Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006550.1 Hibiscus syriacus cultivar Beakdansim tig00016004_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: 1576944
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1121845 original size:18 final size:18
Alignment explanation
Indices: 1121822--1121868 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
1121812 TCTCTTCATG
1121822 GTATCGATACCTACTTCA
1 GTATCGATACCTACTTCA
1121840 GTATCGATACCTACTTCA
1 GTATCGATACCTACTTCA
1121858 GTATCGATACC
1 GTATCGATACC
1121869 ATTTTTGCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.32
Consensus pattern (18 bp):
GTATCGATACCTACTTCA
Found at i:1122879 original size:14 final size:14
Alignment explanation
Indices: 1122862--1122894 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1122852 ATGGTTTAGA
1122862 ATTTAAAGTTTAAG
1 ATTTAAAGTTTAAG
*
1122876 ATTTAAGGTTTAAG
1 ATTTAAAGTTTAAG
1122890 ATTTA
1 ATTTA
1122895 GTATTTAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.45
Consensus pattern (14 bp):
ATTTAAAGTTTAAG
Found at i:1123007 original size:20 final size:20
Alignment explanation
Indices: 1122936--1123065 Score: 63
Period size: 21 Copynumber: 6.3 Consensus size: 20
1122926 TTTTGGGTTA
1122936 AAGGTTTAGTGG-TAAGATTT
1 AAGGTTTA-TGGTTAAGATTT
* * **
1122956 AAGGGTTAATGGTTTAGGGTT
1 AA-GGTTTATGGTTAAGATTT
* *
1122977 -AGAGATCATGGTTAAGATTT
1 AAG-GTTTATGGTTAAGATTT
1122997 AAGGTTTATGGATTAAGA-TT
1 AAGGTTTATGG-TTAAGATTT
*
1123017 AAGTGTTT-TAGATTTAAGATTT
1 AAG-GTTTAT-G-GTTAAGATTT
* *
1123039 -AGGATTAAGGGTTAAGAGTTT
1 AAGG-TTTATGGTTAAGA-TTT
1123060 AAGGTT
1 AAGGTT
1123066 AAAAGTTTAT
Statistics
Matches: 82, Mismatches: 15, Indels: 25
0.67 0.12 0.20
Matches are distributed among these distances:
19 1 0.01
20 37 0.45
21 39 0.48
22 5 0.06
ACGTcount: A:0.32, C:0.01, G:0.28, T:0.39
Consensus pattern (20 bp):
AAGGTTTATGGTTAAGATTT
Found at i:1123012 original size:21 final size:21
Alignment explanation
Indices: 1122984--1123065 Score: 73
Period size: 21 Copynumber: 4.0 Consensus size: 21
1122974 GTTAGAGATC
1122984 ATGG-TTAAGATTTAAGGTTT
1 ATGGATTAAGATTTAAGGTTT
1123004 ATGGATTAAGA-TTAAGTGTTT
1 ATGGATTAAGATTTAAG-GTTT
* *
1123025 -TAGATTTAAGATTT-AGGATT
1 ATGGA-TTAAGATTTAAGGTTT
* *
1123045 AAGGGTTAAGAGTTTAAGGTT
1 ATGGATTAAGA-TTTAAGGTT
1123066 AAAAGTTTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
20 21 0.43
21 22 0.45
22 6 0.12
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.41
Consensus pattern (21 bp):
ATGGATTAAGATTTAAGGTTT
Found at i:1123054 original size:35 final size:35
Alignment explanation
Indices: 1122991--1123059 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
1122981 ATCATGGTTA
* *
1122991 AGATTTAAGGTTTATGGATTAAGATTAAGTGTTTT
1 AGATTTAAGATTTATGGATTAAGATTAAGAGTTTT
*
1123026 AGATTTAAGATTTA-GGATTAAGGGTTAAGAGTTT
1 AGATTTAAGATTTATGGATTAA-GATTAAGAGTTT
1123060 AAGGTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 7 0.23
35 23 0.77
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (35 bp):
AGATTTAAGATTTATGGATTAAGATTAAGAGTTTT
Found at i:1125761 original size:258 final size:259
Alignment explanation
Indices: 1125299--1125806 Score: 797
Period size: 258 Copynumber: 2.0 Consensus size: 259
1125289 AAGTTTTAGG
1125299 TACTTTCTGAATTTGAATCCAAATTTAATTAAAAATTCACTTTGGTCCCTAAATTTAATTAAAAT
1 TACTTTCTGAATTTGAATCCAAATTTAATTAAAAATTCACTTTGGTCCCTAAATTTAATTAAAAT
1125364 TTTAATTTAATCCTCAAAATTAATTTTAAGAAAAAATTAGGCCCTAAATTAAGGTATAACAAAGT
66 TTTAATTTAATCCTCAAAATTAATTTTAAGAAAAAATTAGGCCCTAAATTAAGGTATAACAAAGT
* * * * *
1125429 TAATAGTTTATAGATAGAGTTTAGGGTTTAGGATTTAATATCAATGGTTAGAGATTTGGTGTTTA
131 TAATAGTTTATAGATAAAGTTTAAGCTTTAAGATTTAATATCAATGGTTAAAGATTTGGTGTTTA
* * *
1125494 ATATTTAGGGTTGAGGGTATAGAGTTTAAGG-TTAAGGGTTAATGGTTAAGGTATAAGGTTTGGA
196 ATATTTAGGGTTAAGAGTATAAAGTTT-AGGTTTAAGGGTTAATGGTTAAGGTATAAGGTTTGGA
* * *
1125558 TACTTTCTGAATTTGAATCCAATTTTAATTAAAATTTCATTTTGGTCCCT-AATTTAATT-AAAT
1 TACTTTCTGAATTTGAATCCAAATTTAATTAAAAATTCACTTTGGTCCCTAAATTTAATTAAAAT
* *
1125621 TTTCAATTTAATCCTCAAAATTAATTTTAAGAAAAAATTAGGCCCTAAATTATGGTATGACAAAG
66 TTT-AATTTAATCCTCAAAATTAATTTTAAGAAAAAATTAGGCCCTAAATTAAGGTATAACAAAG
* * * * *
1125686 TTAATAGTTTGTCGTTAAAGTTTAAGCTTTAAGATTTAATATTAGTGGTTAAAGATTTGGTGTTT
130 TTAATAGTTTATAGATAAAGTTTAAGCTTTAAGATTTAATATCAATGGTTAAAGATTTGGTGTTT
* *
1125751 AATGTTTAGGGTTAATAGTATAAAGTTTAGGTTTAAGGGTTAATGGTTAAGGTATA
195 AATATTTAGGGTTAAGAGTATAAAGTTTAGGTTTAAGGGTTAATGGTTAAGGTATA
1125807 TGTTTATATT
Statistics
Matches: 227, Mismatches: 20, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
257 10 0.04
258 170 0.75
259 47 0.21
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.40
Consensus pattern (259 bp):
TACTTTCTGAATTTGAATCCAAATTTAATTAAAAATTCACTTTGGTCCCTAAATTTAATTAAAAT
TTTAATTTAATCCTCAAAATTAATTTTAAGAAAAAATTAGGCCCTAAATTAAGGTATAACAAAGT
TAATAGTTTATAGATAAAGTTTAAGCTTTAAGATTTAATATCAATGGTTAAAGATTTGGTGTTTA
ATATTTAGGGTTAAGAGTATAAAGTTTAGGTTTAAGGGTTAATGGTTAAGGTATAAGGTTTGGA
Found at i:1125811 original size:27 final size:28
Alignment explanation
Indices: 1125752--1125812 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
1125742 TTGGTGTTTA
*
1125752 ATGTTT-AGGGTTAATAGTATAAAGTTT
1 ATGTTTAAGGGTTAATAGTATAAAGTAT
* * *
1125779 AGGTTTAAGGGTTAATGGT-TAAGGTAT
1 ATGTTTAAGGGTTAATAGTATAAAGTAT
1125806 ATGTTTA
1 ATGTTTA
1125813 TATTTAAAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 17 0.61
28 11 0.39
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.43
Consensus pattern (28 bp):
ATGTTTAAGGGTTAATAGTATAAAGTAT
Found at i:1125819 original size:33 final size:34
Alignment explanation
Indices: 1125782--1125846 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
1125772 AAAGTTTAGG
*
1125782 TTTAAGGGTTAATGGTTAAGGTATATG-TTTATA
1 TTTAAAGGTTAATGGTTAAGGTATATGATTTATA
* * *
1125815 TTTAAAGGTTTATGGTTAGGGTTTATGATTTA
1 TTTAAAGGTTAATGGTTAAGGTATATGATTTA
1125847 ATGTTTAGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 23 0.85
34 4 0.15
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.48
Consensus pattern (34 bp):
TTTAAAGGTTAATGGTTAAGGTATATGATTTATA
Found at i:1125891 original size:7 final size:7
Alignment explanation
Indices: 1125819--1125958 Score: 85
Period size: 7 Copynumber: 20.1 Consensus size: 7
1125809 TTTATATTTA
1125819 AAGGTTT
1 AAGGTTT
*
1125826 ATGG-TT
1 AAGGTTT
*
1125832 AGGGTTT
1 AAGGTTT
* *
1125839 ATGATTT
1 AAGGTTT
*
1125846 AATGTTT
1 AAGGTTT
1125853 -AGGTTT
1 AAGGTTT
* *
1125859 TAGGGTT
1 AAGGTTT
*
1125866 AA-ATATT
1 AAGGT-TT
1125873 AAGGATTT
1 AAGG-TTT
1125881 -AGGTTT
1 AAGGTTT
1125887 AAGG-TT
1 AAGGTTT
1125893 AAGGATTT
1 AAGG-TTT
*
1125901 TAGGTTT
1 AAGGTTT
*
1125908 -AGGGTT
1 AAGGTTT
1125914 AAGGATTT
1 AAGG-TTT
*
1125922 TAGGTTT
1 AAGGTTT
1125929 AAGGTTT
1 AAGGTTT
1125936 AAGGATTT
1 AAGG-TTT
1125944 AAGGTTT
1 AAGGTTT
*
1125951 AGGGTTT
1 AAGGTTT
1125958 A
1 A
1125959 GGATTTTATA
Statistics
Matches: 103, Mismatches: 19, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
6 24 0.23
7 59 0.57
8 19 0.18
9 1 0.01
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.44
Consensus pattern (7 bp):
AAGGTTT
Found at i:1125902 original size:21 final size:21
Alignment explanation
Indices: 1125871--1125998 Score: 141
Period size: 21 Copynumber: 6.1 Consensus size: 21
1125861 GGGTTAAATA
1125871 TTAAGGA-TTTAGGTTTAAGG
1 TTAAGGATTTTAGGTTTAAGG
*
1125891 TTAAGGATTTTAGGTTTAGGG
1 TTAAGGATTTTAGGTTTAAGG
1125912 TTAAGGATTTTAGGTTTAAGG
1 TTAAGGATTTTAGGTTTAAGG
* *
1125933 TTTAAGGATTTAAGGTTTAGGG
1 -TTAAGGATTTTAGGTTTAAGG
* ** * * *
1125955 TTTAGGATTTTATATTGATGT
1 TTAAGGATTTTAGGTTTAAGG
* *
1125976 TTAAAGATTTAAGGTTTAAGG
1 TTAAGGATTTTAGGTTTAAGG
1125997 TT
1 TT
1125999 TATATGATAG
Statistics
Matches: 87, Mismatches: 19, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
20 7 0.08
21 61 0.70
22 19 0.22
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.45
Consensus pattern (21 bp):
TTAAGGATTTTAGGTTTAAGG
Found at i:1125925 original size:15 final size:14
Alignment explanation
Indices: 1125905--1125966 Score: 54
Period size: 15 Copynumber: 4.3 Consensus size: 14
1125895 GGATTTTAGG
1125905 TTTAGGGTTAAGGAT
1 TTTAGGGTTAAGG-T
*
1125920 TTTAGGTTTAAGGT
1 TTTAGGGTTAAGGT
* *
1125934 TTAAGGATTTAAGG-
1 TTTAGG-GTTAAGGT
*
1125948 TTTAGGGTTTAGGAT
1 TTTAGGGTTAAGG-T
1125963 TTTA
1 TTTA
1125967 TATTGATGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
13 5 0.13
14 11 0.28
15 23 0.59
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.45
Consensus pattern (14 bp):
TTTAGGGTTAAGGT
Found at i:1126049 original size:14 final size:13
Alignment explanation
Indices: 1126026--1126084 Score: 64
Period size: 14 Copynumber: 4.3 Consensus size: 13
1126016 GGTTAATAGT
1126026 TTAAGGTTTAAGA
1 TTAAGGTTTAAGA
1126039 TTAAGGATTTAAGA
1 TTAAGG-TTTAAGA
* *
1126053 TTAATGGTTAAAGT
1 TTAA-GGTTTAAGA
*
1126067 TTAAGGGTTTAGGA
1 TTAA-GGTTTAAGA
1126081 TTAA
1 TTAA
1126085 TTTATTTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
13 6 0.16
14 30 0.79
15 2 0.05
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (13 bp):
TTAAGGTTTAAGA
Found at i:1126061 original size:28 final size:28
Alignment explanation
Indices: 1126026--1126085 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
1126016 GGTTAATAGT
*
1126026 TTAA-GGTTTAAGATTAAGGATTTAAGA
1 TTAATGGTTAAAGATTAAGGATTTAAGA
* * *
1126053 TTAATGGTTAAAGTTTAAGGGTTTAGGA
1 TTAATGGTTAAAGATTAAGGATTTAAGA
1126081 TTAAT
1 TTAAT
