Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008001.1 Hibiscus syriacus cultivar Beakdansim tig00110458_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: 3902382
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 18
Found at i:1406554 original size:21 final size:21
Alignment explanation
Indices: 1406528--1406577 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
1406518 TTTTGAAAAT
1406528 ACTACTCCCCCTTACTTTAAC
1 ACTACTCCCCCTTACTTTAAC
1406549 ACTACTCCCCCTTACTTTAAC
1 ACTACTCCCCCTTACTTTAAC
1406570 ACTACTCC
1 ACTACTCC
1406578 TCTTTAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.24, C:0.44, G:0.00, T:0.32
Consensus pattern (21 bp):
ACTACTCCCCCTTACTTTAAC
Found at i:1408868 original size:20 final size:21
Alignment explanation
Indices: 1408817--1408876 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
1408807 CAGAACCCCA
*
1408817 GGGGGGTATCGATTCCCTTAT
1 GGGGGGTATCGATTCCCTCAT
* *
1408838 GGGGGGAATCGGTTCCCTCAT
1 GGGGGGTATCGATTCCCTCAT
1408859 -GGGGGTATCGATTCCCTC
1 GGGGGGTATCGATTCCCTC
1408877 TGTACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.47
21 18 0.53
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.28
Consensus pattern (21 bp):
GGGGGGTATCGATTCCCTCAT
Found at i:1412717 original size:22 final size:21
Alignment explanation
Indices: 1412675--1412714 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1412665 TATGAGTTTT
1412675 TCATTTTTCAATTTTAAAACA
1 TCATTTTTCAATTTTAAAACA
1412696 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1412715 ACAATTTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1416689 original size:2 final size:2
Alignment explanation
Indices: 1416682--1416712 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1416672 TATTCTTATT
1416682 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 T
1416713 TTTGCAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1416776 original size:36 final size:36
Alignment explanation
Indices: 1416736--1417248 Score: 285
Period size: 36 Copynumber: 13.6 Consensus size: 36
1416726 TTTAAAATAA
* *
1416736 ATATAATATATAGTTTTTGAAAGCA-TTTCAAAAC--
1 ATATAATATATAGTTTTT-AAAACATTTTGAAAACAT
* * *
1416770 CTAT-ATATATAGTCTTTAAAACATTTTGGAAACATAT
1 ATATAATATATAGTTTTTAAAACATTTT-GAAA-ACAT
*
1416807 ATATAATATATAGTTTTTAAAACATTTTGGAAACAT
1 ATATAATATATAGTTTTTAAAACATTTTGAAAACAT
* * *
1416843 ATATATTATATAGTTTTTAACACATTTTGAAAATAT
1 ATATAATATATAGTTTTTAAAACATTTTGAAAACAT
*
1416879 ATATAATATATAGTTTTTAAAACATTTTGAACACAT
1 ATATAATATATAGTTTTTAAAACATTTTGAAAACAT
* *
1416915 ATATATATTATATATTTTTTAAAACATTTTAAAAACAT
1 ATATA-A-TATATAGTTTTTAAAACATTTTGAAAACAT
* * * *
1416953 ATATATATATATATATATATATATATATATATAGTTTTAAAAAAATTT
1 ATATA-ATATATA-GT-T-T-T-TA-A-A-ACA-TTTTGAAAACA--T
*
1417001 AAAAATATATAATATAGTTTTTAAAACAATTTTTG-AAA-AT
1 --ATATA-AT-ATATAGTTTTTAAAAC-A-TTTTGAAAACAT
* * * *
1417041 ATATACTATATAATTTTGAAAATTATTTTTGAAAA-AT
1 ATATAATATATAGTTTTTAAAA-CA-TTTTGAAAACAT
* * * *
1417078 ATATGTATTATATAGTTTTGAAAATTATTTTTAAAA-AT
1 ATA--TAATATATAGTTTTTAAAA-CATTTTGAAAACAT
* * * *
1417116 ATAAATATTATATAG-TTTGAAAATTATTTTTAAAA-AT
1 AT--ATAATATATAGTTTTTAAAA-CATTTTGAAAACAT
* * *
1417153 ATATATATTATATAGTTTTGAAAATTATTTTTAAAA-AT
1 ATATA-A-TATATAGTTTTTAAAA-CATTTTGAAAACAT
* * * *
1417191 ATATATTATATAGTTTTGAAAATTATTTTTAAAA-AT
1 ATATAATATATAGTTTTTAAAA-CATTTTGAAAACAT
* *
1417227 ATATATTATATAGTTTTGAAAA
1 ATATAATATATAGTTTTTAAAA
1417249 TTATTTTTTA
Statistics
Matches: 409, Mismatches: 38, Indels: 62
0.80 0.07 0.12
Matches are distributed among these distances:
32 5 0.01
33 15 0.04
34 6 0.01
35 4 0.01
36 144 0.35
37 53 0.13
38 110 0.27
39 21 0.05
40 3 0.01
41 1 0.00
42 3 0.01
43 5 0.01
44 7 0.02
45 3 0.01
46 12 0.03
47 1 0.00
48 2 0.00
49 1 0.00
50 8 0.02
51 5 0.01
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.45
Consensus pattern (36 bp):
ATATAATATATAGTTTTTAAAACATTTTGAAAACAT
Found at i:1416778 original size:38 final size:38
Alignment explanation
Indices: 1416774--1417248 Score: 315
Period size: 38 Copynumber: 12.4 Consensus size: 38
1416764 CAAAACCTAT
* *
1416774 ATATATAGTCTTTAAAACATTTTGGAAACATATATATA
1 ATATATAGTTTTTAAAACATTTTGAAAACATATATATA
*
1416812 ATATATAGTTTTTAAAACATTTTGGAAACATATATAT-
1 ATATATAGTTTTTAAAACATTTTGAAAACATATATATA
*
1416849 -TATATAGTTTTTAACACATTTTG-AAA-ATATATATA
1 ATATATAGTTTTTAAAACATTTTGAAAACATATATATA
*
1416884 ATATATAGTTTTTAAAACATTTTGAACACATATATATA
1 ATATATAGTTTTTAAAACATTTTGAAAACATATATATA
* * *
1416922 TTATATATTTTTTAAAACATTTTAAAAACATATATATA
1 ATATATAGTTTTTAAAACATTTTGAAAACATATATATA
* * * * *
1416960 TATATATA-TATATATATATATATATAGTTTTAAAAAAATTTAAAAATA
1 -ATATATAGT-T-T-T-TA-A-A-ACA-TTTTGAAAACA--TATATATA
1417008 TATAATATAGTTTTTAAAACAATTTTTG-AAA-ATATATACT-
1 -AT-ATATAGTTTTTAAAAC-A-TTTTGAAAACATATATA-TA
* * *
1417048 ATATA-A-TTTTGAAAATTATTTTTGAAAA-ATATATGTA
1 ATATATAGTTTTTAAAA-CA-TTTTGAAAACATATATATA
* * * * *
1417085 TTATATAGTTTTGAAAATTATTTTTAAAA-ATATAAATA
1 ATATATAGTTTTTAAAA-CATTTTGAAAACATATATATA
* * * *
1417123 TTATATAG-TTTGAAAATTATTTTTAAAA-ATATATATA
1 ATATATAGTTTTTAAAA-CATTTTGAAAACATATATATA
* * * *
1417160 TTATATAGTTTTGAAAATTATTTTTAAAA-ATATATAT-
1 ATATATAGTTTTTAAAA-CATTTTGAAAACATATATATA
* * *
1417197 -TATATAGTTTTGAAAATTATTTTTAAAA-ATATATAT-
1 ATATATAGTTTTTAAAA-CATTTTGAAAACATATATATA
*
1417233 -TATATAGTTTTGAAAA
1 ATATATAGTTTTTAAAA
1417249 TTATTTTTTA
Statistics
Matches: 386, Mismatches: 26, Indels: 52
0.83 0.06 0.11
Matches are distributed among these distances:
34 8 0.02
35 3 0.01
36 112 0.29
37 52 0.13
38 135 0.35
39 21 0.05
40 5 0.01
41 2 0.01
42 3 0.01
43 5 0.01
44 7 0.02
45 3 0.01
46 12 0.03
47 1 0.00
48 10 0.03
49 6 0.02
50 1 0.00
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (38 bp):
ATATATAGTTTTTAAAACATTTTGAAAACATATATATA
Found at i:1416958 original size:2 final size:2
Alignment explanation
Indices: 1416951--1416985 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1416941 TTTTAAAAAC
1416951 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 A
1416986 GTTTTAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1417108 original size:75 final size:72
Alignment explanation
Indices: 1416998--1417325 Score: 418
Period size: 75 Copynumber: 4.5 Consensus size: 72
1416988 TTTAAAAAAA
* ** * *
1416998 TTTAAAAATATATA--ATATAGTTTTTAAAACAATTTTTGAAAATATATACTATATAATTTTGAA
1 TTTAAAAATATATATTATATAGTTTTGAAAATTATTTTTAAAAATATATATTATATAATTTTGAA
1417061 AATTATT
66 AATTATT
*
