
AACACATTCACAAACGTTAAAAA
Found at i:5977133 original size:23 final size:23
Alignment explanation
Indices: 5977089--5977133 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5977079 AACGAACACC
*
5977089 TTCACGAACGTTAAAAAAACATA
1 TTCACAAACGTTAAAAAAACATA
* *
5977112 TTCACAAATGTTAAATAAACAT
1 TTCACAAACGTTAAAAAAACAT
5977134 GTTTGCGGAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.51, C:0.16, G:0.07, T:0.27
Consensus pattern (23 bp):
TTCACAAACGTTAAAAAAACATA
Found at i:5977483 original size:43 final size:43
Alignment explanation
Indices: 5977422--5977607 Score: 250
Period size: 43 Copynumber: 4.3 Consensus size: 43
5977412 CCGCTAAAGT
* *
5977422 TAGCGGCGTTTTTGGGACAAAGGCCGCAATAGGTCGAGATCTA
1 TAGCGGCGTTTTTTGGACAAACGCCGCAATAGGTCGAGATCTA
*
5977465 TAGCGACGTTTTTTGGACAAACGCCGCAATAGGTCGAGATCTA
1 TAGCGGCGTTTTTTGGACAAACGCCGCAATAGGTCGAGATCTA
* * * * *
5977508 TAACGGCATTTTTGGGACAAACGCCTCAATAGGTCGAGATTTA
1 TAGCGGCGTTTTTTGGACAAACGCCGCAATAGGTCGAGATCTA
* * *
5977551 TAGCGGCG-TTTTTGGAACAAACGCCACAAAAGGT-TAGATCTA
1 TAGCGGCGTTTTTTGG-ACAAACGCCGCAATAGGTCGAGATCTA
5977593 TAGCGGCGTTTTTTG
1 TAGCGGCGTTTTTTG
5977608 ATACACGCGC
Statistics
Matches: 125, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
42 20 0.16
43 105 0.84
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (43 bp):
TAGCGGCGTTTTTTGGACAAACGCCGCAATAGGTCGAGATCTA
Found at i:5978577 original size:21 final size:20
Alignment explanation
Indices: 5978553--5978595 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
5978543 AGCAAGTAAT
5978553 ATTGATAGTATAAAAAACA-AA
1 ATTGAT-GT-TAAAAAACATAA
*
5978574 ATTGATGTTAAGAAACATAA
1 ATTGATGTTAAAAAACATAA
5978594 AT
1 AT
5978596 AGACTAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 6 0.30
21 6 0.30
ACGTcount: A:0.56, C:0.05, G:0.12, T:0.28
Consensus pattern (20 bp):
ATTGATGTTAAAAAACATAA
Found at i:5981491 original size:81 final size:81
Alignment explanation
Indices: 5981213--5981601 Score: 305
Period size: 83 Copynumber: 4.7 Consensus size: 81
5981203 CACAAGTTTA
*** * * * * *
5981213 TAGCGGCGTTTTTACAAAAACGCCACTATATATCTGGGCTATTGCGGCGTTTTATACATAAACGC
1 TAGCGGCGTTTTTGTGAAAACGCCGCTATATAT-TCGGATATTGCGGCG-TTTGTACAAAAACGC
* *
5981278 CACTAAAGTACATGTTTT
64 CACTAAAGTACGTGATTT
* * * *
5981296 TAGCGACGTTTTATGTGAAAACGCCGCTATATATTCGGATATTGCGGCGTTTTTTACATAAAGGC
1 TAGCGGCGTTTT-TGTGAAAACGCCGCTATATATTCGGATATTGCGGCG-TTTGTACAAAAACGC
*
5981361 CACTAAAGTACG-CATTTT
64 CACTAAAGTACGTGA-TTT
***** * ** * * * *
5981379 TAGCGGCGTTTGCACAAAAATGCCATTATATATTTGGATATCGCGGCGTTTGTCCAAAAACACCA
1 TAGCGGCGTTTTTGTGAAAACGCCGCTATATATTCGGATATTGCGGCGTTTGTACAAAAACGCCA
5981444 CTAAAGTACGTGATTT
66 CTAAAGTACGTGATTT
* * * * *
5981460 TGGCGGCGTTTTTGTGAAAACGTCGCTATATATTCGGATATTGCGGCGTTTTTTTACATAAATGC
1 TAGCGGCGTTTTTGTGAAAACGCCGCTATATATTCGGATATTGCGGCG--TTTGTACAAAAACGC
** *
5981525 CACTAAAGTACACGTTTT
64 CACTAAAGTACGTGATTT
***** * * * *
5981543 TAGCGGCGTTTGCACAAAAACACCACTATATATTTGGATATAGCGGCGTTTGT-CAAAAA
1 TAGCGGCGTTTTTGTGAAAACGCCGCTATATATTCGGATATTGCGGCGTTTGTACAAAAA
5981602 ACGTCGCTAC
Statistics
Matches: 239, Mismatches: 62, Indels: 13
0.76 0.20 0.04
Matches are distributed among these distances:
80 5 0.02
81 65 0.27
82 28 0.12
83 124 0.52
84 17 0.07
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (81 bp):
TAGCGGCGTTTTTGTGAAAACGCCGCTATATATTCGGATATTGCGGCGTTTGTACAAAAACGCCA
CTAAAGTACGTGATTT
Found at i:5981545 original size:164 final size:164
Alignment explanation
Indices: 5981208--5981603 Score: 551
Period size: 164 Copynumber: 2.4 Consensus size: 164
5981198 TATTGCACAA
* ** * * * * * *
5981208 GTTTATAGCGGCGTTTTTACAAAAACGCCACTATATATCTGGGCTATTGCGGCGTTTTATACATA
1 GTTTTTAGCGGCGTTTGCACAAAAACGCCACTATATAT-TTGGATATAGCGGCG-TTTGTCCAAA
* *
5981273 AACGCCACTAAAGTACATGTTTTTAGCGACGTTTTATGTGAAAACGCCGCTATATATTCGGATAT
64 AACACCACTAAAGTACATGATTTTAGCGACGTTTTATGTGAAAACGCCGCTATATATTCGGATAT
*
5981338 TGCGGCGTTTTTTACATAAAGGCCACTAAAGTACGC
129 TGCGGCGTTTTTTACATAAAGGCCACTAAAGTACAC
* * * *
5981374 ATTTTTAGCGGCGTTTGCACAAAAATGCCATTATATATTTGGATATCGCGGCGTTTGTCCAAAAA
1 GTTTTTAGCGGCGTTTGCACAAAAACGCCACTATATATTTGGATATAGCGGCGTTTGTCCAAAAA
* * * *
5981439 CACCACTAAAGTACGTGATTTTGGCGGCGTTTT-TGTGAAAACGTCGCTATATATTCGGATATTG
66 CACCACTAAAGTACATGATTTTAGCGACGTTTTATGTGAAAACGCCGCTATATATTCGGATATTG
*
5981503 CGGCGTTTTTTTACATAAATGCCACTAAAGTACAC
131 CGGCG-TTTTTTACATAAAGGCCACTAAAGTACAC
* *
5981538 GTTTTTAGCGGCGTTTGCACAAAAACACCACTATATATTTGGATATAGCGGCGTTTGTCAAAAAA
1 GTTTTTAGCGGCGTTTGCACAAAAACGCCACTATATATTTGGATATAGCGGCGTTTGTCCAAAAA
5981603 C
66 C
5981604 GTCGCTACAT
Statistics