1126086 TTATTTATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 4 0.14
28 24 0.86
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (28 bp):
TTAATGGTTAAAGATTAAGGATTTAAGA
Found at i:1126344 original size:28 final size:27
Alignment explanation
Indices: 1126234--1126414 Score: 91
Period size: 28 Copynumber: 6.5 Consensus size: 27
1126224 CAGGATTTGA
1126234 GTTTAGGGTTAAGGTTTAAAGGTTTAA-G
1 GTTTAGGGTTAAGG-TTAAAGG-TTAAGG
* * *
1126262 GTTTAGGATTTATA-GTTAAGGGTTTAGG
1 GTTTAGG-GTTA-AGGTTAAAGGTTAAGG
* * *
1126290 GTATAAGGTTAAAGGTT-AAGTGATAAGG
1 GTTTAGGGTT-AAGGTTAAAG-GTTAAGG
*
1126318 GTTTAGGGTATAAGGTTAAAGGTTAAGT
1 GTTTAGGGT-TAAGGTTAAAGGTTAAGG
* * * * * *
1126346 GATTAGGATTTAGTGTTTAATGTT-ATG
1 GTTTAGGGTTAAG-GTTAAAGGTTAAGG
* * * *
1126373 ATTTAGAGTTAAGAGTTAAATGTTAAGT
1 GTTTAGGGTTAAG-GTTAAAGGTTAAGG
*
1126401 GTTTATGGTTAAGG
1 GTTTAGGGTTAAGG
1126415 GCTTAATGTT
Statistics
Matches: 111, Mismatches: 32, Indels: 21
0.68 0.20 0.13
Matches are distributed among these distances:
27 30 0.27
28 72 0.65
29 8 0.07
30 1 0.01
ACGTcount: A:0.31, C:0.00, G:0.30, T:0.39
Consensus pattern (27 bp):
GTTTAGGGTTAAGGTTAAAGGTTAAGG
Found at i:1126346 original size:35 final size:35
Alignment explanation
Indices: 1126278--1126358 Score: 144
Period size: 35 Copynumber: 2.3 Consensus size: 35
1126268 GATTTATAGT
1126278 TAAGGGTTTAGGGTATAAGGTTAAAGGTTAAGTGA
1 TAAGGGTTTAGGGTATAAGGTTAAAGGTTAAGTGA
1126313 TAAGGGTTTAGGGTATAAGGTTAAAGGTTAAGTGA
1 TAAGGGTTTAGGGTATAAGGTTAAAGGTTAAGTGA
* *
1126348 TTAGGATTTAG
1 TAAGGGTTTAG
1126359 TGTTTAATGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (35 bp):
TAAGGGTTTAGGGTATAAGGTTAAAGGTTAAGTGA
Found at i:1126421 original size:55 final size:55
Alignment explanation
Indices: 1126319--1126424 Score: 126
Period size: 55 Copynumber: 1.9 Consensus size: 55
1126309 GTGATAAGGG
* * * *
1126319 TTTAGGGTATAAGGTTAAAGGTTAAGTGATTAGGATTTAGTGTTTAATGTTATGA
1 TTTAGAGTATAAGGTTAAAGGTTAAGTGATTAGGATTAAGGGCTTAATGTTATGA
* *
1126374 TTTAGAGT-TAAGAGTTAAATGTTAAGTGTTTATGG-TTAAGGGCTTAATGTT
1 TTTAGAGTATAAG-GTTAAAGGTTAAGTGATTA-GGATTAAGGGCTTAATGTT
1126425 TATAGTTTAG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
54 4 0.09
55 37 0.86
56 2 0.05
ACGTcount: A:0.30, C:0.01, G:0.26, T:0.42
Consensus pattern (55 bp):
TTTAGAGTATAAGGTTAAAGGTTAAGTGATTAGGATTAAGGGCTTAATGTTATGA
Found at i:1126424 original size:21 final size:22
Alignment explanation
Indices: 1126395--1126436 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1126385 GAGTTAAATG
*
1126395 TTAAGTGTTTATGGTTAAGGGC
1 TTAAGTGTTTATAGTTAAGGGC
*
1126417 TTAA-TGTTTATAGTTTAGGG
1 TTAAGTGTTTATAGTTAAGGG
1126437 TTTTAGGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.24, C:0.02, G:0.29, T:0.45
Consensus pattern (22 bp):
TTAAGTGTTTATAGTTAAGGGC
Found at i:1126453 original size:28 final size:27
Alignment explanation
Indices: 1126417--1126473 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
1126407 GGTTAAGGGC
1126417 TTAATGTTTATAG-TTTAGGGTTTTAGG
1 TTAATGTTTA-AGATTTAGGGTTTTAGG
* *
1126444 TTAATAGTTTAAGATTTAGGTTTTTGGG
1 TTAAT-GTTTAAGATTTAGGGTTTTAGG
1126472 TT
1 TT
1126474 TAGGGTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 7 0.27
28 19 0.73
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.53
Consensus pattern (27 bp):
TTAATGTTTAAGATTTAGGGTTTTAGG
Found at i:1126474 original size:21 final size:21
Alignment explanation
Indices: 1126450--1126550 Score: 55
Period size: 21 Copynumber: 4.9 Consensus size: 21
1126440 TAGGTTAATA
*
1126450 GTTTAAGATTT-AGGTTTTTGG
1 GTTTAAGATTTAAGG-TTTTAG
* *
1126471 GTTTAGGGTTTAAGGTTTTAG
1 GTTTAAGATTTAAGGTTTTAG
* * *
1126492 GTTTAAGGTTT-TGGGTTTAG
1 GTTTAAGATTTAAGGTTTTAG
* * * *
1126512 GATTTATG-GTTAATGATTTAG
1 G-TTTAAGATTTAAGGTTTTAG
* *
1126533 GTTTAGGATTTAATGTTT
1 GTTTAAGATTTAAGGTTT
1126551 GAAGTTAAGA
Statistics
Matches: 62, Mismatches: 14, Indels: 8
0.74 0.17 0.10
Matches are distributed among these distances:
20 15 0.24
21 44 0.71
22 3 0.05
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (21 bp):
GTTTAAGATTTAAGGTTTTAG
Found at i:1126487 original size:14 final size:14
Alignment explanation
Indices: 1126429--1126510 Score: 67
Period size: 14 Copynumber: 5.9 Consensus size: 14
1126419 AATGTTTATA
*
1126429 GTTTAGGGTTTTAG
1 GTTTAGGGTTTAAG
* **
1126443 GTTAATAGTTTAAG
1 GTTTAGGGTTTAAG
* * **
1126457 ATTTAGGTTTTTGG
1 GTTTAGGGTTTAAG
1126471 GTTTAGGGTTTAAG
1 GTTTAGGGTTTAAG
1126485 GTTTTA-GGTTTAAG
1 G-TTTAGGGTTTAAG
*
1126499 GTTTTGGGTTTA
1 GTTTAGGGTTTA
1126511 GGATTTATGG
Statistics
Matches: 50, Mismatches: 16, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
13 3 0.06
14 43 0.86
15 4 0.08
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (14 bp):
GTTTAGGGTTTAAG
Found at i:1126509 original size:7 final size:7
Alignment explanation
Indices: 1126242--1126502 Score: 50
Period size: 7 Copynumber: 37.3 Consensus size: 7
1126232 GAGTTTAGGG
1126242 TTAAGGT
1 TTAAGGT
1126249 TTAAAGGT
1 TT-AAGGT
1126257 TTAAGGT
1 TTAAGGT
1126264 TT-AGGAT
1 TTAAGG-T
1126271 TTATA-G-
1 TTA-AGGT
1126277 TTAAGGGT
1 TTAA-GGT
*
1126285 TTAGGGT
1 TTAAGGT
*
1126292 ATAAGGT
1 TTAAGGT
*
1126299 TAAAGG-
1 TTAAGGT
1126305 TTAA-GT
1 TTAAGGT
*
1126311 GATAAGGGT
1 -TTAA-GGT
*
1126320 TTAGGGT
1 TTAAGGT
*
1126327 ATAAGGT
1 TTAAGGT
*
1126334 TAAAGG-
1 TTAAGGT
*
1126340 TTAAGTGA
1 TTAAG-GT
1126348 TT-AGGAT
1 TTAAGG-T
1126355 TT-AGTGT
1 TTAAG-GT
*
1126362 TTAATG-
1 TTAAGGT
* *
1126368 TTATGAT
1 TTAAGGT
1126375 TT-AGAG-
1 TTAAG-GT
1126381 TTAAGAGT
1 TTAAG-GT
* *
1126389 TAAATG-
1 TTAAGGT
1126395 TTAAGTGT
1 TTAAG-GT
*
1126403 TTATGG-
1 TTAAGGT
*
1126409 TTAAGGGC
1 TTAA-GGT
*
1126417 TTAATGT
1 TTAAGGT
1126424 TTATA-GT
1 TTA-AGGT
*
1126431 TTAGGGT
1 TTAAGGT
*
1126438 TTTAGG-
1 TTAAGGT
*
1126444 TTAATAGT
1 TTAA-GGT
*
1126452 TTAAGAT
1 TTAAGGT
1126459 TT-AGGTT
1 TTAAGG-T
**
1126466 TTTGGGT
1 TTAAGGT
*
1126473 TTAGGGT
1 TTAAGGT
1126480 TTAAGGT
1 TTAAGGT
*
1126487 TTTAGGT
1 TTAAGGT
1126494 TTAAGGT
1 TTAAGGT
1126501 TT
1 TT
1126503 TGGGTTTAGG
Statistics
Matches: 182, Mismatches: 42, Indels: 60
0.64 0.15 0.21
Matches are distributed among these distances:
5 2 0.01
6 31 0.17
7 111 0.61
8 35 0.19
9 3 0.02
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.43
Consensus pattern (7 bp):
TTAAGGT
Found at i:1126522 original size:14 final size:14
Alignment explanation
Indices: 1126450--1126595 Score: 63
Period size: 14 Copynumber: 10.5 Consensus size: 14
1126440 TAGGTTAATA
*
1126450 GTTTAAGATTTA-G
1 GTTTAGGATTTATG
* * *
1126463 GTTTTTGGGTTTAGG
1 G-TTTAGGATTTATG
*
1126478 GTTTAAGGTTTTA-G
1 GTTT-AGGATTTATG
1126492 GTTTAAGG-TTT-TGG
1 GTTT-AGGATTTAT-G
1126506 GTTTAGGATTTATG
1 GTTTAGGATTTATG
* *
1126520 GTTAATGATTTA-G
1 GTTTAGGATTTATG
1126533 GTTTAGGATTTAAT-
1 GTTTAGGATTT-ATG
* * *
1126547 GTTT-GAAGTTAAG
1 GTTTAGGATTTATG
* *
1126560 AGTTTAGGATGTAAG
1 -GTTTAGGATTTATG
*
1126575 GTATAGGATTTATG
1 GTTTAGGATTTATG
*
1126589 TTTTAGG
1 GTTTAGG
1126596 GTTAAATGTT
Statistics
Matches: 101, Mismatches: 20, Indels: 23
0.70 0.14 0.16
Matches are distributed among these distances:
12 1 0.01
13 21 0.21
14 64 0.63
15 15 0.15
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (14 bp):
GTTTAGGATTTATG
Found at i:1126627 original size:21 final size:21
Alignment explanation
Indices: 1126556--1126639 Score: 66
Period size: 21 Copynumber: 4.0 Consensus size: 21
1126546 TGTTTGAAGT
*
1126556 TAAGAGTTTAGGATGTAA-GGTA
1 TAAG-GTTTATGAT-TAAGGGTA
* *
1126578 T-AGGATTTATGTTTTAGGGT-
1 TAAGG-TTTATGATTAAGGGTA
*
1126598 TAAATGTTTATGATTAAGGGTA
1 T-AAGGTTTATGATTAAGGGTA
*
1126620 TAAGGTTTAAGATTAAGGGT
1 TAAGGTTTATGATTAAGGGT
1126640 TAAAAATTTA
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
20 4 0.08
21 41 0.84
22 4 0.08
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.39
Consensus pattern (21 bp):
TAAGGTTTATGATTAAGGGTA
Found at i:1126649 original size:21 final size:21
Alignment explanation
Indices: 1126593--1126649 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
1126583 TTTATGTTTT
* *
1126593 AGGGTTAAATGTTTATGATTA
1 AGGGTTAAAAGTTTAAGATTA
*
1126614 AGGG-TATAAGGTTTAAGATTA
1 AGGGTTA-AAAGTTTAAGATTA
*
1126635 AGGGTTAAAAATTTA
1 AGGGTTAAAAGTTTA
1126650 GGGTTTATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.37
Consensus pattern (21 bp):
AGGGTTAAAAGTTTAAGATTA
Found at i:1130904 original size:2 final size:2
Alignment explanation
Indices: 1130897--1130934 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1130887 AATTTTACAT
1130897 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1130935 CCTAATAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1134488 original size:17 final size:17
Alignment explanation
Indices: 1134466--1134506 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
1134456 AAATGCCCTT
1134466 AAAATATTTTTTTTTCA
1 AAAATATTTTTTTTTCA
1134483 AAAATATTTTTTTTTCA
1 AAAATATTTTTTTTTCA
1134500 AAAATAT
1 AAAATAT
1134507 ACTTCTGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (17 bp):
AAAATATTTTTTTTTCA
Found at i:1143602 original size:59 final size:59
Alignment explanation
Indices: 1143510--1143630 Score: 206
Period size: 59 Copynumber: 2.1 Consensus size: 59
1143500 AATAGATGGA
* *
1143510 TAAGTGTCCTATCGAACCCTCCTAGTCGCAATGAAAAGGCAAACTCGATAATATGGCTC
1 TAAGTGTCATATCGAACCCTCCTAGTCGCAATGAAAAGGCAAACTCGATAATATGACTC
* *
1143569 TAAGTGTCATGTCGAACCCTCCTAGTCGCAATGAAAAGGCAAACTTGATAATATGACTC
1 TAAGTGTCATATCGAACCCTCCTAGTCGCAATGAAAAGGCAAACTCGATAATATGACTC
1143628 TAA