1417068 TTTGAAAAATATATGTATTATATAGTTTTGAAAATTATTTTTAAAAATATAAATATTATAT-AGT
1 TTT-AAAAATATA--TATTATATAGTTTTGAAAATTATTTTTAAAAATAT--ATATTATATAATT
1417132 TTGAAAATTATT
61 TTGAAAATTATT
*
1417144 TTTAAAAATATATATATTATATAGTTTTGAAAATTATTTTTAAAAATATATATTATATAGTTTTG
1 TTT-AAAA-ATATATATTATATAGTTTTGAAAATTATTTTTAAAAATATATATTATATAATTTTG
1417209 AAAATTATT
64 AAAATTATT
* * *
1417218 TTTAAAAATATATATTATATAGTTTTGAAAATTATTTTT-TAAATATATATTATGTAGTTTTG-A
1 TTTAAAAATATATATTATATAGTTTTGAAAATTATTTTTAAAAATATATATTATATAATTTTGAA
1417281 AATTATTT
66 AATTA-TT
* * *
1417289 TTTTAAAACATATA-TATATAGTTTT-AAAAATATTTTT
1 TTTAAAAATATATATTATATAGTTTTGAAAATTATTTTT
1417326 TTATATTTTT
Statistics
Matches: 234, Mismatches: 14, Indels: 21
0.87 0.05 0.08
Matches are distributed among these distances:
69 11 0.05
70 20 0.09
71 44 0.19
72 32 0.14
73 15 0.06
74 16 0.07
75 62 0.26
76 21 0.09
77 13 0.06
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (72 bp):
TTTAAAAATATATATTATATAGTTTTGAAAATTATTTTTAAAAATATATATTATATAATTTTGAA
AATTATT
Found at i:1417327 original size:36 final size:36
Alignment explanation
Indices: 1416971--1417325 Score: 442
Period size: 36 Copynumber: 9.9 Consensus size: 36
1416961 ATATATATAT
**
1416971 ATATATATATATATAGTTTT-AAAA--AAATTTAAAA
1 ATATATAT-TATATAGTTTTGAAAATTATTTTTAAAA
* ** *
1417005 ATATATA--ATATAGTTTTTAAAACAATTTTTGAAA
1 ATATATATTATATAGTTTTGAAAATTATTTTTAAAA
* *
1417039 ATATATACTATATAATTTTGAAAATTATTTTTGAAAA
1 ATATATATTATATAGTTTTGAAAATTATTTTT-AAAA
1417076 ATATATGTATTATATAGTTTTGAAAATTATTTTTAAAA
1 ATATA--TATTATATAGTTTTGAAAATTATTTTTAAAA
1417114 ATATAAATATTATATAG-TTTGAAAATTATTTTTAAAAA
1 ATAT--ATATTATATAGTTTTGAAAATTATTTTT-AAAA
1417152 TATATATATTATATAGTTTTGAAAATTATTTTTAAAA
1 -ATATATATTATATAGTTTTGAAAATTATTTTTAAAA
1417189 ATATATATTATATAGTTTTGAAAATTATTTTTAAAA
1 ATATATATTATATAGTTTTGAAAATTATTTTTAAAA
*
1417225 ATATATATTATATAGTTTTGAAAATTATTTTT-TAA
1 ATATATATTATATAGTTTTGAAAATTATTTTTAAAA
* *
1417260 ATATATATTATGTAGTTTTG-AAATTATTTTTTTAAA
1 ATATATATTATATAGTTTTGAAAATTA-TTTTTAAAA
* *
1417296 ACATATA-TATATAGTTTT-AAAAATATTTTT
1 ATATATATTATATAGTTTTGAAAATTATTTTT
1417326 TTATATTTTT
Statistics
Matches: 289, Mismatches: 16, Indels: 32
0.86 0.05 0.09
Matches are distributed among these distances:
31 10 0.03
32 4 0.01
34 32 0.11
35 41 0.14
36 95 0.33
37 39 0.13
38 38 0.13
39 29 0.10
40 1 0.00
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.49
Consensus pattern (36 bp):
ATATATATTATATAGTTTTGAAAATTATTTTTAAAA
Found at i:1417359 original size:34 final size:36
Alignment explanation
Indices: 1417321--1417388 Score: 104
Period size: 37 Copynumber: 1.9 Consensus size: 36
1417311 TTTAAAAATA
1417321 TTTTTTTATATT-TTTTA-TTTATTATTTTTCTACT
1 TTTTTTTATATTATTTTATTTTATTATTTTTCTACT
*
1417355 TTTTTTTATTTTATTTTATTTTTATTATTTTTCT
1 TTTTTTTATATTATTTTA-TTTTATTATTTTTCT
1417389 CGTTTTAGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 11 0.37
35 5 0.17
37 14 0.47
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.79
Consensus pattern (36 bp):
TTTTTTTATATTATTTTATTTTATTATTTTTCTACT
Found at i:1417366 original size:9 final size:9
Alignment explanation
Indices: 1417319--1417386 Score: 64
Period size: 10 Copynumber: 6.8 Consensus size: 9
1417309 GTTTTAAAAA
1417319 TATTTTTTT
1 TATTTTTTT
1417328 ATATTTTTTATT
1 -TA-TTTTT-TT
1417340 TATTATTTTT
1 TATT-TTTTT
1417350 CTACTTTTTTT
1 -TA-TTTTTTT
1417361 TATTTTATTT
1 TATTTT-TTT
*
1417371 TATTTTTAT
1 TATTTTTTT
1417380 TATTTTT
1 TATTTTT
1417387 CTCGTTTTAG
Statistics
Matches: 51, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
9 13 0.25
10 17 0.33
11 17 0.33
12 4 0.08
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (9 bp):
TATTTTTTT
Found at i:1418602 original size:18 final size:17
Alignment explanation
Indices: 1418577--1418610 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1418567 TTTTTTAGTA
1418577 TTTTATTTTATTTTCCT
1 TTTTATTTTATTTTCCT
1418594 TTTTCATTTTATTTTCC
1 TTTT-ATTTTATTTTCC
1418611 CATTCTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTATTTTATTTTCCT
Found at i:1419335 original size:12 final size:12
Alignment explanation
Indices: 1419318--1419342 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1419308 CTCAATGTAC
1419318 TAGTTTTTTTTT
1 TAGTTTTTTTTT
1419330 TAGTTTTTTTTT
1 TAGTTTTTTTTT
1419342 T
1 T
1419343 CTTCAAATAC
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:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (12 bp):
TAGTTTTTTTTT
Found at i:1428184 original size:31 final size:31
Alignment explanation
Indices: 1428145--1428223 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
1428135 AGCCAGGGTG
* *
1428145 CATTCAGATAATGCACATTATGGTCAGGTTA
1 CATTCAGATAATGCACAGTATGGTCAGATTA
* *
1428176 TATTCAGATAATGCACAGTATGGTCAGATTG
1 CATTCAGATAATGCACAGTATGGTCAGATTA
1428207 CATTCAGATAATGCACA
1 CATTCAGATAATGCACA
1428224 AGAGTGTCAG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Consensus pattern (31 bp):
CATTCAGATAATGCACAGTATGGTCAGATTA
Found at i:1428943 original size:65 final size:64
Alignment explanation
Indices: 1428813--1428960 Score: 183
Period size: 65 Copynumber: 2.3 Consensus size: 64
1428803 AATTAAATTG
* * *
1428813 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGATTTTATGAA
1 AACATTGAATGCATTTGATGCATCGATGCACATACCACGCACCGATGCACTGAGGATTTTATG-A
* ** *
1428878 AACATTGAATGCATTTGATGCATCGATGCACCAT-CCACGCATCGATGCACTTTGGCTATTT-TG
1 AACATTGAATGCATTTGATGCATCGATGCA-CATACCACGCACCGATGCACTGAGGAT-TTTATG
1428941 A
64 A
1428942 AACATTGAATGCACTTTGA
1 AACATTGAATGCA-TTTGA
1428961 GAGTCCAACG
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
64 14 0.19
65 53 0.73
66 6 0.08
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.29
Consensus pattern (64 bp):
AACATTGAATGCATTTGATGCATCGATGCACATACCACGCACCGATGCACTGAGGATTTTATGA
Found at i:1435961 original size:21 final size:21
Alignment explanation
Indices: 1435919--1435962 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1435909 ACCCCGGGAG
*
1435919 CTAGCTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
1435940 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
1435961 CT
1 CT
1435963 CCTCCTACGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.41, G:0.16, T:0.34
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:1436304 original size:19 final size:19
Alignment explanation
Indices: 1436280--1436327 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
1436270 ATTTCAATCT