Matches: 203, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
163 35 0.17
164 124 0.61
165 12 0.06
166 32 0.16
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.33
Consensus pattern (164 bp):
GTTTTTAGCGGCGTTTGCACAAAAACGCCACTATATATTTGGATATAGCGGCGTTTGTCCAAAAA
CACCACTAAAGTACATGATTTTAGCGACGTTTTATGTGAAAACGCCGCTATATATTCGGATATTG
CGGCGTTTTTTACATAAAGGCCACTAAAGTACAC
Found at i:5982589 original size:34 final size:35
Alignment explanation
Indices: 5982543--5982617 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 35
5982533 AATTAATAAA
* *
5982543 TTTAATCGATTAATATTAAAAAAGTGATTCAATTC
1 TTTAATCGATTAATACTAAAAAAGTGATCCAATTC
**
5982578 TTTAAT-GATTAATACTCGAAAAGTGATCCAATTC
1 TTTAATCGATTAATACTAAAAAAGTGATCCAATTC
5982612 TTTAAT
1 TTTAAT
5982618 TTTAACTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 30 0.83
35 6 0.17
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (35 bp):
TTTAATCGATTAATACTAAAAAAGTGATCCAATTC
Found at i:5983361 original size:26 final size:25
Alignment explanation
Indices: 5983330--5983380 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
5983320 TAAACTCGTC
* *
5983330 ATTTTTAGTATTTTTTAGATCTTTTA
1 ATTTTTAATATTTTATAGAT-TTTTA
*
5983356 ATTTTTAATGTTTTATAGATTTTTA
1 ATTTTTAATATTTTATAGATTTTTA
5983381 TTATTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.25, C:0.02, G:0.08, T:0.65
Consensus pattern (25 bp):
ATTTTTAATATTTTATAGATTTTTA
Found at i:5983601 original size:31 final size:31
Alignment explanation
Indices: 5983539--5983601 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
5983529 AACAATGAAT
*
5983539 TGATCATTTTGTTACAAATAGATACTGTTAG
1 TGATCATTTTGTTACAAATAGATACTATTAG
* * *
5983570 TGATCATTTTGTTATAAATCGATTCTATTAG
1 TGATCATTTTGTTACAAATAGATACTATTAG
5983601 T
1 T
5983602 AATCCAATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (31 bp):
TGATCATTTTGTTACAAATAGATACTATTAG
Found at i:5983764 original size:2 final size:2
Alignment explanation
Indices: 5983757--5983789 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
5983747 TGGCATTTTC
*
5983757 AT AT AT AT AT AT AT AT AT AT AT AT -T AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5983790 GAAAATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:5984032 original size:11 final size:11
Alignment explanation
Indices: 5984018--5984070 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
5984008 CAAATTCAAG
5984018 AGCTCGATTGA
1 AGCTCGATTGA
5984029 AGCTCGAAACTTG-
1 AGCTCG--A-TTGA
* *
5984042 AGTTCGATTCA
1 AGCTCGATTGA
5984053 AGCTCGATTGA
1 AGCTCGATTGA
5984064 AGCTCGA
1 AGCTCGA
5984071 AACTCGAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 2 0.06
11 23 0.68
13 6 0.18
14 3 0.09
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (11 bp):
AGCTCGATTGA
Found at i:5984105 original size:35 final size:35
Alignment explanation
Indices: 5984018--5984092 Score: 116
Period size: 35 Copynumber: 2.1 Consensus size: 35
5984008 CAAATTCAAG
* *
5984018 AGCTCGATTGAAGCTCGAAACTTGAGTTCGATTCA
1 AGCTCGATTGAAGCTCGAAACTCGACTTCGATTCA
5984053 AGCTCGATTGAAGCTCGAAACTCGAACTT-GATTCA
1 AGCTCGATTGAAGCTCGAAACTCG-ACTTCGATTCA
5984088 AGCTC
1 AGCTC
5984093 TATTTATGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 34 0.92
36 3 0.08
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (35 bp):
AGCTCGATTGAAGCTCGAAACTCGACTTCGATTCA
Found at i:5984148 original size:11 final size:11
Alignment explanation
Indices: 5984045--5984149 Score: 50
Period size: 11 Copynumber: 9.2 Consensus size: 11
5984035 AAACTTGAGT
5984045 TCGATTCAAGC
1 TCGATTCAAGC
*
5984056 TCGATTGAAGC
1 TCGATTCAAGC
*
5984067 TCGAAACTCGAA-C
1 TCG--ATTC-AAGC
*
5984080 TTGATTCAAGC
1 TCGATTCAAGC
* * *
5984091 TCTATTTATGC
1 TCGATTCAAGC
*
5984102 TCGATTCAAAC
1 TCGATTCAAGC
* *
5984113 TCAAATTTAAGC
1 TC-GATTCAAGC
* **
5984125 TCAATTTTGAGC
1 TCGA-TTCAAGC
5984137 TCGATTCAAGC
1 TCGATTCAAGC
5984148 TC
1 TC
5984150 AAACCACACG
Statistics
Matches: 68, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
10 2 0.03
11 42 0.62
12 17 0.25
13 5 0.07
14 2 0.03
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (11 bp):
TCGATTCAAGC
Found at i:5984762 original size:14 final size:14
Alignment explanation
Indices: 5984742--5984775 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5984732 CAGTAGTATG
5984742 CATTTTAAATTATT
1 CATTTTAAATTATT
* *
5984756 TATTTTAATTTATT
1 CATTTTAAATTATT
5984770 CATTTT
1 CATTTT
5984776 TTTTAGTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (14 bp):
CATTTTAAATTATT
Found at i:5985625 original size:11 final size:11
Alignment explanation
Indices: 5985609--5985671 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