1 TAA
1143631 CCAACCTTCC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (59 bp):
TAAGTGTCATATCGAACCCTCCTAGTCGCAATGAAAAGGCAAACTCGATAATATGACTC
Found at i:1149203 original size:27 final size:24
Alignment explanation
Indices: 1149173--1149225 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 24
1149163 TTCTTCTATA
1149173 TTATTTACTTATTTACTTTCTCATTAT
1 TTATTTA-TTATTTA-TTT-TCATTAT
*
1149200 TTATTTATTATTTATTTTTATTAT
1 TTATTTATTATTTATTTTCATTAT
1149224 TT
1 TT
1149226 TATTATTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 8 0.32
25 3 0.12
26 7 0.28
27 7 0.28
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.70
Consensus pattern (24 bp):
TTATTTATTATTTATTTTCATTAT
Found at i:1149211 original size:11 final size:11
Alignment explanation
Indices: 1149195--1149233 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
1149185 TTACTTTCTC
1149195 ATTATTTATTT
1 ATTATTTATTT
1149206 ATTATTTATTT
1 ATTATTTATTT
1149217 -TTA-TTATTTT
1 ATTATTTA-TTT
1149227 ATTATTT
1 ATTATTT
1149234 TCATTATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 3 0.12
10 6 0.24
11 14 0.56
12 2 0.08
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
ATTATTTATTT
Found at i:1149221 original size:17 final size:17
Alignment explanation
Indices: 1149195--1149241 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
1149185 TTACTTTCTC
*
1149195 ATTATTTAT-TTATTAT
1 ATTATTTTTATTATTAT
*
1149211 -TTATTTTTATTATTTT
1 ATTATTTTTATTATTAT
*
1149227 ATTATTTTCATTATT
1 ATTATTTTTATTATT
1149242 TCTAAATCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 7 0.27
16 6 0.23
17 13 0.50
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTATTTTTATTATTAT
Found at i:1149225 original size:9 final size:9
Alignment explanation
Indices: 1149200--1149242 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
1149190 TTCTCATTAT
1149200 TTATTTATTA
1 TTATTT-TTA
1149210 TTTATTTTTA
1 -TTATTTTTA
1149220 TTA-TTTTA
1 TTATTTTTA
*
1149228 TTATTTTCA
1 TTATTTTTA
1149237 TTATTT
1 TTATTT
1149243 CTAAATCCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
8 8 0.27
9 13 0.43
10 3 0.10
11 6 0.20
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (9 bp):
TTATTTTTA
Found at i:1149243 original size:8 final size:7
Alignment explanation
Indices: 1149200--1149233 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
1149190 TTCTCATTAT
1149200 TTATTTA
1 TTATTTA
1149207 TTATTTA
1 TTATTTA
1149214 TT-TTTA
1 TTATTTA
1149220 TTATTTTA
1 TTA-TTTA
1149228 TTATTT
1 TTATTT
1149234 TCATTATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.24
7 12 0.48
8 7 0.28
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTATTTA
Found at i:1152897 original size:17 final size:19
Alignment explanation
Indices: 1152852--1152903 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
1152842 ATTATGTAAA
*
1152852 TATTAAAAAGTATAATAATT
1 TATTTAAAA-TATAATAATT
*
1152872 TATTTAAAAT-TAATCATT
1 TATTTAAAATATAATAATT
1152890 TA-TTAAAATATAAT
1 TATTTAAAATATAAT
1152904 TTTAATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 7 0.24
18 13 0.45
19 1 0.03
20 8 0.28
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
TATTTAAAATATAATAATT
Found at i:1153561 original size:2 final size:2
Alignment explanation
Indices: 1153554--1153584 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1153544 AAGTTCCACA
*
1153554 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1153585 AGTATAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1154432 original size:3 final size:3
Alignment explanation
Indices: 1154426--1154450 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1154416 GTTAACCACC
1154426 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
1154451 GGCCGGCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:1159397 original size:60 final size:61
Alignment explanation
Indices: 1159299--1159474 Score: 144
Period size: 60 Copynumber: 2.9 Consensus size: 61
1159289 CCTAAATTAT
* * * *
1159299 AATCTTCATTTTAAATTGGTTCTTAAATTTTTGAATATT-TCAATTTCATCCCCAATCTATG
1 AATCTTCATTCTAAATTGGTTCTTAAACTTTTAAATATTCT-AATTTCATCCCCAAACTATG
* * *
1159360 AATC-TCATTCTAAATTTG-TCTTTAAACTTTTAAATATTCTAATTTTATCCCTAAACTATG
1 AATCTTCATTCTAAATTGGTTC-TTAAACTTTTAAATATTCTAATTTCATCCCCAAACTATG
* * * * *** * * * *
1159420 -ACCATCTTTCTAAATTGTTTCCCGAATTTTTGAATGTTCCAATTTCATCCCCAAA
1 AATCTTCATTCTAAATTGGTTCTTAAACTTTTAAATATTCTAATTTCATCCCCAAA
1159475 TTCATCAAAA
Statistics
Matches: 91, Mismatches: 20, Indels: 9
0.76 0.17 0.08
Matches are distributed among these distances:
59 4 0.04
60 80 0.88
61 7 0.08
ACGTcount: A:0.30, C:0.19, G:0.06, T:0.45
Consensus pattern (61 bp):
AATCTTCATTCTAAATTGGTTCTTAAACTTTTAAATATTCTAATTTCATCCCCAAACTATG
Found at i:1159657 original size:29 final size:29
Alignment explanation
Indices: 1159599--1159664 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
1159589 ATATACATAT
1159599 AGTTTGGGAAAAAATTGAAATGTTCAAAA
1 AGTTTGGGAAAAAATTGAAATGTTCAAAA
* *
1159628 AGTTTGGGAATGAGATTGAAATGTTC-AAA
1 AGTTTGGGAA-AAAATTGAAATGTTCAAAA
1159657 AGTTTGGG
1 AGTTTGGG
1159665 GGACCAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 21 0.62
30 13 0.38
ACGTcount: A:0.39, C:0.03, G:0.27, T:0.30
Consensus pattern (29 bp):
AGTTTGGGAAAAAATTGAAATGTTCAAAA
Found at i:1170062 original size:23 final size:23
Alignment explanation
Indices: 1170024--1170073 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
1170014 TAGATTTAGG
* *
1170024 TTTT-TTTTAAAGTTTTTATTAT
1 TTTTATTTTAAAGTTTTAAATAT
1170046 TTTTATTTTATAA-TTTTAAATAT
1 TTTTATTTTA-AAGTTTTAAATAT
1170069 TTTTA
1 TTTTA
1170074 GAAAGCTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 4 0.17
23 18 0.75
24 2 0.08
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (23 bp):
TTTTATTTTAAAGTTTTAAATAT
Found at i:1175161 original size:20 final size:20
Alignment explanation
Indices: 1175133--1175172 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1175123 ATGTTTAATG
*
1175133 AAAAAGATACCATTTGTTAC
1 AAAAAGATACCAATTGTTAC
* *
1175153 AAAAGGATATCAATTGTTAC
1 AAAAAGATACCAATTGTTAC
1175173 CAATTGTTGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (20 bp):
AAAAAGATACCAATTGTTAC
Found at i:1187924 original size:20 final size:20
Alignment explanation
Indices: 1187884--1187921 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1187874 AAAAATTTTA
1187884 TTTTGATTTTCAAAATCAAT
1 TTTTGATTTTCAAAATCAAT
1187904 TTTTG-TTTTCAAAATCAA
1 TTTTGATTTTCAAAATCAA
1187922 ATTAATTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50
Consensus pattern (20 bp):
TTTTGATTTTCAAAATCAAT
Found at i:1189891 original size:20 final size:20
Alignment explanation
Indices: 1189863--1189934 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
1189853 TAATGTTCAT
* * * *
1189863 TACTGTTCACACAGTATCGG
1 TACTATTCATACAATATCGA
*
1189883 TACTATTCATACAATATTGA
1 TACTATTCATACAATATCGA
1189903 TACTATTCATACAATATCGA
1 TACTATTCATACAATATCGA
*
1189923 T-CTATTTATACA
1 TACTATTCATACA
1189935 GTATAATAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 10 0.22
20 35 0.78
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (20 bp):
TACTATTCATACAATATCGA
Found at i:1190934 original size:159 final size:159
Alignment explanation
Indices: 1190765--1191067 Score: 396
Period size: 159 Copynumber: 1.9 Consensus size: 159
1190755 AACAAAAAGG
* ** *
1190765 ACTTAAAATGAATG-AGCAATCGAAGGAATGAG-AAATCATGCAAATTTGAAGGGTTGCA-TTGA
1 ACTTAAAATGAATGAAG-AATCGAAGGAATGAGAAAATCATGCAAAGTTGAAGGACT-AAGTTG-
* * * * *
1190827 AAAAAATATAAAATTTGTTATCAAATAGAGAAATTGAATATACATAGGTGTTCTACAATGATTTA
63 AAAAAATAGAAAATTTGTTATCAAAAAGAGAAATTGAAGATACATAGGTATTCTAAAATGATTTA
*
1190892 GGTGCATGTGGTTCAAACTTGGTTAAAAATGA
128 GGAGCATGTGGTTCAAACTTGGTTAAAAATGA
*
1190924 ACTTAAAATGAATGAAGAATTGAAGGAATGAGAAAATCATGCAAAGTTGAAGGACTAAGTTGAAA
1 ACTTAAAATGAATGAAGAATCGAAGGAATGAGAAAATCATGCAAAGTTGAAGGACTAAGTTGAAA
* * * * * *
1190989 AAATAGAAAATTTGTTATTAAAAAGAGGAATTGAAGATTCATATGTATTTTAAAATGCTTTAGGA
66 AAATAGAAAATTTGTTATCAAAAAGAGAAATTGAAGATACATAGGTATTCTAAAATGATTTAGGA
*
1191054 GTATGTGGTTCAAA
131 GCATGTGGTTCAAA
1191068 TTTAGTAAAA
Statistics
Matches: 123, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
159 98 0.80
160 25 0.20
ACGTcount: A:0.44, C:0.07, G:0.20, T:0.29
Consensus pattern (159 bp):
ACTTAAAATGAATGAAGAATCGAAGGAATGAGAAAATCATGCAAAGTTGAAGGACTAAGTTGAAA
AAATAGAAAATTTGTTATCAAAAAGAGAAATTGAAGATACATAGGTATTCTAAAATGATTTAGGA
GCATGTGGTTCAAACTTGGTTAAAAATGA
Found at i:1191709 original size:285 final size:285
Alignment explanation
Indices: 1191199--1191769 Score: 1088
Period size: 285 Copynumber: 2.0 Consensus size: 285
1191189 TTAAATTGTA
*
1191199 GCTCGACTCAAAATTTGACTCGATGGTTCGAATTGGATCAAATAACTCAACTTAAATAATTTGAA
1 GCTCGACTCAAAAATTGACTCGATGGTTCGAATTGGATCAAATAACTCAACTTAAATAATTTGAA
*
1191264 ATTGAAAAAAAATTATTTTTTAAGTCGAGTCTAGTTTTTCTCACCCCAAAAATTATTATTCTATC
66 ATTGAAAAAAAATTATTTTTTAAGTCGAGTCTAGTTTTGCTCACCCCAAAAATTATTATTCTATC
* *
1191329 TAAATTTTAGGGTAAAATATATAAATAATCCCTAAACTTTTAGGGCGTTTGCATTTTGGTCACCT
131 TAAATTTCAGGGTAAAATATATAAATAATCCCTAAACTTTTAGGGCATTTGCATTTTGGTCACCT
*
1191394 AACTTTTGAAACTTGCAATATAATCATCGAACTTTTAGTTTATTTTCAGTAAGGTCTCTGTCGTT
196 AACTTTTGAAACTTGCAATATAATCATCGAACTTTTAGTTCATTTTCAGTAAGGTCTCTGTCGTT
1191459 ACCTCCCGTTAGTTTTAGTTGATGT
261 ACCTCCCGTTAGTTTTAGTTGATGT
1191484 GCTCGACTCAAAAATTGACTCGATGGTTCGAATTGGATCAAATAACTCAACTTAAATAATTTGAA
1 GCTCGACTCAAAAATTGACTCGATGGTTCGAATTGGATCAAATAACTCAACTTAAATAATTTGAA