*
1436280 TGGATTGTTTTGATGTTTC
1 TGGATTGTTTTAATGTTTC
1436299 TGGATTGTTTTAATGTTTC
1 TGGATTGTTTTAATGTTTC
*
1436318 TAGATTGTTT
1 TGGATTGTTT
1436328 GTTTTGGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.15, C:0.04, G:0.23, T:0.58
Consensus pattern (19 bp):
TGGATTGTTTTAATGTTTC
Found at i:1437173 original size:17 final size:19
Alignment explanation
Indices: 1437145--1437193 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1437135 TATTTTGAAA
1437145 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1437163 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1437182 CACCGATGCACT
1 CATCGATGCACT
1437194 GAGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1438080 original size:21 final size:22
Alignment explanation
Indices: 1438056--1438101 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1438046 TTTTTTTTTT
* *
1438056 AATTATGAATA-TTTGTATTAA
1 AATTATAAATATTTTATATTAA
1438077 AATTATAAATATTTTATATTAA
1 AATTATAAATATTTTATATTAA
1438099 AAT
1 AAT
1438102 AAAATTTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (22 bp):
AATTATAAATATTTTATATTAA
Found at i:1445743 original size:15 final size:15
Alignment explanation
Indices: 1445723--1445752 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1445713 CCACCTGCCC
1445723 GTTCAGCATCCTTAA
1 GTTCAGCATCCTTAA
1445738 GTTCAGCATCCTTAA
1 GTTCAGCATCCTTAA
1445753 ATAGCCAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (15 bp):
GTTCAGCATCCTTAA
Found at i:1453338 original size:28 final size:28
Alignment explanation
Indices: 1453299--1453353 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
1453289 GGGTTTAAAC
1453299 CCCCAATGGGGTTGCCTTGAGGGATGTA
1 CCCCAATGGGGTTGCCTTGAGGGATGTA
1453327 CCCCAATGGGGTTGCCTTGAGGGATGT
1 CCCCAATGGGGTTGCCTTGAGGGATGT
1453354 CTTGTGACCT
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:0.16, C:0.22, G:0.36, T:0.25
Consensus pattern (28 bp):
CCCCAATGGGGTTGCCTTGAGGGATGTA
Found at i:1466737 original size:29 final size:29
Alignment explanation
Indices: 1466702--1466783 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
1466692 AAACTAAATT
* * *
1466702 GATGTCATTACTTACGTCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
1466731 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
1466760 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1466784 GTTAGGTGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 43 0.90
30 5 0.10
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:1469012 original size:24 final size:22
Alignment explanation
Indices: 1468985--1469041 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 22
1468975 TTTTTTTTTA
*
1468985 AAAATTATATTTTAGATACTAAAC
1 AAAA-TATAATTTAGATA-TAAAC
1469009 AAAATATAATTTAGATAT-AA-
1 AAAATATAATTTAGATATAAAC
*
1469029 AACATATAATTTA
1 AAAATATAATTTA
1469042 TCTTTTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.39
21 2 0.06
22 1 0.03
23 12 0.39
24 4 0.13
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.37
Consensus pattern (22 bp):
AAAATATAATTTAGATATAAAC
Found at i:1469021 original size:23 final size:20
Alignment explanation
Indices: 1468983--1469041 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 20
1468973 AATTTTTTTT
* *
1468983 TAAAAATTATATTTTAGATA
1 TAAAAAATATAATTTAGATA
1469003 CTAAACAAAATATAATTTAGATA
1 -T-AA-AAAATATAATTTAGATA
*
1469026 TAAAACATATAATTTA
1 TAAAAAATATAATTTA
1469042 TCTTTTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 12 0.36
21 3 0.09
22 3 0.09
23 15 0.45
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.37
Consensus pattern (20 bp):
TAAAAAATATAATTTAGATA
Found at i:1469226 original size:12 final size:12
Alignment explanation
Indices: 1469209--1469277 Score: 52
Period size: 12 Copynumber: 5.7 Consensus size: 12
1469199 TAATTTATTA
1469209 TATTATTAAATT
1 TATTATTAAATT
*
1469221 TATTATT-ATTAT
1 TATTATTAAAT-T
*
1469233 TATTATTATA-T
1 TATTATTAAATT
*
1469244 TATTATTAGTATAT
1 TATTATTA-AAT-T
*
1469258 TATTATTAAAAT
1 TATTATTAAATT
*
1469270 AATTATTA
1 TATTATTA
1469278 CAAACCCATT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
11 11 0.24
12 25 0.54
13 1 0.02
14 9 0.20
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (12 bp):
TATTATTAAATT
Found at i:1469249 original size:17 final size:18
Alignment explanation
Indices: 1469203--1469265 Score: 71
Period size: 17 Copynumber: 3.7 Consensus size: 18
1469193 TTCATTTAAT
*
1469203 TTATTA-TATTATTA-AA
1 TTATTATTATTATTAGTA
*
1469219 TTTATTATTATTATTATTA
1 -TTATTATTATTATTAGTA
1469238 TTA-TATTATTATTAGTA
1 TTATTATTATTATTAGTA
1469255 -TATTATTATTA
1 TTATTATTATTA
1469266 AAATAATTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
16 2 0.05
17 27 0.66
18 11 0.27
19 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TTATTATTATTATTAGTA
Found at i:1469277 original size:3 final size:3
Alignment explanation
Indices: 1469203--1469265 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
1469193 TTCATTTAAT
*
1469203 TTA TTA -TA TTA TTA -AA TTTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1469246 TTA TTA GTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
1469266 AAATAATTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
2 7 0.13
3 44 0.85
4 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1469689 original size:21 final size:20
Alignment explanation
Indices: 1469652--1469691 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
1469642 CAAAAAACAG
1469652 AAAAGAAGAAAACAGGAAAA
1 AAAAGAAGAAAACAGGAAAA
1469672 AAAAGAAAGAAGAA-AGGAAA
1 AAAAG-AAGAA-AACAGGAAA
1469692 GCTTACCGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 11 0.61
22 2 0.11
ACGTcount: A:0.75, C:0.03, G:0.23, T:0.00
Consensus pattern (20 bp):
AAAAGAAGAAAACAGGAAAA
Found at i:1470881 original size:29 final size:29
Alignment explanation
Indices: 1470845--1470909 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
1470835 TATGATAAAA
*
1470845 AATCAATGTGACTATTGAACTTTAAATTG
1 AATCAATGTGACTACTGAACTTTAAATTG
1470874 AATCAATGTGACTACTGAACTTTAAATTG
1 AATCAATGTGACTACTGAACTTTAAATTG
1470903 AATCAAT
1 AATCAAT
1470910 CAGACCACTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (29 bp):
AATCAATGTGACTACTGAACTTTAAATTG
Found at i:1472118 original size:22 final size:22
Alignment explanation
Indices: 1472075--1472118 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1472065 ATTATATTGT
*
1472075 ATGAACAGTACCGTAAATAGTA
1 ATGAACAGTACCGTAAACAGTA
* *