5985599 GTATTATAGA
5985609 ATTTTTAATAT
1 ATTTTTAATAT
5985620 ATTTTTAA-A-
1 ATTTTTAATAT
5985629 ATTTTATAAT-T
1 ATTTT-TAATAT
*** *
5985640 ATCAATAATGT
1 ATTTTTAATAT
5985651 ATTTTTAATAT
1 ATTTTTAATAT
5985662 ATTTTTAATA
1 ATTTTTAATA
5985672 ATGTAATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 28 0.68
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:5987663 original size:6 final size:6
Alignment explanation
Indices: 5987652--5987688 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
5987642 ATTTGCAAAC
5987652 CTAAAT CTAAAT CTAAAT CTAAAT CTAAAT CTAAAT C
1 CTAAAT CTAAAT CTAAAT CTAAAT CTAAAT CTAAAT C
5987689 CTCTCATTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (6 bp):
CTAAAT
Found at i:5993255 original size:199 final size:199
Alignment explanation
Indices: 5992873--5993429 Score: 633
Period size: 199 Copynumber: 2.8 Consensus size: 199
5992863 AGTCAAACTT
* * ** ** **
5992873 GGTCTTCTTCTTGAC-TAAAGACTTCGGTTTGAAAATTTGACCAGAAAGTAGTTCCTTACTGTTA
1 GGTCTTCTTCTTGACTTAAAGACCTCAGTTT--AAATTCAAATAGAAAGTAGTTCCTCGCTGTTA
* * ** * ** *
5992937 CTACGCGGTTGATATGCCTTCGAGCTGAATGAAATTGAACTCAAAAGTTTTTGTTGACAGATAAC
64 CCATGCGGTTGATACACCCTCGAGCTGAATGAAATCAAACTCGAAAGTTTTTGTTGACAGATAAC
* * *
5993002 CCTTCT-GTCCTTGAGCTATGTCATAGATTAGGCTAAGAGATAATTCCTTATTGCTAAATCACAA
129 CCTTCTCG-CCTTGAGCTATAT-GTAAATTAGGCTAAGAGATAATTCCTTATTGCTAAATCACAA
5993066 CCAACCTA
192 CCAACCTA
* * * *
5993074 GGTCTTCTTCTTGAGTTAAAGACCTCGGTTT-ACTTC-AATAAGAAAGTAGTTCCTCGCTATTAC
1 GGTCTTCTTCTTGACTTAAAGACCTCAGTTTAAATTCAAAT-AGAAAGTAGTTCCTCGCTGTTAC
* *
5993137 CATGCGGTTGATACACCCTCGAGCTGAATGAAATCAAACTCGAAAGTTTTTATTAACAGATAACC
65 CATGCGGTTGATACACCCTCGAGCTGAATGAAATCAAACTCGAAAGTTTTTGTTGACAGATAACC
* ** *
5993202 CTTCTCGCCTTGAGCTATAATGTAAATTCA-GTTGGGAGATAGTTCCTTATTGCTAAATCACAAC
130 CTTCTCGCCTTGAGCTAT-ATGTAAATT-AGGCTAAGAGATAATTCCTTATTGCTAAATCACAAC
5993266 CAACCTA
193 CAACCTA
* * * *
5993273 GGTCTTCTTCTTGACTTAAAGACCTCAGTTTAAAATTCAAATGGTAAGTAGTTACTCGCTGCTAC
1 GGTCTTCTTCTTGACTTAAAGACCTCAGTTT-AAATTCAAATAGAAAGTAGTTCCTCGCTGTTAC
* *
5993338 CATGCGGTTGATACACCCTCGATCTGAAT-AGAATCAAACAT-GAAAGTTTTCGTTGACAGATAA
65 CATGCGGTTGATACACCCTCGAGCTGAATGA-AATCAAAC-TCGAAAGTTTTTGTTGACAGATAA
* *
5993401 CCCTTCTCGCTTTGAGCTATGCTGTAAAT
128 CCCTTCTCGCCTTGAGCTAT-ATGTAAAT
5993430 GGTTCCTTTA
Statistics
Matches: 305, Mismatches: 41, Indels: 20
0.83 0.11 0.05
Matches are distributed among these distances:
198 1 0.00
199 165 0.54
200 4 0.01
201 117 0.38
202 18 0.06
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.32
Consensus pattern (199 bp):
GGTCTTCTTCTTGACTTAAAGACCTCAGTTTAAATTCAAATAGAAAGTAGTTCCTCGCTGTTACC
ATGCGGTTGATACACCCTCGAGCTGAATGAAATCAAACTCGAAAGTTTTTGTTGACAGATAACCC
TTCTCGCCTTGAGCTATATGTAAATTAGGCTAAGAGATAATTCCTTATTGCTAAATCACAACCAA
CCTA
Found at i:5997293 original size:13 final size:13
Alignment explanation
Indices: 5997275--5997299 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5997265 AACATATATT
5997275 ATATTTTTAAAAA
1 ATATTTTTAAAAA
5997288 ATATTTTTAAAA
1 ATATTTTTAAAA
5997300 CTATATACTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATTTTTAAAAA
Found at i:5997427 original size:35 final size:35
Alignment explanation
Indices: 5997268--5997639 Score: 320
Period size: 35 Copynumber: 10.3 Consensus size: 35
5997258 ACCATATAAC
* * *
5997268 ATATATTATAT-TTTTAAAAAATATTTTTAAAACT
1 ATATATTATATGTTTTTAAAAATGTTTTCAAAACT
* * * ****
5997302 ATATACTATATGTTTTCAAATAT-TAAAAAAGAACT
1 ATATATTATATGTTTTTAAAAATGTTTTCAA-AACT
* *
5997337 ATATATTATATGTTTTCAAAAATACATTTTCAAAAACT
1 ATATATTATATGTTTTTAAAAAT--GTTTTC-AAAACT
* * *
5997375 ATATTATATATATGTTTTTTAAAACGTTTTCAAAACC
1 ATA-TAT-TATATGTTTTTAAAAATGTTTTCAAAACT
* *
5997412 ATATATTATATGTTTTCAAAAATATTTTCAAAACT
1 ATATATTATATGTTTTTAAAAATGTTTTCAAAACT
* *
5997447 ATATATTATATACGTTTTT-AAAATGTTTTTAAAACC
1 ATATATTATAT--GTTTTTAAAAATGTTTTCAAAACT
* **
5997483 AAATATTATGCGTTTTTAAAAATGTTTTCAAAACT
1 ATATATTATATGTTTTTAAAAATGTTTTCAAAACT
*
5997518 ATATATTATATACATTTTT-AAAATGTTTTCCAAAACT
1 ATATATTATAT--GTTTTTAAAAATGTTTT-CAAAACT
* * *
5997555 ATATATTATATATTTTCAACAAACGTTTTCAAAACT
1 ATATATTATATGTTTTTAA-AAATGTTTTCAAAACT
* *
5997591 ATATATTATATATATTTTCAAAAAATGTTTTCAAAATT
1 ATATATTATATGT-TTTT--AAAAATGTTTTCAAAACT
*
5997629 ATTTATTATAT
1 ATATATTATAT
5997640 ATGTTATCGA
Statistics
Matches: 277, Mismatches: 42, Indels: 34
0.78 0.12 0.10
Matches are distributed among these distances:
34 19 0.07
35 97 0.35
36 56 0.20
37 47 0.17
38 37 0.13
39 7 0.03
40 14 0.05
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (35 bp):
ATATATTATATGTTTTTAAAAATGTTTTCAAAACT