1191549 ATTGAAAAAAAATTATTTTTTAAGTCGAGTCTAGTTTTGCTCACCCCAAAAATTATTATTCTATC
66 ATTGAAAAAAAATTATTTTTTAAGTCGAGTCTAGTTTTGCTCACCCCAAAAATTATTATTCTATC
*
1191614 TAAATTTCAGGGTAAAATATATAAATAATCCCTGAACTTTTAGGGCATTTGCATTTTGGTCACCT
131 TAAATTTCAGGGTAAAATATATAAATAATCCCTAAACTTTTAGGGCATTTGCATTTTGGTCACCT
1191679 AACTTTTGAAACTTGCAATATAATCATCGAACTTTTAGTTCATTTTCAGTAAGGTCTCTGTCGTT
196 AACTTTTGAAACTTGCAATATAATCATCGAACTTTTAGTTCATTTTCAGTAAGGTCTCTGTCGTT
1191744 ACCTCCCGTTAGTTTTAGTTGATGT
261 ACCTCCCGTTAGTTTTAGTTGATGT
1191769 G
1 G
1191770 GCACTTGACT
Statistics
Matches: 280, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
285 280 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (285 bp):
GCTCGACTCAAAAATTGACTCGATGGTTCGAATTGGATCAAATAACTCAACTTAAATAATTTGAA
ATTGAAAAAAAATTATTTTTTAAGTCGAGTCTAGTTTTGCTCACCCCAAAAATTATTATTCTATC
TAAATTTCAGGGTAAAATATATAAATAATCCCTAAACTTTTAGGGCATTTGCATTTTGGTCACCT
AACTTTTGAAACTTGCAATATAATCATCGAACTTTTAGTTCATTTTCAGTAAGGTCTCTGTCGTT
ACCTCCCGTTAGTTTTAGTTGATGT
Found at i:1192324 original size:3 final size:3
Alignment explanation
Indices: 1192316--1192348 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1192306 TGTGTGTGAG
1192316 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1192349 GGGGTTAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1194483 original size:39 final size:39
Alignment explanation
Indices: 1194429--1194508 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
1194419 GTCTAAATCA
1194429 AACACATACTTCTTATTACAATTTATCTTTGTGTTAGGG
1 AACACATACTTCTTATTACAATTTATCTTTGTGTTAGGG
1194468 AACACATACTTCTTATTACAATTTATCTTTGTGTTAGGG
1 AACACATACTTCTTATTACAATTTATCTTTGTGTTAGGG
1194507 AA
1 AA
1194509 AGGAGTTTGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (39 bp):
AACACATACTTCTTATTACAATTTATCTTTGTGTTAGGG
Found at i:1197101 original size:2 final size:2
Alignment explanation
Indices: 1197096--1197124 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1197086 GAATCAATGA
1197096 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1197125 ACACTAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1199606 original size:59 final size:59
Alignment explanation
Indices: 1199514--1199631 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
1199504 ATGCATGATA
1199514 GCATAAAAGGCTTAATAGGGATGGTGGGGATGGTTTTAATATTAAAGTTTAAATTTGGG
1 GCATAAAAGGCTTAATAGGGATGGTGGGGATGGTTTTAATATTAAAGTTTAAATTTGGG
*
1199573 GCATAAAAGGCTTAATATGGATGGTGGGGATGGTTTTAATATTAAAGTTTAAATTTGGG
1 GCATAAAAGGCTTAATAGGGATGGTGGGGATGGTTTTAATATTAAAGTTTAAATTTGGG
1199632 CTATTTAAAG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (59 bp):
GCATAAAAGGCTTAATAGGGATGGTGGGGATGGTTTTAATATTAAAGTTTAAATTTGGG
Found at i:1200205 original size:47 final size:46
Alignment explanation
Indices: 1200136--1200267 Score: 183
Period size: 47 Copynumber: 2.8 Consensus size: 46
1200126 TACTGTTTAG
1200136 TAGTATATAGACACTCAATAATCTCATAGTATACCATTAAGAGTATA
1 TAGTATATAGACACTCAATAATC-CATAGTATACCATTAAGAGTATA
* * * *
1200183 TAGTAAATAAACACTCAATAATCCTATATTATACTATTAAGAGTATA
1 TAGTATATAGACACTCAATAATCC-ATAGTATACCATTAAGAGTATA
* *
1200230 TAGTATATCGATACTCAATAATCCCATAGTATACCATT
1 TAGTATATAGACACTCAATAAT-CCATAGTATACCATT
1200268 TAATGGTATA
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
46 1 0.01
47 70 0.96
48 2 0.03
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.33
Consensus pattern (46 bp):
TAGTATATAGACACTCAATAATCCATAGTATACCATTAAGAGTATA
Found at i:1202950 original size:24 final size:24
Alignment explanation
Indices: 1202923--1203020 Score: 117
Period size: 24 Copynumber: 4.1 Consensus size: 24
1202913 TATATCAAAA
* *
1202923 ATCAAAACATAATCCAGGTCAAGT
1 ATCAAATCAGAATCCAGGTCAAGT
* *
1202947 ATCAGATCAAAATCCAGGTCAAGT
1 ATCAAATCAGAATCCAGGTCAAGT
1202971 ATTC-AATCAGAATCCAGGTCAAGT
1 A-TCAAATCAGAATCCAGGTCAAGT
** *
1202995 ATCCGATCAGAATCCAGGTCAGGT
1 ATCAAATCAGAATCCAGGTCAAGT
1203019 AT
1 AT
1203021 TATAATAGAA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
23 2 0.03
24 61 0.94
25 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAATCAGAATCCAGGTCAAGT
Found at i:1202968 original size:12 final size:13
Alignment explanation
Indices: 1202933--1203015 Score: 61
Period size: 12 Copynumber: 6.8 Consensus size: 13
1202923 ATCAAAACAT
1202933 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
1202946 TAT-CAGATCAA-
1 AATCCAGGTCAAG
1202957 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* * *
1202970 TATTCA-ATC-AG
1 AATCCAGGTCAAG
1202981 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
1202994 TATCC-GATC-AG
1 AATCCAGGTCAAG
1203005 AATCCAGGTCA
1 AATCCAGGTCA
1203016 GGTATTATAA
Statistics
Matches: 50, Mismatches: 14, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
11 14 0.28
12 24 0.48
13 12 0.24
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (13 bp):
AATCCAGGTCAAG
Found at i:1203030 original size:24 final size:24
Alignment explanation
Indices: 1202933--1203021 Score: 126
Period size: 24 Copynumber: 3.7 Consensus size: 24
1202923 ATCAAAACAT
*
1202933 AATCCAGGTCAAGTA-TCAGATCAA
1 AATCCAGGTCAAGTATTCA-ATCAG
1202957 AATCCAGGTCAAGTATTCAATCAG
1 AATCCAGGTCAAGTATTCAATCAG
* *
1202981 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATTCAATCAG
*
1203005 AATCCAGGTCAGGTATT
1 AATCCAGGTCAAGTATT
1203022 ATAATAGAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
24 56 0.95
25 3 0.05
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (24 bp):
AATCCAGGTCAAGTATTCAATCAG
Found at i:1204598 original size:20 final size:19
Alignment explanation
Indices: 1204551--1204590 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1204541 GAATTATTCC
*
1204551 TTAACAAACTTTTAGCATC
1 TTAACAAACTTTTAGCATA
*
1204570 TTAACAAACTTTTAGTATA
1 TTAACAAACTTTTAGCATA
1204589 TT
1 TT
1204591 GCACAAACCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (19 bp):
TTAACAAACTTTTAGCATA
Found at i:1208393 original size:19 final size:20
Alignment explanation
Indices: 1208361--1208398 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
1208351 ACTACTATAT
1208361 TACTTGCATCGA-TTGTGTA
1 TACTTGCATCGATTTGTGTA
1208380 TACTTGCA-CAGATTTGTGT
1 TACTTGCATC-GATTTGTGT
1208399 GCCTCAACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 1 0.06
19 10 0.59
20 6 0.35
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (20 bp):
TACTTGCATCGATTTGTGTA
Found at i:1214244 original size:11 final size:12
Alignment explanation
Indices: 1214222--1214246 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1214212 CCTCTTCATA
1214222 TTTTTCCTTTTT
1 TTTTTCCTTTTT
1214234 TTTTTCCTTTTT
1 TTTTTCCTTTTT
1214246 T
1 T
1214247 CTTCTAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTCCTTTTT
Found at i:1222633 original size:12 final size:13
Alignment explanation
Indices: 1222605--1222633 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1222595 CTTCTTTGAC
1222605 TTTGCACTTCATT
1 TTTGCACTTCATT
1222618 TTTGCACTTC-TT
1 TTTGCACTTCATT
1222630 TTTG
1 TTTG
1222634 TATTTTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.10, C:0.21, G:0.10, T:0.59
Consensus pattern (13 bp):
TTTGCACTTCATT
Found at i:1226152 original size:22 final size:22
Alignment explanation
Indices: 1226122--1226179 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
1226112 TCAACTATTT
* *
1226122 GACCATTGACTTTGACCGGTTA
1 GACCGTTGACTTTGACCGGTCA
*
1226144 GACCGTTGACTTTAACCGGTCA
1 GACCGTTGACTTTGACCGGTCA
* *
1226166 TACTGTTGACTTTG
1 GACCGTTGACTTTG
1226180 CCCAAAAAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.34
Consensus pattern (22 bp):
GACCGTTGACTTTGACCGGTCA
Found at i:1226330 original size:18 final size:17
Alignment explanation
Indices: 1226297--1226330 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1226287 TTATCTTTGG
*
1226297 ATTTAAGTTGGTTTCTC
1 ATTTAAGTTAGTTTCTC
1226314 ATTTAAGTTCAGTTTCT
1 ATTTAAGTT-AGTTTCT
1226331 GATGTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.21, C:0.12, G:0.15, T:0.53
Consensus pattern (17 bp):
ATTTAAGTTAGTTTCTC
Found at i:1228158 original size:19 final size:19
Alignment explanation
Indices: 1228126--1228205 Score: 63
Period size: 19 Copynumber: 4.2 Consensus size: 19
1228116 GTCTGACCTC
** *
1228126 TGATTTCTGCTATGAACTT
1 TGATTTCTATTATGATCTT
1228145 TGATTTCTATTATGATCTCT
1 TGATTTCTATTATGATCT-T
* * *
1228165 T-ATTTCTGTTCTGATCTC
1 TGATTTCTATTATGATCTT
* * *
1228183 TGATTTCTACTCTGATTTT
1 TGATTTCTATTATGATCTT
1228202 TGAT
1 TGAT
1228206 ATCTCCATTT
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
18 1 0.02
19 46 0.94
20 2 0.04
ACGTcount: A:0.17, C:0.16, G:0.12, T:0.54
Consensus pattern (19 bp):
TGATTTCTATTATGATCTT
Found at i:1231455 original size:24 final size:24
Alignment explanation
Indices: 1231427--1231475 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1231417 AACTGTCGTT
* * *
1231427 TAGAATTTGCACCGAAGTGCGACA
1 TAGAATATACACCGAAGTGCCACA
1231451 TAGAATATACACCGAAGTGCCACA
1 TAGAATATACACCGAAGTGCCACA
1231475 T
1 T
1231476 TGATTTGTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.20
Consensus pattern (24 bp):
TAGAATATACACCGAAGTGCCACA
Found at i:1231506 original size:23 final size:23
Alignment explanation
Indices: 1231480--1231539 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
1231470 CCACATTGAT
*
1231480 TTGTCCCGAAGGATAACGTAGAA
1 TTGTCCCGAAGGATAACATAGAA
* * **
1231503 TTGTCCCAAATGACCACATAGAA
1 TTGTCCCGAAGGATAACATAGAA
*
1231526 TTGTTCCGAAGGAT
1 TTGTCCCGAAGGAT
1231540 CGTGTAGAAC
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (23 bp):