1472097 ATGAACTGTACCGTGAACAGTA
1 ATGAACAGTACCGTAAACAGTA
1472119 CCGATTCTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (22 bp):
ATGAACAGTACCGTAAACAGTA
Found at i:1472835 original size:63 final size:62
Alignment explanation
Indices: 1472713--1472835 Score: 176
Period size: 63 Copynumber: 2.0 Consensus size: 62
1472703 TATAATAATC
* * *
1472713 TGTCCATATGTCCCGATGAACATAGGTAAACTGTCCATATGTCCCGAAAGACATAGGTAAAT
1 TGTCCATATGTCCCAAAGAACATAGGTAAACTGTCCATATGTCCCAAAAGACATAGGTAAAT
* *
1472775 TGTCCATATGTCCCAAA-AGACATAGGTAATATTGTTCATATGTCCCAAAAGACATAGGTAA
1 TGTCCATATGTCCCAAAGA-ACATAGGTAA-ACTGTCCATATGTCCCAAAAGACATAGGTAA
1472836 TACCTCGACT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
61 1 0.02
62 25 0.46
63 28 0.52
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (62 bp):
TGTCCATATGTCCCAAAGAACATAGGTAAACTGTCCATATGTCCCAAAAGACATAGGTAAAT
Found at i:1472837 original size:32 final size:31
Alignment explanation
Indices: 1472713--1472835 Score: 176
Period size: 31 Copynumber: 3.9 Consensus size: 31
1472703 TATAATAATC
* * *
1472713 TGTCCATATGTCCC-GATGAACATAGGTAAAC
1 TGTCCATATGTCCCAAAAG-ACATAGGTAAAT
*
1472744 TGTCCATATGTCCCGAAAGACATAGGTAAAT
1 TGTCCATATGTCCCAAAAGACATAGGTAAAT
1472775 TGTCCATATGTCCCAAAAGACATAGGTAATAT
1 TGTCCATATGTCCCAAAAGACATAGGTAA-AT
*
1472807 TGTTCATATGTCCCAAAAGACATAGGTAA
1 TGTCCATATGTCCCAAAAGACATAGGTAA
1472836 TACCTCGACT
Statistics
Matches: 85, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
31 53 0.62
32 32 0.38
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (31 bp):
TGTCCATATGTCCCAAAAGACATAGGTAAAT
Found at i:1474244 original size:10 final size:10
Alignment explanation
Indices: 1474229--1474264 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
1474219 GGAGAGGAAG
1474229 AAGAAGAAAT
1 AAGAAGAAAT
*
1474239 AAGAAGAAAG
1 AAGAAGAAAT
1474249 AAGAAG-AAT
1 AAGAAGAAAT
1474258 AAGAAGA
1 AAGAAGA
1474265 GAGTTTTCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (10 bp):
AAGAAGAAAT
Found at i:1477336 original size:20 final size:19
Alignment explanation
Indices: 1477296--1477352 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 19
1477286 AACTTTTACA
*
1477296 TTTGATTTTTTTATTTTAT
1 TTTGATTTTTTTATTTAAT
1477315 TTTG-TTTTTTTATATTCAAT
1 TTTGATTTTTTTAT-TT-AAT
1477335 TTT-ATTTATCTTTATTTA
1 TTTGATTT-T-TTTATTTA
1477353 TCCATTTTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
18 9 0.28
19 6 0.19
20 9 0.28
21 3 0.09
22 5 0.16
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.74
Consensus pattern (19 bp):
TTTGATTTTTTTATTTAAT
Found at i:1478887 original size:11 final size:11
Alignment explanation
Indices: 1478871--1478895 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1478861 ACTCGAATTA
1478871 AAAATAGATCG
1 AAAATAGATCG
1478882 AAAATAGATCG
1 AAAATAGATCG
1478893 AAA
1 AAA
1478896 TAATTTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.08, G:0.16, T:0.16
Consensus pattern (11 bp):
AAAATAGATCG
Found at i:1478958 original size:21 final size:21
Alignment explanation
Indices: 1478907--1478952 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
1478897 AATTTGAAAA
1478907 ACATAGGAGTTAAAAATAATT
1 ACATAGGAGTTAAAAATAATT
1478928 ACATAGGAGTTAAAAATAATT
1 ACATAGGAGTTAAAAATAATT
1478949 ACAT
1 ACAT
1478953 TAGAGTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.52, C:0.07, G:0.13, T:0.28
Consensus pattern (21 bp):
ACATAGGAGTTAAAAATAATT
Found at i:1483128 original size:3 final size:3
Alignment explanation
Indices: 1483113--1483165 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
1483103 TTATCCCGTT
* * * * *
1483113 TTA TTA TTT TTA TTA TTA TTA TAA TAA TAA TTA TTA TTTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
1483159 TTA TTA T
1 TTA TTA T
1483166 ATTTACAGGC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1484562 original size:27 final size:30
Alignment explanation
Indices: 1484496--1484566 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 30
1484486 TGTTTTAATT
* * *
1484496 TTATGTTTTATATATTGATTATTATTACTA
1 TTATGTTTTATTTATTGATTATAAATACTA
1484526 TTAT-TATTTATTTATT-A-TATAAATA-TA
1 TTATGT-TTTATTTATTGATTATAAATACTA
1484553 TTATGTTTTATTTA
1 TTATGTTTTATTTA
1484567 AAATCCTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
27 14 0.39
28 7 0.19
29 2 0.06
30 13 0.36
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.62
Consensus pattern (30 bp):
TTATGTTTTATTTATTGATTATAAATACTA
Found at i:1485358 original size:11 final size:11
Alignment explanation
Indices: 1485342--1485375 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1485332 TATTCATATG
*
1485342 AATAAAATTAA
1 AATAAAAATAA
1485353 AATAAAAATAA
1 AATAAAAATAA
1485364 AATAAAGAATAA
1 AATAAA-AATAA
1485376 TAATTAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:1486762 original size:3 final size:3
Alignment explanation
Indices: 1486754--1486796 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1486744 TTTCGGGCCT
1486754 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1486797 GGGACAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1488446 original size:14 final size:14
Alignment explanation
Indices: 1488427--1488457 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1488417 AAAGTCCCTT
1488427 TTCAAAGGAAAATC
1 TTCAAAGGAAAATC
1488441 TTCAAAGGAAAATC
1 TTCAAAGGAAAATC
1488455 TTC
1 TTC
1488458 TTGGTTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (14 bp):
TTCAAAGGAAAATC
Found at i:1489184 original size:225 final size:224
Alignment explanation
Indices: 1488784--1489261 Score: 813
Period size: 225 Copynumber: 2.1 Consensus size: 224
1488774 GTAAATTATC
* * *
1488784 TATCCTTTTTATAAAAGTGTCCATACTTA-TTCAATGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCAATGTGAAAACATATTTATTATTATATTTAGT
1488848 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAAATCAAATAATTTTTGT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAAATCAAATAATTTTTGT
1488913 GTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAATTGAAA
131 GTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAA
1488977 CATAAATTACATAACTTTCAAAAAAGTATA
196 CATAAATTACATAACTTT-AAAAAAGTATA
* *
1489007 TATCATTTTTA-AAAAGTGTCCATACTTATTTCACTGTTG-AAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCAATG-TGAAAACATATTTATTATTATATTTAG
*
1489070 TTAATATTGTTAAATTT-AATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATC-AAA-AATCAAATAAT-TT
*
1489134 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