Found at i:5997481 original size:36 final size:36
Alignment explanation
Indices: 5997333--5997640 Score: 265
Period size: 37 Copynumber: 8.4 Consensus size: 36
5997323 ATTAAAAAAG
* *
5997333 AACTATATATTATAT--GTTTTCAAAAATACATTTTCAAA
1 AACTATATATTATATACGTTTT-TAAAAT--GTTTTC-AA
* *
5997371 AACTATAT-TATATATATGTTTTTTAAAACGTTTTCAA
1 AACTATATAT-TATATACG-TTTTTAAAATGTTTTCAA
* * *
5997408 AACCATATATTATAT--GTTTTCAAAAATATTTTCAA
1 AACTATATATTATATACGTTTT-TAAAATGTTTTCAA
*
5997443 AACTATATATTATATACGTTTTTAAAATGTTTTTAA
1 AACTATATATTATATACGTTTTTAAAATGTTTTCAA
* * *
5997479 AACCAAATA-T-TATGCGTTTTTAAAAATGTTTTCAA
1 AACTATATATTATATACGTTTTT-AAAATGTTTTCAA
*
5997514 AACTATATATTATATACATTTTTAAAATGTTTTCCAA
1 AACTATATATTATATACGTTTTTAAAATGTTTT-CAA
* *
5997551 AACTATATATTATATA--TTTTCAACAAACGTTTTCAA
1 AACTATATATTATATACGTTTT-TA-AAATGTTTTCAA
** *
5997587 AACTATATATTATATATATTTTCAAAAAATGTTTTCAA
1 AACTATATATTATATACGTTTT--TAAAATGTTTTCAA
* *
5997625 AATTATTTATTATATA
1 AACTATATATTATATA
5997641 TGTTATCGAA
Statistics
Matches: 228, Mismatches: 25, Indels: 34
0.79 0.09 0.12
Matches are distributed among these distances:
34 14 0.06
35 50 0.22
36 49 0.21
37 56 0.25
38 48 0.21
39 2 0.01
40 5 0.02
41 4 0.02
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (36 bp):
AACTATATATTATATACGTTTTTAAAATGTTTTCAA
Found at i:5997489 original size:71 final size:71
Alignment explanation
Indices: 5997267--5997626 Score: 361
Period size: 71 Copynumber: 5.0 Consensus size: 71
5997257 AACCATATAA
* * * * **
5997267 CATATATTATAT-TTTTAAAAAATATTTTTAAAACTATATACTATAT--GTTTTCAAATAT-TAA
1 CATATATTATATGTTTTCAAAAATATTTTCAAAACTATATATTATATACGTTTTTAAA-ATGTTT
**
5997328 AAAAGAAC
65 TCAA-AAC
* * *
5997336 TATATATTATATGTTTTCAAAAATACATTTTCAAAAACTATAT-TATATATATGTTTTTTAAAAC
1 CATATATTATATGTTTTCAAAAAT--ATTTTC-AAAACTATATAT-TATATACG-TTTTTAAAAT
5997400 GTTTTCAAAAC
61 GTTTTCAAAAC
5997411 CATATATTATATGTTTTCAAAAATATTTTCAAAACTATATATTATATACGTTTTTAAAATGTTTT
1 CATATATTATATGTTTTCAAAAATATTTTCAAAACTATATATTATATACGTTTTTAAAATGTTTT
*
5997476 TAAAAC
66 CAAAAC
* ** * * *
5997482 CAAATATTATGCGTTTTTAAAAATGTTTTCAAAACTATATATTATATACATTTTTAAAATGTTTT
1 CATATATTATATGTTTTCAAAAATATTTTCAAAACTATATATTATATACGTTTTTAAAATGTTTT
5997547 CCAAAAC
66 -CAAAAC
* * ** ** *
5997554 TATATATTATATATTTTCAACAAACGTTTTCAAAACTATATATTATATATATTTTCAAAAAATGT
1 CATATATTATATGTTTTCAA-AAATATTTTCAAAACTATATATTATATACGTTTT--TAAAATGT
5997619 TTTCAAAA
63 TTTCAAAA
5997627 TTATTTATTA
Statistics
Matches: 247, Mismatches: 30, Indels: 23
0.82 0.10 0.08
Matches are distributed among these distances:
69 11 0.04
70 10 0.04
71 78 0.32
72 41 0.17
73 54 0.22
74 5 0.02
75 38 0.15
76 10 0.04
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (71 bp):
CATATATTATATGTTTTCAAAAATATTTTCAAAACTATATATTATATACGTTTTTAAAATGTTTT
CAAAAC
Found at i:5997680 original size:41 final size:37
Alignment explanation
Indices: 5997333--5997682 Score: 137
Period size: 35 Copynumber: 9.5 Consensus size: 37
5997323 ATTAAAAAAG
* *
5997333 AACTATA-TAT-TATATGTTTTCAAAAATACATTTTCAAA
1 AACTATATTATATATATATTTTCAAAAA-ATATTTTC--A
* ** **
5997371 AACTATATTATATATATGTTTT-TTAAAACGTTTTCAA
1 AACTATATTATATATATATTTTCAAAAAATATTTTC-A
* *
5997408 AACCATA-TAT-TATATGTTTTC-AAAAATATTTTCAA
1 AACTATATTATATATATATTTTCAAAAAATATTTTC-A
* ** *
5997443 AACTATA-TAT-TATATACGTTTTTAAAATGT-TTTTAA
1 AACTATATTATATATATA--TTTTCAAAAAATATTTTCA
* * *** * *
5997479 AACCA-AATAT-TATGCGTTTT-TAAAAATGTTTTCAA
1 AACTATATTATATATATATTTTCAAAAAATATTTTC-A
* * *
5997514 AACTATA-TATTATATACATTTT--TAAAATGTTTTCCAA
1 AACTATATTA-TATATATATTTTCAAAAAATATTTT-C-A
* **
5997551 AACTATA-TAT-TATATATTTTCAACAAACGTTTTCAA
1 AACTATATTATATATATATTTTCAAAAAATATTTTC-A
*
5997587 AACTATA-TATTATATATATTTTCAAAAAATGTTTTCA
1 AACTATATTA-TATATATATTTTCAAAAAATATTTTCA
* *
5997624 AAAT-TATT-TATTATATATGTTATCGAAAAAAATATTTTTA
1 AACTATATTATA-TATATAT-TT-TC--AAAAAATATTTTCA
5997664 AACTATATTATATATATAT
1 AACTATATTATATATATAT
5997683 ATATACTAAA
Statistics
Matches: 252, Mismatches: 35, Indels: 47
0.75 0.10 0.14
Matches are distributed among these distances:
33 4 0.02
34 8 0.03
35 54 0.21
36 48 0.19
37 52 0.21
38 42 0.17
39 6 0.02
40 25 0.10
41 11 0.04
42 2 0.01
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (37 bp):
AACTATATTATATATATATTTTCAAAAAATATTTTCA
Found at i:6002535 original size:28 final size:28
Alignment explanation
Indices: 6002495--6002549 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
6002485 AAAATTTTGA
6002495 AGTCTTGTTGATGTTAGATAATCCATGG
1 AGTCTTGTTGATGTTAGATAATCCATGG
6002523 AGTCTTGTTGATGTTAGATAATCCATG
1 AGTCTTGTTGATGTTAGATAATCCATG