TTGTCCCGAAGGATAACATAGAA
Found at i:1234544 original size:22 final size:22
Alignment explanation
Indices: 1234516--1234569 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
1234506 ATTGACTTTT
1234516 TGGTCAAAGTCAAAGTAAACGC
1 TGGTCAAAGTCAAAGTAAACGC
* * *
1234538 TGGTCAATGTCAAAGTCAACTC
1 TGGTCAAAGTCAAAGTAAACGC
*
1234560 TAGTCAAAGT
1 TGGTCAAAGT
1234570 AAATGGTAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (22 bp):
TGGTCAAAGTCAAAGTAAACGC
Found at i:1237734 original size:30 final size:33
Alignment explanation
Indices: 1237698--1237769 Score: 96
Period size: 35 Copynumber: 2.2 Consensus size: 33
1237688 AAAATTGAAT
1237698 TAAACGGGAAC-G-GA-GAAAAACCGTTTATGC
1 TAAACGGGAACGGAGAGGAAAAACCGTTTATGC
*
1237728 TAAACGGGGACGGAGACGGGAAAAACCGTTTATGC
1 TAAACGGGAACGGAGA--GGAAAAACCGTTTATGC
1237763 TAAACGG
1 TAAACGG
1237770 AGACGAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
30 10 0.28
31 1 0.03
32 2 0.06
35 23 0.64
ACGTcount: A:0.38, C:0.17, G:0.31, T:0.15
Consensus pattern (33 bp):
TAAACGGGAACGGAGAGGAAAAACCGTTTATGC
Found at i:1237758 original size:35 final size:36
Alignment explanation
Indices: 1237707--1237774 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
1237697 TTAAACGGGA
*
1237707 ACGGAGAAAAACCGTTTATGCTAAACGGGGACGGAG
1 ACGGAGAAAAACCGTTTATGCTAAACGGAGACGGAG
1237743 ACGG-GAAAAACCGTTTATGCTAAACGGAGACG
1 ACGGAGAAAAACCGTTTATGCTAAACGGAGACG
1237775 AATTTGGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 27 0.87
36 4 0.13
ACGTcount: A:0.37, C:0.18, G:0.31, T:0.15
Consensus pattern (36 bp):
ACGGAGAAAAACCGTTTATGCTAAACGGAGACGGAG
Found at i:1237912 original size:15 final size:14
Alignment explanation
Indices: 1237892--1237933 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
1237882 AATTAGAAAA
1237892 ATATATATAATATTT
1 ATATATAT-ATATTT
*
1237907 ATATATTTA-ATTT
1 ATATATATATATTT
*
1237920 AAATATATATATTT
1 ATATATATATATTT
1237934 CCGGCCCGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 11 0.48
14 5 0.22
15 7 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATATATATATATTT
Found at i:1248788 original size:6 final size:6
Alignment explanation
Indices: 1248777--1250297 Score: 1762
Period size: 6 Copynumber: 254.3 Consensus size: 6
1248767 ATCACATTGT
1248777 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATG-
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
* * * * * * * *
1248824 GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
* * * * * * * *
1248872 GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
* * * * * * * *
1248920 GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
* * * * * * * *
1248968 GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
* * * * * * * *
1249016 GTATGG GTATGG GTATGG GTATGG GTATGG GTATG- G-GTGG GTATGG
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
* * * * * * * *
1249062 GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
* * * * * * * *
1249110 GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
* * * * * * * *
1249158 GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
*
1249206 GTATGG GTATGA GT-TGA GGT-TGA GTATGA GTATGA GTATGA GTATGA
1 GTATGA GTATGA GTATGA -GTATGA GTATGA GTATGA GTATGA GTATGA
1249253 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATG-
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
* * * * * * *
1249300 GTATG- GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
* * * * * * * *
1249347 GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
* * * * * * * *
1249395 GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
* * * * * * * *
1249443 GTATGG GTATGG GTATGG GTATGGGG GTATGG GTATGG GTATGG GTATGG
1 GTATGA GTATGA GTATGA GTAT--GA GTATGA GTATGA GTATGA GTATGA
* * * * * * * *
1249493 GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
* * * * * * * *
1249541 GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG GTATGG
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
*
1249589 GTATGG GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
1249637 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
1249685 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
* * *
1249733 GTATGA GTATGA GTAGGA GTATGA GTATGA GTACGA GTATGA GTACGA
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
*
1249781 GTATGA GTATGA GTACGA GTATGA GTATGA GTATGA GTATGA GTATGA
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
* * * *
1249829 GTATGA GTATGA GTATGA GTACGA GTACGA GTACGA GTACGA GTATGA
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
*
1249877 GTATGA GTACGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
* * * * * *
1249925 GTACGA GTACGA GTACGA GTACGA GTACGA GTATGA GTATGA GTACGA
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
1249973 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
1250021 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
1250069 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
1250117 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
1250165 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
* * *
1250213 GTATGA GTATGA GTATCA GTATGA GTATCA GTATGA GTATCA GTATGA
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA
* *
1250261 GTATCA GTA-GA GTATCA GTATGA GTATGA GTATGA GT
1 GTATGA GTATGA GTATGA GTATGA GTATGA GTATGA GT
1250298 GAGAGTTTAA
Statistics
Matches: 1476, Mismatches: 30, Indels: 18
0.97 0.02 0.01
Matches are distributed among these distances:
4 2 0.00
5 26 0.02
6 1442 0.98
8 6 0.00
ACGTcount: A:0.26, C:0.01, G:0.41, T:0.32
Consensus pattern (6 bp):
GTATGA
Found at i:1255801 original size:23 final size:23
Alignment explanation
Indices: 1255731--1255793 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1255721 TCGATGGTTT
1255731 TACGCGGTCCTTCGGGACAATTC
1 TACGCGGTCCTTCGGGACAATTC
* **
1255754 TATGTTGTCCTTCGGGACAATTC
1 TACGCGGTCCTTCGGGACAATTC
*
1255777 TACGCGGTCATTCGGGA
1 TACGCGGTCCTTCGGGA
1255794 TAAATCTATG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.17, C:0.25, G:0.27, T:0.30
Consensus pattern (23 bp):
TACGCGGTCCTTCGGGACAATTC
Found at i:1255813 original size:46 final size:47
Alignment explanation
Indices: 1255731--1255827 Score: 119
Period size: 46 Copynumber: 2.1 Consensus size: 47
1255721 TCGATGGTTT
* * *
1255731 TACGCGGTCCTTCGGGACAATTCTATGTTGTCCTTCGG-GACA-ATTC
1 TACGCGGTCATTCGGGACAAATCTATGTTGGCCTTCGGTG-CATATTC
*
1255777 TACGCGGTCATTCGGGATAAATCTATG-TGGCACTTCGGTGCATATTC
1 TACGCGGTCATTCGGGACAAATCTATGTTGGC-CTTCGGTGCATATTC
1255824 TACG
1 TACG
1255828 TAACACTTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
45 3 0.07
46 32 0.73
47 9 0.20
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.32
Consensus pattern (47 bp):
TACGCGGTCATTCGGGACAAATCTATGTTGGCCTTCGGTGCATATTC
Found at i:1258141 original size:2 final size:2
Alignment explanation
Indices: 1258134--1258172 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1258124 GAATACGGTA
1258134 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1258173 AATTTAAAAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1260172 original size:2 final size:2
Alignment explanation
Indices: 1260165--1260193 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1260155 GTTTCTTAAT
1260165 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 T
1260194 TAACAATTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1261250 original size:2 final size:2
Alignment explanation
Indices: 1261243--1261301 Score: 50
Period size: 2 Copynumber: 30.0 Consensus size: 2
1261233 ATTATTTTTA
* * * * *
1261243 AT AT AT AT AT AT AT AT AA AT A- AT AT TT TT AGT AT TT TT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
1261284 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1261302 TTAATTTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
1 2 0.04
2 44 0.92
3 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1261289 original size:39 final size:40
Alignment explanation
Indices: 1261235--1261319 Score: 138
Period size: 39 Copynumber: 2.1 Consensus size: 40
1261225 TGTTGGTTAT
1261235 TATTTTTAATATATATATATATATA-A-ATAATATTTTTAG
1 TATTTTTAATATATATATATATATATATATAAT-TTTTTAG
*
1261274 TATTTTTAATATATATATATATATATATTTAATTTTTTAG
1 TATTTTTAATATATATATATATATATATATAATTTTTTAG
1261314 TATTTT
1 TATTTT
1261320 ATATTTCATT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
39 25 0.58
40 14 0.33
41 4 0.09
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (40 bp):
TATTTTTAATATATATATATATATATATATAATTTTTTAG
Found at i:1266989 original size:32 final size:31
Alignment explanation
Indices: 1266953--1267043 Score: 128
Period size: 31 Copynumber: 2.9 Consensus size: 31
1266943 TTAATTGATT
* *
1266953 GTGTGACACATATCACGTCATCATTTTAGGTG
1 GTGTGACACATATTACGTCATCATTTT-GGTA
1266985 GTGTGACACATATTACGTCATCATTTTGGTA
1 GTGTGACACATATTACGTCATCATTTTGGTA
* * *
1267016 GCGTGACACATGTTACATCATCATTTTG
1 GTGTGACACATATTACGTCATCATTTTG
1267044 ACGACGTAAC
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
31 28 0.52
32 26 0.48
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (31 bp):
GTGTGACACATATTACGTCATCATTTTGGTA
Found at i:1267081 original size:17 final size:17
Alignment explanation
Indices: 1267059--1267106 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
1267049 GTAACATGTA
**
1267059 CCACATCATCTTTTGTG
1 CCACATCATCAATTGTG
1267076 CCACATCATCAATTGTG
1 CCACATCATCAATTGTG
1267093 CCACATCATCAATT
1 CCACATCATCAATT