127 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
1489199 GAAACATAAATTACATAACTTTAAAAAAGTATA
192 GAAACATAAATTACATAACTTTAAAAAAGTATA
1489232 TATCATTTTTATAAAAGTGTCCATACTTAT
1 TATCATTTTTATAAAAGTGTCCATACTTAT
1489262 AAAAGTAGGT
Statistics
Matches: 241, Mismatches: 7, Indels: 11
0.93 0.03 0.04
Matches are distributed among these distances:
222 44 0.18
223 57 0.24
224 13 0.05
225 79 0.33
226 48 0.20
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.40
Consensus pattern (224 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCAATGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAAATCAAATAATTTTTGT
GTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAA
CATAAATTACATAACTTTAAAAAAGTATA
Found at i:1489569 original size:20 final size:20
Alignment explanation
Indices: 1489523--1489581 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
1489513 TGTATCGATC
* *
1489523 CAAAATGAT-ATACCAGTAA
1 CAAAATGATAAAACCGGTAA
1489542 -AAATATGATAAAACCGGTAA
1 CAAA-ATGATAAAACCGGTAA
1489562 CAAAATGATAAAACCGGTAA
1 CAAAATGATAAAACCGGTAA
1489582 AACGTTACCG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 3 0.09
19 5 0.14
20 24 0.69
21 3 0.09
ACGTcount: A:0.54, C:0.14, G:0.14, T:0.19
Consensus pattern (20 bp):
CAAAATGATAAAACCGGTAA
Found at i:1489617 original size:179 final size:181
Alignment explanation
Indices: 1489328--1489761 Score: 615
Period size: 180 Copynumber: 2.4 Consensus size: 181
1489318 GATCCAAATT
* * * *
1489328 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATA-GAAATGAT
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTA-ACAAAATGAT
* * * *
1489392 AAAACCGGTCAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTT
65 AAAACCGGTAAAACGCTACCGGATACATTAAAAGTGTCGATACTTT-ATATAAGGATCGACACTT
* * **
1489457 CGTGAATTT-AAA-AGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
129 CGTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTCAA
* *
1489508 AAAAATGTATCGATCCAAAATGATATACCA-GTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* * *
1489572 AAACCGGTAAAACGTTACCGGATATATTAAAAGTGTCGATACTTTATATAAGGATCGACACTTTG
66 AAACCGGTAAAACGCTACCGGATACATTAAAAGTGTCGATACTTTATATAAGGATCGACACTTCG
** *
1489637 TGAATTTAAAAGAGAAGCAGTTATAGCGCCTATAATGTGTCGATACTTCAA
131 TGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTCAA
* * *
1489688 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1489753 AAACCGGTA
66 AAACCGGTA
1489762 TCAAAATGAT
Statistics
Matches: 225, Mismatches: 25, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
178 27 0.12
179 71 0.32
180 85 0.38
181 42 0.19
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.26
Consensus pattern (181 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
AAACCGGTAAAACGCTACCGGATACATTAAAAGTGTCGATACTTTATATAAGGATCGACACTTCG
TGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTCAA
Found at i:1489741 original size:20 final size:20
Alignment explanation
Indices: 1489718--1489781 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
1489708 CGATATAACA
1489718 GGTA-AAAATATGATAAAACC
1 GGTATAAAA-ATGATAAAACC
*
1489738 GGTATCAAAATGATAAAACC
1 GGTATAAAAATGATAAAACC
*
1489758 GGTATCAAAATGATAAAACC
1 GGTATAAAAATGATAAAACC
1489778 GGTA
1 GGTA
1489782 AAATGATACC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
20 39 0.93
21 3 0.07
ACGTcount: A:0.50, C:0.12, G:0.17, T:0.20
Consensus pattern (20 bp):
GGTATAAAAATGATAAAACC
Found at i:1492035 original size:21 final size:21
Alignment explanation
Indices: 1492008--1492072 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
1491998 AATACAATCA
*
1492008 AGAGTCGAAGAAAAACTTGAT
1 AGAGTCGAAGAAAAACTTGAG
* * * *
1492029 CGAGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAAAAACTTGAG
* *
1492050 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAAAAACTTGAG
1492071 AG
1 AG
1492073 GCATAAGGGG
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.40, C:0.14, G:0.29, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAAAAACTTGAG
Found at i:1492147 original size:32 final size:33
Alignment explanation
Indices: 1492106--1492170 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1492096 AAATAGATGG
*
1492106 AGTGGTGAAAG-AGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
1492138 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1492171 TATTAAGATG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 11 0.38
33 18 0.62
ACGTcount: A:0.28, C:0.00, G:0.49, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1493980 original size:19 final size:19
Alignment explanation
Indices: 1493956--1494002 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 19
1493946 AATGTAGGGT
1493956 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1493975 TAA-TTT-TATACGATTTA
1 TAATTTTGTATAAGATTTA
*
1493992 TATTTTTGTAT
1 TAATTTTGTAT
1494003 GTGAATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 12 0.50
18 6 0.25
19 6 0.25
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1494640 original size:199 final size:199
Alignment explanation
Indices: 1494121--1495861 Score: 2818
Period size: 199 Copynumber: 8.9 Consensus size: 199
1494111 CAATATGGCC
* * *
1494121 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
* *
1494186 CCAAAAGTATAATGT-ATATGTAATTTTTCAATCTAACCGGTACAAGTCTACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
1494250 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
1494315 TGGAA
195 TGGAA
1494320 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
* *
1494384 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATATCGGTTTTATGAGAT
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
1494449 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
1494514 GGAA
196 GGAA
1494518 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1494583 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
* **
1494648 AATATGTCTAAATAATGTGTCG--A-T-AT-T--TTT-T-TCCA-A-----AAT---GAATGGAA
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAAT-GAA
1494695 ---AA
195 TGGAA
* ** * ** * ** * ** * * ** *
1494697 CAGGGTGCACCCATAAAGTGTCGATCCAT--ATATAAAAAGTGTCGATC---CCAAAATCATCGA
1 AACAGGGTGCACCCATAAAGT-G-TCGATCCATATATAAAAAGT-G-TCGATCCCAAA--ATC-A
* *
1494757 ---ACCCAAAA-GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTT
59 TCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTT
1494818 ATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAG
124 ATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAG
1494882 AATGAATGGAA
189 AATGAATGGAA
1494893 AACAGGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1494956 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1495021 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
1495086 GGAA
196 GGAA
1495090 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1495155 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1495220 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
1495285 GGAA
196 GGAA
1495289 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
* *
1495354 CAAAAGTATAGTGTAATATGTAATTTTTCAATCTAACCGGTATAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1495419 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
1495484 GGAA
196 GGAA
1495488 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
1495553 CAAAAGTATAATGTAATATGTAATTTTCCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1495618 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
1495683 GGAA
196 GGAA
*
1495687 AACAGGGTGCACCCATAAAGTGTCGATTCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
1495752 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1495817 AATATGTCTAAATAATGTGTCGACACGT--TATAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACAC-TAATATAGTTTGTGTCGATA
1495862 CTAATTTAAA
Statistics
Matches: 1436, Mismatches: 63, Indels: 87
0.91 0.04 0.05
Matches are distributed among these distances:
177 82 0.06
178 11 0.01
179 22 0.02
180 6 0.00
181 13 0.01
182 4 0.00
184 4 0.00
185 1 0.00
186 3 0.00
187 1 0.00
189 1 0.00
190 3 0.00
191 2 0.00
192 6 0.00
193 7 0.00
194 17 0.01
195 14 0.01
196 118 0.08
197 69 0.05
198 189 0.13
199 862 0.60
200 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (199 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
GGAA
Found at i:1494703 original size:177 final size:178
Alignment explanation
Indices: 1494485--1495043 Score: 766
Period size: 177 Copynumber: 3.0 Consensus size: 178
1494475 TAATATAGTT
*
1494485 TGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATA
1 TGTGTCGATATTTTTTTTCCAAAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATA
1494550 TATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAAT
66 TATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAAT
1494615 CTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAA
131 CTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAA
1494663 TGTGTCGATA-TTTTTTTCCAAAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATA
1 TGTGTCGATATTTTTTTTCCAAAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATA
1494727 TATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAAT
66 TATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAAT
1494792 CTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAA
131 CTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAA
* * ** * ** * ** *
1494840 TGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAAT-GAATGGAAAACAGGGTGCA
1 TGTGTCG--A-T-AT-T--TTT-TTTCCA-A----AAT---GAATGGAA---AACAGGGTGCACC
** *
1494904 CCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
47 CATAAA--GTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
1494967 TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAA
110 TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAA
1495032 ATAA
175 ATAA
1495036 TGTGTCGA
1 TGTGTCGA
1495044 CACTAATATA
Statistics
Matches: 344, Mismatches: 15, Indels: 28
0.89 0.04 0.07
Matches are distributed among these distances:
177 173 0.50
178 10 0.03
179 1 0.00
180 1 0.00
181 1 0.00
183 1 0.00
185 3 0.01
186 4 0.01
187 1 0.00
191 1 0.00
193 3 0.01
194 5 0.01
196 130 0.38
198 10 0.03
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.31
Consensus pattern (178 bp):
TGTGTCGATATTTTTTTTCCAAAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATA
TATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAAT
CTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAA
Found at i:1495515 original size:398 final size:398
Alignment explanation
Indices: 1494121--1495861 Score: 3135
Period size: 398 Copynumber: 4.4 Consensus size: 398
1494111 CAATATGGCC
* * *
1494121 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
* *
1494186 CCAAAAGTATAATGT-ATATGTAATTTTTCAATCTAACCGGTACAAGTCTACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
1494250 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
1494315 TGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATC
195 TGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
*
1494379 GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATATCGGTTTTAT
260 GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT
* *
1494444 GAGATAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAA
325 GAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAA
1494509 TGAATGGAA
390 TGAATGGAA
1494518 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1494583 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
1494648 AATATGTC-----------T----A--AATA-A---TGTGTCGATA-TTTTTTTCCAAAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
1494691 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
196 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
1494756 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
261 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
1494821 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAAT
326 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAAT
1494885 GAATGGAA
391 GAATGGAA
1494893 AACAGGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1494956 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1495021 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
1495086 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
196 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
1495151 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
261 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
1495216 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAAT
326 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAAT
1495281 GAATGGAA
391 GAATGGAA
1495289 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
* *
1495354 CAAAAGTATAGTGTAATATGTAATTTTTCAATCTAACCGGTATAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1495419 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
1495484 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