6002550 ATCAAATGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.11, G:0.24, T:0.40
Consensus pattern (28 bp):
AGTCTTGTTGATGTTAGATAATCCATGG
Found at i:6004725 original size:69 final size:69
Alignment explanation
Indices: 6004614--6004888 Score: 518
Period size: 69 Copynumber: 4.0 Consensus size: 69
6004604 CTGCTAAGAA
* *
6004614 AGTAAGATGCTAATGCGACAGAAAAAGTACTTGATACACACTAATCAAATTTGAGAGAGAAATTA
1 AGTAAGATGCTAATGTGACAGAAAAAGTACTTGATACACACTAATCAAATTTGAGAGACAAATTA
6004679 TTTC
66 TTTC
6004683 AGTAAGATGCTAATGTGACAGAAAAAGTACTTGATACACACTAATCAAATTTGAGAG--AAATTA
1 AGTAAGATGCTAATGTGACAGAAAAAGTACTTGATACACACTAATCAAATTTGAGAGACAAATTA
6004746 TTTC
66 TTTC
6004750 AGTAAGATGCTAATGTGACAGAAAAAGTACTTGATACACACTAATCAAATTTGAGAGACAAATTA
1 AGTAAGATGCTAATGTGACAGAAAAAGTACTTGATACACACTAATCAAATTTGAGAGACAAATTA
6004815 TTTC
66 TTTC
6004819 AGTAAGATGCTAATGTGACAGAAAAAGTACTTGATACACACTAATCAAATTTGAGAGACAAATTA
1 AGTAAGATGCTAATGTGACAGAAAAAGTACTTGATACACACTAATCAAATTTGAGAGACAAATTA
6004884 TTTC
66 TTTC
6004888 A
1 A
6004889 CAGAAAACGG
Statistics
Matches: 203, Mismatches: 1, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
67 67 0.33
69 136 0.67
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (69 bp):
AGTAAGATGCTAATGTGACAGAAAAAGTACTTGATACACACTAATCAAATTTGAGAGACAAATTA
TTTC
Found at i:6004858 original size:136 final size:137
Alignment explanation
Indices: 6004614--6004888 Score: 516
Period size: 136 Copynumber: 2.0 Consensus size: 137
6004604 CTGCTAAGAA
*
6004614 AGTAAGATGCTAATGCGACAGAAAAAGTACTTGATACACACTAATCAAATTTGAGAGAGAAATTA
1 AGTAAGATGCTAATGCGACAGAAAAAGTACTTGATACACACTAATCAAATTTGAGAGACAAATTA
6004679 TTTCAGTAAGATGCTAATGTGACAGAAAAAGTACTTGATACACACTAATCAAATTTGAGAG-AAA
66 TTTCAGTAAGATGCTAATGTGACAGAAAAAGTACTTGATACACACTAATCAAATTTGAGAGAAAA
6004743 TTATTTC
131 TTATTTC
*
6004750 AGTAAGATGCTAATGTGACAGAAAAAGTACTTGATACACACTAATCAAATTTGAGAGACAAATTA
1 AGTAAGATGCTAATGCGACAGAAAAAGTACTTGATACACACTAATCAAATTTGAGAGACAAATTA
6004815 TTTCAGTAAGATGCTAATGTGACAGAAAAAGTACTTGATACACACTAATCAAATTTGAGAGACAA
66 TTTCAGTAAGATGCTAATGTGACAGAAAAAGTACTTGATACACACTAATCAAATTTGAGAGA-AA
6004880 ATTATTTC
130 ATTATTTC
6004888 A
1 A
6004889 CAGAAAACGG
Statistics
Matches: 135, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
136 124 0.92
138 11 0.08
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (137 bp):
AGTAAGATGCTAATGCGACAGAAAAAGTACTTGATACACACTAATCAAATTTGAGAGACAAATTA
TTTCAGTAAGATGCTAATGTGACAGAAAAAGTACTTGATACACACTAATCAAATTTGAGAGAAAA
TTATTTC
Found at i:6005950 original size:124 final size:124
Alignment explanation
Indices: 6005793--6006027 Score: 434
Period size: 124 Copynumber: 1.9 Consensus size: 124
6005783 AATAACCTGT
6005793 AAGGCTCAAAACCCAAAAGCCCACTACATATTTATTTATTTGTAAAATGACCTGTTACAATATTC
1 AAGGCTCAAAACCCAAAAGCCCACTACATATTTATTTATTTGTAAAATGACCTGTTACAATATTC
*
6005858 CCTCACCCGAAACAATCTTTAACCTCAACGATTAAAATAGAAAATAGAAGGAGAAGAAG
66 CCTCACCCGAAACAATCCTTAACCTCAACGATTAAAATAGAAAATAGAAGGAGAAGAAG
*
6005917 AAGGCTCAAAACTCAAAAGCCCACTACATATTTATTTATTTGTAAAATGACCTGTTACAATATTC
1 AAGGCTCAAAACCCAAAAGCCCACTACATATTTATTTATTTGTAAAATGACCTGTTACAATATTC
* *
6005982 CTTCGCCCGAAACAATCCTTAACCTCAACGATTAAAATAGAAAATA
66 CCTCACCCGAAACAATCCTTAACCTCAACGATTAAAATAGAAAATA
6006028 TAAATTATAT
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
124 107 1.00
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.26
Consensus pattern (124 bp):
AAGGCTCAAAACCCAAAAGCCCACTACATATTTATTTATTTGTAAAATGACCTGTTACAATATTC
CCTCACCCGAAACAATCCTTAACCTCAACGATTAAAATAGAAAATAGAAGGAGAAGAAG
Found at i:6006056 original size:7 final size:7
Alignment explanation
Indices: 6006046--6006114 Score: 61
Period size: 7 Copynumber: 9.9 Consensus size: 7
6006036 ATACTATAGT
6006046 TAGAAAA
1 TAGAAAA
*
6006053 TAGAAAG
1 TAGAAAA
*
6006060 TAGAAGA
1 TAGAAAA
*
6006067 -AGAATA
1 TAGAAAA
6006073 -AGAAGAA
1 TAGAA-AA
* *
6006080 GAAGAAGA
1 -TAGAAAA
6006088 TAGAAAA
1 TAGAAAA
6006095 TAGAAAA
1 TAGAAAA
6006102 TAGAAAA
1 TAGAAAA
6006109 TAGAAA
1 TAGAAA
6006115 TTATATACTA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
6 9 0.18
7 37 0.73
8 1 0.02
9 4 0.08
ACGTcount: A:0.67, C:0.00, G:0.22, T:0.12
Consensus pattern (7 bp):
TAGAAAA
Found at i:6006149 original size:3 final size:3
Alignment explanation
Indices: 6006137--6006208 Score: 135
Period size: 3 Copynumber: 23.7 Consensus size: 3
6006127 GCTAGAAAAT
6006137 AGA AGAA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
6006183 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
6006209 CCAAACAATT
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 65 0.96
4 3 0.04