1267107 AAAACATATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.27, C:0.31, G:0.08, T:0.33
Consensus pattern (17 bp):
CCACATCATCAATTGTG
Found at i:1270984 original size:41 final size:40
Alignment explanation
Indices: 1270924--1271030 Score: 115
Period size: 42 Copynumber: 2.6 Consensus size: 40
1270914 GCCCGAAGGT
* * * *
1270924 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGC
1 CTTAT-GATGGCCCAAAGGACTTAGCATCATGCTCGAAAGA
* *
1270965 CTTATAGATGACCCAAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTAT-GATGGCCCAAAGGACTT-AGCATCATGCTCGAAAGA
*
1271007 CTTACTGATGGCCTAAAGGACTTA
1 CTTA-TGATGGCCCAAAGGACTTA
1271031 AGATGATTCA
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 20 0.37
42 33 0.61
43 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (40 bp):
CTTATGATGGCCCAAAGGACTTAGCATCATGCTCGAAAGA
Found at i:1271260 original size:39 final size:39
Alignment explanation
Indices: 1271170--1271841 Score: 963
Period size: 39 Copynumber: 17.2 Consensus size: 39
1271160 AAGAAAAATA
* * *
1271170 ATCTCAAGTGAGAT-AAATCTTCTGTTTCTAGTG-AATT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* *
1271207 ATCTCCAGCGAGATAAAATCTTTTGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
*
1271246 ATCTCAAGCGAGATAAAATCTTCTATTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* *
1271285 ATCTAAAGCGAGATAAAATCTTCTGTTTCAAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
*
1271324 ATCTCAAGCGAGATAAAATCTTATGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* * *
1271363 ATCTCAAGAGAGATAGAATCTTTTGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
*
1271402 ATCTCAAGCGAGATAAAATCTTATGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
1271441 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* * *
1271480 ATTTCAAGCGAGACAAAATCTT-TAGTTTCAAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCT-GTTTCGAGTGAAACT
* *
1271519 ATCTCAAACGAGATAAAATCTTCTGTTTTGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* ** *
1271558 ATCTTAAAAGAGATAAAATCTTCTGTTTCAAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* * *
1271597 ATCTGAAGCGAGATAAAATCTTCTATTTTGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
1271636 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* *
1271675 ATCTCAAGCGAGAAAAAAATCTTTTGTTTCGAGTGAAACT
1 ATCTCAAGCGAG-ATAAAATCTTCTGTTTCGAGTGAAACT
* *
1271715 ATCTTAAGCGAGATAAAATTTTCTGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* * *
1271754 ATCTTAAACGAGATAAAAAATCTTATGTTTCGAGTGAAACT
1 ATCTCAAGCGAGAT--AAAATCTTCTGTTTCGAGTGAAACT
* * * *
1271795 ATATCAAGCGAGATGAAATCTTCTATTTTGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
1271834 ATCTCAAG
1 ATCTCAAG
1271842 TGTAATACCC
Statistics
Matches: 569, Mismatches: 59, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
37 12 0.02
38 18 0.03
39 468 0.82
40 37 0.07
41 34 0.06
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (39 bp):
ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
Found at i:1271296 original size:19 final size:19
Alignment explanation
Indices: 1271235--1271296 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
1271225 TCTTTTGTTT
*
1271235 CGAGTGAAACTATCTCAAG
1 CGAGTGAAACTATCTAAAG
* ***
1271254 CGAGATAAAATCT-TCTATTT
1 CGAG-TGAAA-CTATCTAAAG
1271274 CGAGTGAAACTATCTAAAG
1 CGAGTGAAACTATCTAAAG
1271293 CGAG
1 CGAG
1271297 ATAAAATCTT
Statistics
Matches: 31, Mismatches: 9, Indels: 6
0.67 0.20 0.13
Matches are distributed among these distances:
18 2 0.06
19 16 0.52
20 11 0.35
21 2 0.06
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (19 bp):
CGAGTGAAACTATCTAAAG
Found at i:1271444 original size:22 final size:22
Alignment explanation
Indices: 1271380--1271444 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 22
1271370 GAGAGATAGA
*
1271380 ATCTTTTGTTTCGAGTGAAACT
1 ATCTTATGTTTCGAGTGAAACT
* *
1271402 ATCTCAAG---CGAGAT-AAA--
1 ATCTTATGTTTCGAG-TGAAACT
1271419 ATCTTATGTTTCGAGTGAAACT
1 ATCTTATGTTTCGAGTGAAACT
1271441 ATCT
1 ATCT
1271445 CAAGCGAGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 14
0.62 0.10 0.28
Matches are distributed among these distances:
17 6 0.19
19 8 0.26
20 8 0.26
22 9 0.29
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (22 bp):
ATCTTATGTTTCGAGTGAAACT
Found at i:1272763 original size:14 final size:15
Alignment explanation
Indices: 1272731--1272770 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
1272721 AGTCCAGTCA
*
1272731 CCGAGTCAACTCGGT
1 CCGAGTCAACTCCGT
1272746 CCGAGTCAAC-CCGT
1 CCGAGTCAACTCCGT
1272760 CCGAGTCAACT
1 CCGAGTCAACT
1272771 TGTTGACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.23, C:0.38, G:0.23, T:0.17
Consensus pattern (15 bp):
CCGAGTCAACTCCGT
Found at i:1279649 original size:12 final size:12
Alignment explanation
Indices: 1279624--1279693 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
1279614 ACAGATATAT
* *
1279624 CAGAAATCAAAA
1 CAGAATTCAGAA
1279636 CAGAATTCAGAA
1 CAGAATTCAGAA
* *
1279648 CA-TATATCAAAA
1 CAGAAT-TCAGAA
* *
1279660 CAGAATCCAGAT
1 CAGAATTCAGAA
*
1279672 CAGAAATCAGAA
1 CAGAATTCAGAA
*
1279684 CATAATTCAG
1 CAGAATTCAG
1279694 GTTATGTATC
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
11 2 0.05
12 39 0.91
13 2 0.05
ACGTcount: A:0.53, C:0.19, G:0.11, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1279659 original size:24 final size:24
Alignment explanation
Indices: 1279624--1279693 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
1279614 ACAGATATAT
1279624 CAGAAATCAAAACAGAATTCAGAA
1 CAGAAATCAAAACAGAATTCAGAA
* * * *
1279648 CATATATCAAAACAGAATCCAGAT
1 CAGAAATCAAAACAGAATTCAGAA
* *
1279672 CAGAAATCAGAACATAATTCAG
1 CAGAAATCAAAACAGAATTCAG
1279694 GTTATGTATC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.53, C:0.19, G:0.11, T:0.17
Consensus pattern (24 bp):
CAGAAATCAAAACAGAATTCAGAA
Found at i:1279728 original size:24 final size:24
Alignment explanation
Indices: 1279675--1279730 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
1279665 TCCAGATCAG
* * *
1279675 AAATCAGAACATAATTCAGGTTAT
1 AAATCAGAACATAATTCAAGTCAA
**
1279699 GTATCAGAACATAATTCAAGTCAA
1 AAATCAGAACATAATTCAAGTCAA
1279723 AAATCAGA
1 AAATCAGA
1279731 TAAAATATTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.25
Consensus pattern (24 bp):
AAATCAGAACATAATTCAAGTCAA
Found at i:1281844 original size:17 final size:17
Alignment explanation
Indices: 1281824--1281856 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1281814 GCATATCAAC
1281824 AGAAATTACATAAAAAT
1 AGAAATTACATAAAAAT
1281841 AGAAATTACATAAAAA
1 AGAAATTACATAAAAA
1281857 ACGGAGCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.21
Consensus pattern (17 bp):
AGAAATTACATAAAAAT
Found at i:1284396 original size:12 final size:12
Alignment explanation
Indices: 1284371--1284440 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
1284361 ACGGAGATAT
* *
1284371 CAGAAATCAAAA
1 CAGAATTCAGAA
1284383 CAGAATTCAGAA
1 CAGAATTCAGAA
*
1284395 CA-TATATCAGAA
1 CAGAAT-TCAGAA
* *
1284407 CAGAATCCAGAT
1 CAGAATTCAGAA
* *
1284419 CAGAAATCTGAA
1 CAGAATTCAGAA
*
1284431 CATAATTCAG
1 CAGAATTCAG
1284441 GTAATGTATT
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
11 2 0.05
12 39 0.91
13 2 0.05
ACGTcount: A:0.50, C:0.19, G:0.13, T:0.19
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1284431 original size:24 final size:24
Alignment explanation
Indices: 1284369--1284432 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
1284359 AAACGGAGAT
* *
1284369 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATCCAG
* * *
1284393 AACATATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATCCAG
*
1284417 ATCAGAAATCTGAACA
1 ATCAGAAATCAGAACA
1284433 TAATTCAGGT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.52, C:0.19, G:0.12, T:0.17
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATCCAG
Found at i:1288972 original size:2 final size:2
Alignment explanation
Indices: 1288965--1289001 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1288955 TCATTTTAAA
1288965 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1289002 CCCCATCCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1289218 original size:12 final size:12
Alignment explanation
Indices: 1289183--1289224 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1289173 CAGAATTCAA
1289183 AACATATATCAG
1 AACATATATCAG
*
1289195 AACAGA-ATTCAG
1 AACATATA-TCAG
1289207 AACATATATCAG
1 AACATATATCAG
*
1289219 GACATA
1 AACATA
1289225 ATCGGATCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 1 0.04
12 23 0.92
13 1 0.04
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (12 bp):
AACATATATCAG
Found at i:1289218 original size:24 final size:24
Alignment explanation
Indices: 1289166--1289276 Score: 91
Period size: 24 Copynumber: 4.7 Consensus size: 24
1289156 GATATCAGAA
* *
1289166 ATCAAAACAGAATTCAAAACATAT
1 ATCAGAACAGAATTCAGAACATAT
1289190 ATCAGAACAGAATTCAGAACATAT
1 ATCAGAACAGAATTCAGAACATAT
* * * * * *
1289214 ATCAGGACATAA-TCGGATCAGAA
1 ATCAGAACAGAATTCAGAACATAT
* * *
1289237 ATCAGAACAAAATTCAGGTA-ATGT
1 ATCAGAACAGAATTCA-GAACATAT
*
1289261 ATTAGAACAGAATTCA
1 ATCAGAACAGAATTCA
1289277 AGTCGGAAAT
Statistics
Matches: 67, Mismatches: 18, Indels: 4
0.75 0.20 0.04
Matches are distributed among these distances:
23 17 0.25
24 49 0.73
25 1 0.01
ACGTcount: A:0.50, C:0.15, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGAACATAT
Found at i:1298076 original size:36 final size:36
Alignment explanation
Indices: 1298020--1298100 Score: 99