196 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
*
1495549 AACCCAAAAGTATAATGTAATATGTAATTTTCCAATCTAACCGGTACAATTATACCGGTTTTATG
261 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
1495614 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAAT
326 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAAT
1495679 GAATGGAA
391 GAATGGAA
*
1495687 AACAGGGTGCACCCATAAAGTGTCGATTCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
1495752 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1495817 AATATGTCTAAATAATGTGTCGACACGT--TATAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACAC-TAATATAGTTTGTGTCGATA
1495862 CTAATTTAAA
Statistics
Matches: 1299, Mismatches: 17, Indels: 56
0.95 0.01 0.04
Matches are distributed among these distances:
373 107 0.08
375 107 0.08
376 147 0.11
379 1 0.00
380 4 0.00
382 1 0.00
384 1 0.00
386 1 0.00
388 1 0.00
390 4 0.00
391 1 0.00
394 10 0.01
395 197 0.15
396 68 0.05
397 132 0.10
398 516 0.40
399 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (398 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAAT
GAATGGAA
Found at i:1495804 original size:597 final size:592
Alignment explanation
Indices: 1494121--1495861 Score: 3103
Period size: 597 Copynumber: 3.0 Consensus size: 592
1494111 CAATATGGCC
* * *
1494121 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
* *
1494186 CCAAAAGTATAATGT-ATATGTAATTTTTCAATCTAACCGGTACAAGTCTACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
1494250 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAA
1494315 TGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCG
194 TGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATA-AAAAGTGTCGATCCCAAAATCATCG
* *
1494380 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATATCGGTTTTATG
258 AACCCAAAAGTATAATGTAATATGTAATTTTCCAATCTAACCGGTACAATTATACCGGTTTTATG
* *
1494445 AGATAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAAT
323 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAAT
1494510 GAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATC
388 GAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATC
*
1494575 ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT
453 ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTT
1494640 TATGAGAGAATATGTC----T-A-------A-A---TA-A---TGTGTCGATATTTTTTTCCAAA
518 TATGAGAGAATATGTCTAAATAATGTGTCGACACGTTATAGTTTGTGTCGATATTTTTTTCCAAA
1494685 ATGAATGGAA
583 ATGAATGGAA
1494695 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1494760 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1494825 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
1494890 GAAAACAGGGTGCACCCATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAAC
196 GAAAACAGGGTGCACCCATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAAC
*
1494955 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
261 CCAAAAGTATAATGTAATATGTAATTTTCCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
1495020 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
326 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
1495085 TGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
391 TGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
*
1495150 GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT
456 GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTAT
*
1495215 GAGAGAATATGTCTAAATAATGTGTCGACAC-TAATATAGTTTGTGTCGATATTTTTTTTCCAGA
521 GAGAGAATATGTCTAAATAATGTGTCGACACGT--TATAGTTTGTGTCGATA-TTTTTTTCCAAA
1495279 ATGAATGGAA
583 ATGAATGGAA
1495289 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
* *
1495354 CAAAAGTATAGTGTAATATGTAATTTTTCAATCTAACCGGTATAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1495419 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
1495484 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
195 GGAAAACAGGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCG
1495549 AACCCAAAAGTATAATGTAATATGTAATTTTCCAATCTAACCGGTACAATTATACCGGTTTTATG
258 AACCCAAAAGTATAATGTAATATGTAATTTTCCAATCTAACCGGTACAATTATACCGGTTTTATG
1495614 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAAT
323 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAAT
*
1495679 GAATGGAAAACAGGGTGCACCCATAAAGTGTCGATTCATATATAAAAAGTGTCGATCCCAAAATC
388 GAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATC
1495744 ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTT
453 ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTT
1495809 TATGAGAGAATATGTCTAAATAATGTGTCGACACGTTATAGTTTGTGTCGATA
518 TATGAGAGAATATGTCTAAATAATGTGTCGACACGTTATAGTTTGTGTCGATA
1495862 CTAATTTAAA
Statistics
Matches: 1126, Mismatches: 14, Indels: 32
0.96 0.01 0.03
Matches are distributed among these distances:
572 298 0.26
573 73 0.06
574 153 0.14
576 1 0.00
577 1 0.00
584 1 0.00
585 1 0.00
589 2 0.00
590 1 0.00
593 10 0.01
594 195 0.17
595 51 0.05
596 17 0.02
597 321 0.29
598 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (592 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
GAAAACAGGGTGCACCCATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAAC
CCAAAAGTATAATGTAATATGTAATTTTCCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
TGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTAT
GAGAGAATATGTCTAAATAATGTGTCGACACGTTATAGTTTGTGTCGATATTTTTTTCCAAAATG
AATGGAA
Found at i:1497346 original size:3 final size:3
Alignment explanation
Indices: 1497338--1497406 Score: 57
Period size: 3 Copynumber: 23.0 Consensus size: 3
1497328 TGAAGCTGAC
* * * ** * * *
1497338 GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT GAC GAC GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
1497386 GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT
1497407 CCAAACAAGT
Statistics
Matches: 51, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.35, C:0.07, G:0.35, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:1497349 original size:12 final size:12
Alignment explanation
Indices: 1497334--1497406 Score: 65
Period size: 12 Copynumber: 6.1 Consensus size: 12
1497324 AAGATGAAGC
1497334 TGACGATGATGA
1 TGACGATGATGA
* *
1497346 TGACGATGAAGC
1 TGACGATGATGA
* *
1497358 TGGCGATGAAGA
1 TGACGATGATGA
* * *
1497370 TGATGACGACGA
1 TGACGATGATGA
*
1497382 TGATGATGATGA
1 TGACGATGATGA
*
1497394 TGAAGATGATGA
1 TGACGATGATGA
1497406 T
1 T
1497407 CCAAACAAGT
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 50 1.00