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:6006159 original size:83 final size:82
Alignment explanation
Indices: 6006015--6006174 Score: 259
Period size: 83 Copynumber: 1.9 Consensus size: 82
6006005 CTCAACGATT
* * * *
6006015 AAAATAGAAAATATAAATTATATACTATAGTTAGAAAATAGAAAGTAGAAGAAGAATAAGAAGAA
1 AAAATAGAAAATAGAAATTATATACTATAGCTAGAAAATAGAAAGAAGAAGAAGAAGAAGAAGAA
6006080 GAAGAAGATAGAAAATAG
66 GAAGAAGA-AGAAAATAG
6006098 AAAATAGAAAATAGAAATTATATACTATAGCTAGAAAATAG-AAGAAAGAAGAAGAAGAAGAAGA
1 AAAATAGAAAATAGAAATTATATACTATAGCTAGAAAATAGAAAG-AAGAAGAAGAAGAAGAAGA
6006162 AGAAGAAGAAGAA
65 AGAAGAAGAAGAA
6006175 GAAGAAGAAG
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
82 7 0.10
83 65 0.90
ACGTcount: A:0.62, C:0.02, G:0.19, T:0.16
Consensus pattern (82 bp):
AAAATAGAAAATAGAAATTATATACTATAGCTAGAAAATAGAAAGAAGAAGAAGAAGAAGAAGAA
GAAGAAGAAGAAAATAG
Found at i:6006318 original size:3 final size:3
Alignment explanation
Indices: 6006310--6006907 Score: 699
Period size: 3 Copynumber: 201.7 Consensus size: 3
6006300 CTATATATTT
6006310 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* ** **
6006358 AGA AG- AGA AGA AGA AG- AGA AG- AGA AGAA AGA AGA AGGC CCA CTA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA A-GA AGA AGA
6006402 TAGA AGA AGA AGA AGA AGA AGA A-A GAGA AGA AGA AG- AGA AGA AGA
1 -AGA AGA AGA AGA AGA AGA AGA AGA -AGA AGA AGA AGA AGA AGA AGA
* * * *
6006447 AGA AGG AGA AGA AGA AGA AGA AGA AGG AG- AGA AGA AGG AG- AGG AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
6006493 AGA AG- AGA AGA AGG AGA AGA AGA AG- AGA AGA AG- AGA AGA AGA GAGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA -AGA
* * *
6006539 AGA AGG AGA AGA AGG AGA AGA AGA AGA AGG AGA AGA AG- AGA AGA AG-
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * * * *
6006585 AGA AGG AGA AGA AGA AGA AGA AGG AGA AGA AGG AGA AGA AGG AGA AGG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * *
6006633 AGA AGA AGAA AGG AGA AGA AG- AGA GAGA AGA AG- AGG AGA AGA AGG
1 AGA AGA AG-A AGA AGA AGA AGA AGA -AGA AGA AGA AGA AGA AGA AGA
* * * * * *
6006678 AGA AGG AGG AGA AG- AGA AGG AGG AGA AG- AGG AGA AGA GAGA AGG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA -AGA AGA
* *
6006722 AGA AGA A-A GAGA AGA AGA AGG AGA AGA AGA AGA AGG AGA AGA AGA
1 AGA AGA AGA -AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* *
6006767 AGA AGG AGA AGA AGA AGG AGA AGA AGA AGA AGAA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA AGA
*
6006813 AGA AGA AGA AGA AGA AGG AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
6006861 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
6006908 CCGAACAATT
Statistics
Matches: 516, Mismatches: 52, Indels: 54
0.83 0.08 0.09
Matches are distributed among these distances:
2 32 0.06
3 462 0.90
4 22 0.04
ACGTcount: A:0.60, C:0.01, G:0.39, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:6007086 original size:7 final size:7
Alignment explanation
Indices: 6007074--6007118 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
6007064 CTCAAGGATT
6007074 AAAATAG
1 AAAATAG
6007081 AAAATAG
1 AAAATAG
6007088 AAAATAG
1 AAAATAG
*
6007095 GAAATAG
1 AAAATAG
6007102 AAAATAG
1 AAAATAG
6007109 AAAATAG
1 AAAATAG
6007116 AAA
1 AAA
6007119 TTATATACTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (7 bp):
AAAATAG
Found at i:6007931 original size:21 final size:21
Alignment explanation
Indices: 6007905--6007967 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
6007895 ATATAAAATT
* *
6007905 TGTCCCAAAAGACCTCATGTA
1 TGTCCCGAAAGACCTCATATA
*
6007926 TGTCCCGAATGACCTCATATA
1 TGTCCCGAAAGACCTCATATA
* *
6007947 TATCCCGAAGGACCTCATATA
1 TGTCCCGAAAGACCTCATATA
6007968 ACCCTCGACT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25
Consensus pattern (21 bp):
TGTCCCGAAAGACCTCATATA
Found at i:6015820 original size:19 final size:19
Alignment explanation
Indices: 6015760--6015820 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
6015750 TTTGTGCAGA
* *
6015760 GGGAATCGATACCCTCATG
1 GGGAATCGATACCCCCCTG
* *
6015779 AGGGAACCGAT-TCCCCCTAG
1 -GGGAATCGATACCCCCCT-G
6015799 GGGAATCGATACCCCCCTG
1 GGGAATCGATACCCCCCTG
6015818 GGG
1 GGG
6015821 TTCTGGATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.23, C:0.31, G:0.30, T:0.16
Consensus pattern (19 bp):
GGGAATCGATACCCCCCTG
Found at i:6020923 original size:12 final size:12
Alignment explanation
Indices: 6020908--6020980 Score: 64
Period size: 12 Copynumber: 6.3 Consensus size: 12
6020898 TTAATTTTAT
6020908 TTATTATAAATA
1 TTATTATAAATA
6020920 TTATTATAAATA
1 TTATTATAAATA
*