Period size: 36 Copynumber: 2.2 Consensus size: 36
1298010 AATTAAACGG
*
1298020 GGACGGAGAAAAACCATTTATGCTAAACGAGGACGA
1 GGACGGGGAAAAACCATTTATGCTAAACGAGGACGA
* * * * * *
1298056 GGATGGGGAAAAACCGTTTATGTTAAATGGGGACGG
1 GGACGGGGAAAAACCATTTATGCTAAACGAGGACGA
1298092 GGACGGGGA
1 GGACGGGGA
1298101 CGAGTTTAGT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.35, C:0.12, G:0.37, T:0.16
Consensus pattern (36 bp):
GGACGGGGAAAAACCATTTATGCTAAACGAGGACGA
Found at i:1298438 original size:25 final size:25
Alignment explanation
Indices: 1298388--1298438 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
1298378 AAATTCTCAC
* *
1298388 GATTTTTTAAGCGGGGATGGGTACG
1 GATTTTTTAAACGGGGAAGGGTACG
*
1298413 GATTTTTTAAATGGGGACAGGG-ACG
1 GATTTTTTAAACGGGGA-AGGGTACG
1298438 G
1 G
1298439 GGGGATCAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.24, C:0.08, G:0.39, T:0.29
Consensus pattern (25 bp):
GATTTTTTAAACGGGGAAGGGTACG
Found at i:1299383 original size:27 final size:27
Alignment explanation
Indices: 1299345--1299435 Score: 137
Period size: 27 Copynumber: 3.3 Consensus size: 27
1299335 GTCACCGACC
* * *
1299345 CGGTGGCTGGCGTGTGAGGGCCATGAG
1 CGGTGGCCGGCGTATAAGGGCCATGAG
1299372 CGGTGGCCGGCGTATAAGGGCCATGAG
1 CGGTGGCCGGCGTATAAGGGCCATGAG
*
1299399 CGGTGGCCGGCGTATAAGGGCCGGTGAG
1 CGGTGGCCGGCGTATAAGGGCC-ATGAG
1299427 CGGTGGCCG
1 CGGTGGCCG
1299436 AGTGAGTCGT
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
27 46 0.78
28 13 0.22
ACGTcount: A:0.13, C:0.22, G:0.49, T:0.15
Consensus pattern (27 bp):
CGGTGGCCGGCGTATAAGGGCCATGAG
Found at i:1299873 original size:33 final size:33
Alignment explanation
Indices: 1299836--1299905 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 33
1299826 TGATTTATTG
*
1299836 CACTTTTATCA-TTCT-ATTTTATTTTAATTTAGC
1 CACTTTTAT-ATTTCTGA-TTTATTTGAATTTAGC
*
1299869 CACTTTTATATTTCTGATTTATTTGAATTTAGT
1 CACTTTTATATTTCTGATTTATTTGAATTTAGC
1299902 CACT
1 CACT
1299906 GACTTTTACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 1 0.03
33 31 0.94
34 1 0.03
ACGTcount: A:0.24, C:0.14, G:0.06, T:0.56
Consensus pattern (33 bp):
CACTTTTATATTTCTGATTTATTTGAATTTAGC
Found at i:1300110 original size:22 final size:22
Alignment explanation
Indices: 1300085--1300148 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
1300075 TTAGTTATCG
1300085 TATTTATTTTATTTTTATTTGT
1 TATTTATTTTATTTTTATTTGT
* *
1300107 TATTTATGTTGTTTTT-TTT-T
1 TATTTATTTTATTTTTATTTGT
* * *
1300127 TACTT-TTTTATTATTACTTGT
1 TATTTATTTTATTTTTATTTGT
1300148 T
1 T
1300149 GTTTTAGTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
19 7 0.21
20 7 0.21
21 5 0.15
22 14 0.42
ACGTcount: A:0.16, C:0.03, G:0.06, T:0.75
Consensus pattern (22 bp):
TATTTATTTTATTTTTATTTGT
Found at i:1304952 original size:16 final size:18
Alignment explanation
Indices: 1304912--1304953 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
1304902 ATCTGTAATT
1304912 TTACCTTCCCATACAGAAA
1 TTACCTTCCCATA-AGAAA
*
1304931 TAACCTTCCCAT-A-AAA
1 TTACCTTCCCATAAGAAA
1304947 TTACCTT
1 TTACCTT
1304954 TTTCAGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 9 0.43
17 1 0.05
19 11 0.52
ACGTcount: A:0.36, C:0.31, G:0.02, T:0.31
Consensus pattern (18 bp):
TTACCTTCCCATAAGAAA
Found at i:1305316 original size:2 final size:2
Alignment explanation
Indices: 1305309--1305338 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1305299 TCCTTTCAAA
*
1305309 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1305339 CCCTTGTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1305636 original size:12 final size:12
Alignment explanation
Indices: 1305619--1305695 Score: 54
Period size: 12 Copynumber: 6.4 Consensus size: 12
1305609 CACAAGAAAG
1305619 AAAAAGAAGAGA
1 AAAAAGAAGAGA
1305631 AAAAAGAA-AGGAA
1 AAAAAGAAGA-G-A
1305644 AAAATAGAAGA-A
1 AAAA-AGAAGAGA
** *
1305656 AATGAGAAAAAGA
1 AAAAAG-AAGAGA
*
1305669 AAAAAAAAGA-A
1 AAAAAGAAGAGA
1305680 AAAAAG-AGAGA
1 AAAAAGAAGAGA
1305691 AAAAA
1 AAAAA
1305696 TTAAAAAGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 15
0.68 0.11 0.21
Matches are distributed among these distances:
10 3 0.06
11 15 0.30
12 18 0.36
13 9 0.18
14 4 0.08
15 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (12 bp):
AAAAAGAAGAGA
Found at i:1305636 original size:18 final size:18
Alignment explanation
Indices: 1305615--1305705 Score: 51
Period size: 16 Copynumber: 4.7 Consensus size: 18
1305605 AAGCCACAAG
1305615 AAAGAAAAAGAAGAGAAA
1 AAAGAAAAAGAAGAGAAA
*
1305633 AAAGAAAGGAAAAAATAGAAGAAA
1 AAAG--A--AAAAGA-AG-AGAAA
*
1305657 ATGAGAAAAAGAA-A-AAA
1 A-AAGAAAAAGAAGAGAAA
*
1305674 AAAGAAAAAAAGAGAGAAA
1 AAAGAAAAAGA-AGAGAAA
*
1305693 AAATTAAAAAGAA
1 AAA-GAAAAAGAA
1305706 AAAATAAGAA
Statistics
Matches: 55, Mismatches: 7, Indels: 21
0.66 0.08 0.25
Matches are distributed among these distances:
16 8 0.15
17 5 0.09
18 6 0.11
19 7 0.13
20 8 0.15
21 5 0.09
22 5 0.09
23 3 0.05
24 6 0.11
25 2 0.04
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (18 bp):
AAAGAAAAAGAAGAGAAA
Found at i:1305657 original size:10 final size:9
Alignment explanation
Indices: 1305616--1305722 Score: 64
Period size: 10 Copynumber: 11.9 Consensus size: 9
1305606 AGCCACAAGA
1305616 AAGAAAAAG
1 AAGAAAAAG
1305625 AAGAGAAAA-
1 AAGA-AAAAG
*
1305634 AAG-AAAGG
1 AAGAAAAAG
1305642 AA-AAAATAG
1 AAGAAAA-AG
*
1305651 AAGAAAATG
1 AAGAAAAAG
1305660 -AGAAAAAG
1 AAGAAAAAG
*
1305668 AAAAAAAAAG
1 -AAGAAAAAG
1305678 AA-AAAAAG
1 AAGAAAAAG
1305686 AGAGAAAAA-
1 A-AGAAAAAG
**
1305695 ATTAAAAAG
1 AAGAAAAAG
*
1305704 AAAAAATAAG
1 AAGAAA-AAG
1305714 AAAGAAAAA
1 -AAGAAAAA
1305723 TAGATAGATC
Statistics
Matches: 76, Mismatches: 10, Indels: 23
0.70 0.09 0.21
Matches are distributed among these distances:
7 3 0.04
8 24 0.32
9 19 0.25
10 25 0.33
11 5 0.07
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.05
Consensus pattern (9 bp):
AAGAAAAAG
Found at i:1305667 original size:27 final size:28
Alignment explanation
Indices: 1305615--1305694 Score: 83
Period size: 28 Copynumber: 2.8 Consensus size: 28
1305605 AAGCCACAAG
1305615 AAAGAAAAAGAAGAGA-AAAAAGAAAGGAAAA
1 AAAGAAAAA-AAGAGAGAAAAAG-AA--AAAA
* *
1305646 AATAGAAGAAAA-TGAGAAAAAGAAAAAA
1 AA-AGAAAAAAAGAGAGAAAAAGAAAAAA
1305674 AAAGAAAAAAAGAGAGAAAAA
1 AAAGAAAAAAAGAGAGAAAAA
1305695 ATTAAAAAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
27 8 0.19
28 14 0.33
30 4 0.10
31 10 0.24
32 6 0.14
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (28 bp):
AAAGAAAAAAAGAGAGAAAAAGAAAAAA
Found at i:1305692 original size:36 final size:35
Alignment explanation
Indices: 1305628--1305721 Score: 100
Period size: 36 Copynumber: 2.5 Consensus size: 35
1305618 GAAAAAGAAG
*
1305628 AGAAAAAAGAAAGGAAAAAATAGAAGAAAATGA-GAAAA
1 AGAAAAAA-AAA-GAAAAAA-AGAAGAAAA-AATGAAAA
*
1305666 AGAAAAAAAAAGAAAAAAAGAGAGAAAAAATTAAAA
1 AGAAAAAAAAAGAAAAAAAGA-AGAAAAAATGAAAA
*
1305702 AGAAAAAATAAGAAAGAAAA
1 AGAAAAAAAAAGAAA-AAAA
1305722 ATAGATAGAT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
35 4 0.08
36 31 0.62
37 7 0.14
38 8 0.16
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (35 bp):
AGAAAAAAAAAGAAAAAAAGAAGAAAAAATGAAAA
Found at i:1305705 original size:14 final size:14
Alignment explanation
Indices: 1305612--1305722 Score: 68
Period size: 14 Copynumber: 8.6 Consensus size: 14
1305602 AAAAAGCCAC
1305612 AAGAAAGAAA-AAG-
1 AAGAAA-AAATAAGA
*
1305625 AAGAGAAAA-AAGA
1 AAGAAAAAATAAGA
1305638 AAGGAAAAAAT-AG-
1 AA-GAAAAAATAAGA
*
1305651 AAG--AAAATGAGA
1 AAGAAAAAATAAGA
1305663 AA-AAGAAAA-AA-A
1 AAGAA-AAAATAAGA
1305675 AAG-AAAAA-AAGA
1 AAGAAAAAATAAGA
*
1305687 GAGAAAAAATTAA-A
1 AAGAAAAAA-TAAGA
1305701 AAGAAAAAATAAGA
1 AAGAAAAAATAAGA
1305715 AAGAAAAA
1 AAGAAAAA
1305723 TAGATAGATC
Statistics
Matches: 79, Mismatches: 5, Indels: 27
0.71 0.05 0.24
Matches are distributed among these distances:
10 5 0.06
11 8 0.10
12 16 0.20
13 18 0.23
14 30 0.38
15 2 0.03
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (14 bp):
AAGAAAAAATAAGA
Found at i:1305707 original size:13 final size:14
Alignment explanation
Indices: 1305674--1305723 Score: 52
Period size: 13 Copynumber: 3.7 Consensus size: 14
1305664 AAAGAAAAAA
1305674 AAAGAAAAA--AAG
1 AAAGAAAAATTAAG
*
1305686 AGAGAAAAAATTAA-
1 AAAG-AAAAATTAAG
*
1305700 AAAGAAAAAATAAG
1 AAAGAAAAATTAAG
1305714 AAAGAAAAAT
1 AAAGAAAAAT
1305724 AGATAGATCC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
12 3 0.10
13 13 0.43
14 12 0.40
15 2 0.07
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (14 bp):
AAAGAAAAATTAAG
Found at i:1305721 original size:26 final size:24
Alignment explanation
Indices: 1305613--1305722 Score: 84
Period size: 26 Copynumber: 4.5 Consensus size: 24
1305603 AAAAGCCACA
*
1305613 AGAAAG-AAAAAGAAGAGAAAAAAG
1 AGAAAGAAAAAAAAAGA-AAAAAAG
* **
1305637 A-AAGGAAAAAATAGAAGAAAATGAG
1 AGAAAGAAAAAA-A-AAGAAAAAAAG
*
1305662 AAAAAGAAAAAAAAAGAAAAAAAG
1 AGAAAGAAAAAAAAAGAAAAAAAG
1305686 AGAGAA-AAAATTAAAAAGAAAAAATA-
1 AGA-AAGAAAA--AAAAAGAAAAAA-AG
1305712 AGAAAGAAAAA
1 AGAAAGAAAAA
1305723 TAGATAGATC
Statistics
Matches: 69, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
23 3 0.04
24 22 0.32
25 11 0.16
26 32 0.46
27 1 0.01
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (24 bp):
AGAAAGAAAAAAAAAGAAAAAAAG
Found at i:1307904 original size:41 final size:42
Alignment explanation
Indices: 1307818--1307904 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
1307808 GAGCCATTAG
* * * * *
1307818 TAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTA
1 TAAGTCTTTCGAGCAAGATGCATAAATCATTCGGGCCATCCA
1307860 TAAGTCTTTCGAGCAAGATG-ATAAGA-CATTCGGGCCATCCA
1 TAAGTCTTTCGAGCAAGATGCATAA-ATCATTCGGGCCATCCA
1307901 TAAG
1 TAAG
1307905 ACCTTCGGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 19 0.49
42 20 0.51
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.30
Consensus pattern (42 bp):
TAAGTCTTTCGAGCAAGATGCATAAATCATTCGGGCCATCCA
Found at i:1308522 original size:23 final size:22
Alignment explanation
Indices: 1308478--1308528 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
1308468 TCTAATATTG
*
1308478 TTTTTCCTTTTTACTTTCTTTT
1 TTTTTCCTTTTTACTTGCTTTT
* *
1308500 TTTTTTCTTTTTCACTTGGTTTT
1 TTTTTCCTTTTT-ACTTGCTTTT
*
1308523 TGTTTC
1 TTTTTC
1308529 GGTTTAGGGG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.04, C:0.16, G:0.06, T:0.75
Consensus pattern (22 bp):
TTTTTCCTTTTTACTTGCTTTT
Found at i:1314832 original size:24 final size:24
Alignment explanation
Indices: 1314800--1314847 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1314790 TGGTATCCAT
1314800 TAAACACTTATTTGTGATATAAGC
1 TAAACACTTATTTGTGATATAAGC
1314824 TAAACACTTATTTGTGATATAAGC
1 TAAACACTTATTTGTGATATAAGC
1314848 CAAAAAGGAA
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:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (24 bp):
TAAACACTTATTTGTGATATAAGC
Found at i:1315789 original size:24 final size:24
Alignment explanation
Indices: 1315755--1315820 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
1315745 CTCTTGTGGT
* *
1315755 TGGCTGCTGCTGAGGCTGAGATTG
1 TGGCTGTTGCTGAGGCTGAGACTG
1315779 TGGCTGTTGCTGAGGCTGAGACTG
1 TGGCTGTTGCTGAGGCTGAGACTG
*
1315803 TGGCGGTTGC-GAAGGCTG
1 TGGCTGTTGCTG-AGGCTG
1315821 TATTGGCTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 1 0.03
24 37 0.97
ACGTcount: A:0.12, C:0.17, G:0.44, T:0.27
Consensus pattern (24 bp):
TGGCTGTTGCTGAGGCTGAGACTG
Found at i:1320316 original size:19 final size:20
Alignment explanation
Indices: 1320292--1320330 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
1320282 AAGAAAGTCA
1320292 ACGGTCAACGGTC-ACGGTC
1 ACGGTCAACGGTCAACGGTC
1320311 ACGGTCAACGGTCAACGGTC
1 ACGGTCAACGGTCAACGGTC
1320331 GGGTCGGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (20 bp):
ACGGTCAACGGTCAACGGTC
Found at i:1320317 original size:26 final size:24
Alignment explanation
Indices: 1320288--1320347 Score: 84
Period size: 26 Copynumber: 2.4 Consensus size: 24
1320278 GTCAAAGAAA
1320288 GTCAACGGTCAACGGTCACGGTCACG
1 GTCAACGGTCAACGGTC-CGGTC-CG
* *
1320314 GTCAACGGTCAACGGTCGGGTCGG
1 GTCAACGGTCAACGGTCCGGTCCG
1320338 GTCAACGGTC
1 GTCAACGGTC
1320348 GGGTCGGGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 11 0.34
25 4 0.12
26 17 0.53
ACGTcount: A:0.20, C:0.28, G:0.35, T:0.17
Consensus pattern (24 bp):
GTCAACGGTCAACGGTCCGGTCCG
Found at i:1320342 original size:17 final size:17
Alignment explanation
Indices: 1320320--1320411 Score: 175
Period size: 17 Copynumber: 5.4 Consensus size: 17
1320310 CACGGTCAAC
1320320 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1320337 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1320354 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1320371 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
1320388 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1320405 GGTCAAC
1 GGTCAAC
1320412 CCAGTTCAGA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
17 74 1.00
ACGTcount: A:0.14, C:0.24, G:0.45, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:1320347 original size:7 final size:7
Alignment explanation
Indices: 1320288--1320330 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
1320278 GTCAAAGAAA
1320288 GTCAACG
1 GTCAACG
1320295 GTCAACG
1 GTCAACG
1320302 GTC-ACG
1 GTCAACG
1320308 GTC-ACG
1 GTCAACG
1320314 GTCAACG
1 GTCAACG
1320321 GTCAACG
1 GTCAACG
1320328 GTC
1 GTC
1320331 GGGTCGGGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 12 0.34
7 23 0.66
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:1320444 original size:10 final size:10
Alignment explanation
Indices: 1320415--1320475 Score: 65
Period size: 9 Copynumber: 6.3 Consensus size: 10
1320405 GGTCAACCCA
*
1320415 GTTCAGACCG
1 GTTCAAACCG
1320425 G-TCAAACCG
1 GTTCAAACCG
*
1320434 GTTCGAACCG
1 GTTCAAACCG
1320444 G-TCAAACCG
1 GTTCAAACCG
*
1320453 GTTCAAAACTG
1 GTTC-AAACCG
1320464 G-TCAAACCG
1 GTTCAAACCG
1320473 GTT
1 GTT
1320476 TTCGAGCAAC
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
9 22 0.52
10 14 0.33
11 6 0.14
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.20
Consensus pattern (10 bp):
GTTCAAACCG
Found at i:1320468 original size:20 final size:19
Alignment explanation
Indices: 1320405--1320475 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
1320395 AGTCGGGTCG
* * *
1320405 GGTCAACCCAGTTCAGACC
1 GGTCAAACCGGTTCAAACC
*
1320424 GGTCAAACCGGTTCGAACC
1 GGTCAAACCGGTTCAAACC
*
1320443 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AAACC
1320463 GGTCAAACCGGTT
1 GGTCAAACCGGTT
1320476 TTCGAGCAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
19 29 0.64
20 16 0.36
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCAAACC
Found at i:1327653 original size:13 final size:14
Alignment explanation
Indices: 1327635--1327664 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1327625 GTCAAATAAA
1327635 GTCAACGGTC-ACG
1 GTCAACGGTCAACG
1327648 GTCAACGGTCAACG
1 GTCAACGGTCAACG
1327662 GTC
1 GTC
1327665 GGGTCGGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:1327655 original size:7 final size:7
Alignment explanation
Indices: 1327635--1327664 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1327625 GTCAAATAAA
1327635 GTCAACG
1 GTCAACG
1327642 GTC-ACG
1 GTCAACG
1327648 GTCAACG
1 GTCAACG
1327655 GTCAACG
1 GTCAACG
1327662 GTC
1 GTC
1327665 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:1327675 original size:30 final size:29
Alignment explanation
Indices: 1327641--1327705 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 29
1327631 TAAAGTCAAC
*
1327641 GGTCAC-GGTCAACGGTCAACGGTCGGGTCG
1 GGTCACGGGTC-A-GGTCAACAGTCGGGTCG
1327671 GGTCAACGGGTCAGGTCAACAGTCGGGTCG
1 GGTC-ACGGGTCAGGTCAACAGTCGGGTCG
1327701 GGTCA
1 GGTCA
1327706 ACCCGGTTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
29 1 0.03
30 24 0.75
31 3 0.09
32 4 0.12
ACGTcount: A:0.18, C:0.25, G:0.40, T:0.17
Consensus pattern (29 bp):
GGTCACGGGTCAGGTCAACAGTCGGGTCG
Found at i:1327676 original size:17 final size:16
Alignment explanation
Indices: 1327654--1327707 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
1327644 CACGGTCAAC
1327654 GGTCAACGGTCGGGTCG
1 GGTCAAC-GTCGGGTCG
*
1327671 GGTCAA---CGGGTCA
1 GGTCAACGTCGGGTCG
1327684 GGTCAACAGTCGGGTCG
1 GGTCAAC-GTCGGGTCG
1327701 GGTCAAC
1 GGTCAAC
1327708 CCGGTTCAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
13 12 0.39
17 19 0.61
ACGTcount: A:0.19, C:0.24, G:0.41, T:0.17
Consensus pattern (16 bp):
GGTCAACGTCGGGTCG
Found at i:1327725 original size:19 final size:19
Alignment explanation
Indices: 1327701--1327773 Score: 110
Period size: 19 Copynumber: 3.8 Consensus size: 19
1327691 AGTCGGGTCG
*
1327701 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
1327720 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
* *
1327739 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
1327759 GGTCAAACCGGTTCA
1 GGTCAAACCGGTTCA
1327774 AAACTGGTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
19 33 0.66
20 17 0.34
ACGTcount: A:0.27, C:0.30, G:0.25, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:1327739 original size:10 final size:10
Alignment explanation
Indices: 1327703--1327791 Score: 87
Period size: 9 Copynumber: 9.1 Consensus size: 10
1327693 TCGGGTCGGG
*
1327703 TCAACCCGGT
1 TCAAACCGGT
*
1327713 TCAGACCGG-
1 TCAAACCGGT
1327722 TCAAACCGGT
1 TCAAACCGGT
*
1327732 TCAGACCGG-
1 TCAAACCGGT
1327741 TCAAACCGGT
1 TCAAACCGGT
*
1327751 TCAAAACTGG-
1 TC-AAACCGGT
1327761 TCAAACCGGT
1 TCAAACCGGT
*
1327771 TCAAAACTGGT
1 TC-AAACCGGT
1327782 T-AAACCGGT
1 TCAAACCGGT
1327791 T
1 T
1327792 TTCCAGCAGC
Statistics
Matches: 65, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
9 30 0.46
10 21 0.32
11 14 0.22
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.20
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:1327764 original size:20 final size:19
Alignment explanation
Indices: 1327701--1327791 Score: 110
Period size: 20 Copynumber: 4.7 Consensus size: 19
1327691 AGTCGGGTCG
* *
1327701 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAAACC
*
1327720 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAAACC
*
1327739 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AAACC
*
1327759 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AAACC
*
1327779 GGTTAAACCGGTT
1 GGTCAAACCGGTT
1327792 TTCCAGCAGC
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
19 32 0.48
20 35 0.52
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (19 bp):
GGTCAAACCGGTTCAAACC
Found at i:1329968 original size:24 final size:26
Alignment explanation
Indices: 1329923--1329974 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
1329913 TTTTAATAAT
*
1329923 ATAAAAATTATATATTTAAAATT-AA
1 ATAAAAATGATATATTTAAAATTCAA
*
1329948 ATAAAAATGATAT-TTTGAAATTCAA
1 ATAAAAATGATATATTTAAAATTCAA
1329973 AT
1 AT
1329975 TTTAACTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (26 bp):
ATAAAAATGATATATTTAAAATTCAA
Done.