6020932 TTA-TAT-TATA
1 TTATTATAAATA
*
6020942 TT-TTATATATTA
1 TTATTATA-AATA
*
6020954 TTATTATTAATA
1 TTATTATAAATA
* *
6020966 ATATAATAAAT-
1 TTATTATAAATA
6020977 TTAT
1 TTAT
6020981 ATTACAGGCC
Statistics
Matches: 48, Mismatches: 9, Indels: 9
0.73 0.14 0.14
Matches are distributed among these distances:
10 8 0.17
11 6 0.12
12 30 0.62
13 4 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTATTATAAATA
Found at i:6022351 original size:2 final size:2
Alignment explanation
Indices: 6022344--6022382 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
6022334 CTTTAATTAT
6022344 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6022383 TTGTTTAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6022639 original size:2 final size:2
Alignment explanation
Indices: 6022627--6022663 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
6022617 ATATCTTATT
*
6022627 TA TA AA TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6022664 TTTTCTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:6022681 original size:142 final size:137
Alignment explanation
Indices: 6022343--6022681 Score: 359
Period size: 142 Copynumber: 2.4 Consensus size: 137
6022333 ACTTTAATTA
* * * * *
6022343 TTATATATATATATATATATATATATATATATATATATATTTGTTT-AAATAATA-ATATTTATT
1 TTATAAATATATATATATATATATATATAT-TA-ATATATTTTTTTAAAATTATATTTATTTATG
* *
6022406 TTTTTATATTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTCATTTTCTGATATTCTTAAATAA
64 TTTTAATATTAAGAAATGGGCTGTCTTAAAACACCTAGAAGTCATTTTCTGATATTCTTAAATAA
6022471 ATAAATATC
129 ATAAATATC
* * * *
6022480 CTATAAAT-TATATATAT-TAT-TTTATTTTAAT-TATTTTTATAGAAATGTTTTATTAATATTT
1 TTATAAATATATATATATATATATATATATTAATATATTTTT-T-TAAA------ATT-ATATTT
*
6022541 ATTTATGTTTTAATATTAAGAAATGGGCTGTCTTAAAACACCTAGAAGTCTTTTTCTGATATT-T
57 ATTTATGTTTTAATATTAAGAAATGGGCTGTCTTAAAACACCTAGAAGTCATTTTCTGATATTCT
*
6022605 CTAAGTAAATAAATATC
122 -TAAATAAATAAATATC
6022622 TTATTTATAAATATATATATATATATATATATATTAATATATTTTTCTTAAAATTATATT
1 ----TTATAAATATATATATATATATATATATATTAATATATTTTT-TTAAAATTATATT
6022682 AATAAATTTA
Statistics
Matches: 164, Mismatches: 18, Indels: 35
0.76 0.08 0.16
Matches are distributed among these distances:
131 6 0.04
132 3 0.02
133 2 0.01
134 7 0.04
135 3 0.02
136 9 0.05
137 6 0.04
140 2 0.01
141 4 0.02
142 80 0.49
143 3 0.02
146 7 0.04
147 9 0.05
148 3 0.02
149 12 0.07
150 8 0.05
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.49
Consensus pattern (137 bp):
TTATAAATATATATATATATATATATATATTAATATATTTTTTTAAAATTATATTTATTTATGTT
TTAATATTAAGAAATGGGCTGTCTTAAAACACCTAGAAGTCATTTTCTGATATTCTTAAATAAAT
AAATATC
Found at i:6023177 original size:29 final size:28
Alignment explanation
Indices: 6023135--6023226 Score: 78
Period size: 28 Copynumber: 3.2 Consensus size: 28
6023125 AAAAATTCAT
* *
6023135 ATATTTAATTTATAATTCTTTATTTTCAAA
1 ATATTT-ATATATAATT-ATTATTTTCAAA
* * *
6023165 ATTTTTATATATACTTATTATTTTCATA
1 ATATTTATATATAATTATTATTTTCAAA
* **
6023193 ATATTTATATGTATATTATT-TTTTCTTA
1 ATATTTATATATA-ATTATTATTTTCAAA
6023221 ATATTT
1 ATATTT
6023227 TTATTTTATT
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
28 34 0.65
29 13 0.25
30 5 0.10
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (28 bp):
ATATTTATATATAATTATTATTTTCAAA
Found at i:6023209 original size:26 final size:27
Alignment explanation
Indices: 6023142--6023214 Score: 80
Period size: 28 Copynumber: 2.8 Consensus size: 27
6023132 CATATATTTA
*
6023142 ATTTATA-ATTCT-TTATTTTCAAAAT
1 ATTTATATATACTATTATTTTCAAAAT
* *
6023167 TTTTATATATACTTATTATTTTCATAAT
1 ATTTATATATAC-TATTATTTTCAAAAT
*
6023195 ATTTATATGTA-TATTATTTT
1 ATTTATATATACTATTATTTT
6023215 TTCTTAATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
25 6 0.15
26 12 0.30
27 1 0.03
28 21 0.52
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.60
Consensus pattern (27 bp):
ATTTATATATACTATTATTTTCAAAAT
Found at i:6023216 original size:28 final size:30
Alignment explanation
Indices: 6023154--6023226 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 30
6023144 TTATAATTCT
*
6023154 TTATTTTCA-AA-ATTTTTATATATACTTA
1 TTATTTTCATAATATTTATATATATACTTA
*
6023182 TTATTTTCATAATATTTATATGTATA-TTA
1 TTATTTTCATAATATTTATATATATACTTA
*
6023211 TT-TTTTCTTAATATTT
1 TTATTTTCATAATATTT
6023227 TTATTTTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
28 22 0.55
29 7 0.17
30 11 0.28
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (30 bp):
TTATTTTCATAATATTTATATATATACTTA
Found at i:6028711 original size:12 final size:12
Alignment explanation
Indices: 6028694--6028723 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
6028684 CAGAACAAGC
6028694 AAAAGCAAAGGG
1 AAAAGCAAAGGG
6028706 AAAAGCAAAGGG
1 AAAAGCAAAGGG
6028718 AAAAGC
1 AAAAGC
6028724 TACAGTGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.60, C:0.10, G:0.30, T:0.00
Consensus pattern (12 bp):
AAAAGCAAAGGG
Found at i:6036928 original size:113 final size:113
Alignment explanation
Indices: 6036601--6037276 Score: 864
Period size: 114 Copynumber: 6.0 Consensus size: 113
6036591 TAGTAAAGAT
* ** *
6036601 TCGAATCCATCACTCAATGGAT-ACACA-TGCCAGGTAGAGTTCATAATGAGAAGAACCCATCTG
1 TCGAATTCATCACTTGATGGATCA-ACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTG
6036664 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
**
6036713 TCGAATTCATCACTCAATGGATCAACA-TGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCGAATTCATCACTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
* *
6036777 AGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* *
6036825 TCGAATTCATCACTTGATGGATCAACATTGCCAGGTAGAGTTCGTAATGAAAAGAACTCATCTGA
1 TCGAATTCATCACTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
* * * *
6036890 AGAAGGAAGAAAAAATTCATAATGAGAAGAATTTGTTCAAACCTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC-AACCTTTTGC
* ** *
6036939 TTGAATTCATCACTTGATGGATCAACATTGCCAGAAAGAGTTCATAATGAGAAGAAATCATCTGA
1 TCGAATTCATCACTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
* * * *
6037004 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACTTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC-AACCTTTTGC
* * * * * *
6037053 TTGAATTCATCATTTGATGGATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTTATCTG
1 TCGAATTCATCACTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTG
*
6037117 AAG-AGGAAAAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * *** * * * *
6037165 AT-GACTCTATCATAGAAGGAGATAGATCAACATTTCCA-GAAGTGTTCATAATGAGAAGAACTC
1 -TCGA--AT-TCAT--CACTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTC
6037228 ATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
60 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
6037277 GCCTTAATTA
Statistics
Matches: 507, Mismatches: 45, Indels: 20
0.89 0.08 0.03
Matches are distributed among these distances:
112 141 0.28
113 103 0.20
114 174 0.34
115 5 0.01
116 64 0.13
117 20 0.04
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (113 bp):
TCGAATTCATCACTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:6037031 original size:24 final size:23
Alignment explanation
Indices: 6036988--6037032 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
6036978 GTTCATAATG
*
6036988 AGAAGAAATCATCTGAAGAAGGA
1 AGAAGAAATCATATGAAGAAGGA
6037011 AGAAGAAATTCATAATG-AGAAG
1 AGAAGAAA-TCAT-ATGAAGAAG
6037033 AATTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 9 0.47
25 2 0.11
ACGTcount: A:0.53, C:0.07, G:0.24, T:0.16
Consensus pattern (23 bp):
AGAAGAAATCATATGAAGAAGGA
Found at i:6037656 original size:12 final size:12
Alignment explanation
Indices: 6037639--6037725 Score: 50
Period size: 12 Copynumber: 6.7 Consensus size: 12
6037629 TATCCATTTG
6037639 TTTTTATTTATA
1 TTTTTATTTATA
*
6037651 TTTTTATTATTAGTT
1 TTTTTA-T-TTA-TA
6037666 TTATTTATTATAAATA
1 TT-TTTATT-T--ATA
**
6037682 TTTTTATAAATA
1 TTTTTATTTATA
6037694 TTTTTATTTAT-
1 TTTTTATTTATA
*
6037705 TTATTATTTATTA
1 TTTTTATTTA-TA
*
6037718 TTATTATT
1 TTTTTATT
6037726 ATTAATATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
11 9 0.15
12 19 0.32
13 9 0.15
14 4 0.07
15 10 0.17
16 7 0.12
17 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (12 bp):
TTTTTATTTATA
Found at i:6037683 original size:13 final size:12
Alignment explanation
Indices: 6037667--6037700 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
6037657 TTATTAGTTT
6037667 TATTTATTATAAA
1 TATTT-TTATAAA
6037680 TATTTTTATAAA
1 TATTTTTATAAA
6037692 TATTTTTAT
1 TATTTTTAT
6037701 TTATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 16 0.76
13 5 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TATTTTTATAAA
Found at i:6037684 original size:31 final size:29
Alignment explanation
Indices: 6037641--6037723 Score: 96
Period size: 31 Copynumber: 2.8 Consensus size: 29
6037631 TCCATTTGTT
6037641 TTTATTT-ATATTTTTATTATTAGTTTTA
1 TTTATTTAATATTTTTATTATTAGTTTTA
* * *
6037669 TTTATTATAAATATTTTTATAAATATTTTTA
1 TTTATT-T-AATATTTTTATTATTAGTTTTA
*
6037700 TTTATTTATTATTTATTATTATTA
1 TTTATTTAATATTT-TTATTATTA
6037724 TTATTAATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
28 6 0.13
29 7 0.16
30 8 0.18
31 24 0.53
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (29 bp):
TTTATTTAATATTTTTATTATTAGTTTTA
Done.