ACGTcount: A:0.34, C:0.08, G:0.34, T:0.23
Consensus pattern (12 bp):
TGACGATGATGA
Found at i:1499214 original size:183 final size:182
Alignment explanation
Indices: 1498903--1499389 Score: 850
Period size: 183 Copynumber: 2.7 Consensus size: 182
1498893 CAATGCTATC
* *
1498903 GTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATCTTGT
1 GTATAAATATACCGGTTTTATGCACGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGT
* * *
1498968 GTCGGTACTTTATGTCTAGATTGGAAGAAAAATGTGTCGATACATTGTTAAAAAGTGTCGACATT
66 GTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATT-TAAAAAAGTATCGACATT
*
1499033 TACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCG
130 TACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCG
1499086 GTATAAATATACCGGTTTTATGCACGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGT
1 GTATAAATATACCGGTTTTATGCACGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGT
*
1499151 GTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTATCGACATT
66 GTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATAC-ATTTAAAAAAGTATCGACATT
*
1499216 TACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAACCG
130 TACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCG
*
1499269 GTATAAATATACCGGTTTTATG-AGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTG
1 GTATAAATATACCGGTTTTATGCA-CGAATAGGTCTACAACCTATATCGACACTTTTTAATATTG
1499333 TGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGT
65 TGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA-CATTTAAAAAAGT
1499390 GTCGGTAATT
Statistics
Matches: 291, Mismatches: 10, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
182 1 0.00
183 286 0.98
184 4 0.01
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Consensus pattern (182 bp):
GTATAAATATACCGGTTTTATGCACGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGT
GTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTTAAAAAAGTATCGACATTT
ACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCG
Found at i:1502285 original size:23 final size:23
Alignment explanation
Indices: 1502254--1502326 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
1502244 ATAGGTAAAA
*
1502254 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1502277 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1502300 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
1502323 ATAT
1 ATAT
1502327 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1502771 original size:18 final size:18
Alignment explanation
Indices: 1502750--1502786 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1502740 GTAATTGGAG
1502750 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1502768 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1502786 T
1 T
1502787 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1502794 original size:24 final size:24
Alignment explanation
Indices: 1502742--1502788 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1502732 TTTCATATGT
* *
1502742 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
1502766 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
1502789 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:1503106 original size:38 final size:38
Alignment explanation
Indices: 1503042--1503126 Score: 127
Period size: 39 Copynumber: 2.2 Consensus size: 38
1503032 TTCGATGCTC
*
1503042 ATCAAAATCCAAAGCTATATGGTGCCAAGC-AAAGGAA
1 ATCAAAATCCAAAGCTATATGATGCCAAGCAAAAGGAA
* *
1503079 ATCAAAATTCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCT-ATATGATGCCAAGCAAAAGGAA
1503118 ATCAAAATC
1 ATCAAAATC
1503127 TACAACTTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
37 14 0.33
38 13 0.31
39 15 0.36
ACGTcount: A:0.48, C:0.19, G:0.14, T:0.19
Consensus pattern (38 bp):
ATCAAAATCCAAAGCTATATGATGCCAAGCAAAAGGAA
Found at i:1503578 original size:23 final size:23
Alignment explanation
Indices: 1503547--1503619 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
1503537 ATAGGTAAAA
*
1503547 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1503570 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1503593 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
1503616 ATAT
1 ATAT
1503620 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1504005 original size:22 final size:23
Alignment explanation
Indices: 1503977--1504043 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
1503967 GTAAAAATAG
1503977 ATGTAATAGGTAGCGCTTATA-A
1 ATGTAATAGGTAGCGCTTATATA
* * *
1503999 ATGTAATATGTATCGTTTATATA
1 ATGTAATAGGTAGCGCTTATATA
* *
1504022 ATGTAATAGGTAGTGGTTATAT
1 ATGTAATAGGTAGCGCTTATAT
1504044 TGTAAAGTGT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 18 0.49
23 19 0.51
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.40
Consensus pattern (23 bp):
ATGTAATAGGTAGCGCTTATATA
Found at i:1504182 original size:424 final size:426
Alignment explanation
Indices: 1503345--1504812 Score: 2672
Period size: 426 Copynumber: 3.5 Consensus size: 426
1503335 GTTAATGTTG
*
1503345 TTAAATAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAAT
1 TTAAATAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATTTTTTGTGCAAAT
1503410 GAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAATTGAAACATA
66 GAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAAATTGAAACATA
*
1503475 AATTACAT-ACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
130 AATTACATAACTTTAAAAGAAGTATCAATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
1503539 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAA
195 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAA
1503604 TAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
260 TAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATA-TTTTTTCACTGT
1503669 GGAAAACATTAATTTAAGGTTATC-TTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
324 GGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
1503733 GTCTAATGATTTATTTTTTACGTTACTATATA-TATTA
389 GTCTAATGATTTATTTTTTACGTTACTATATATTATTA
*
1503770 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAA
1 TTAAA-TAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATTTTTTGTGCAAA
1503835 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATA
65 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATA
*
1503900 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
130 AATTACATAACTTTAAAAGAAGTATCAATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
*
1503965 AGGTAAAAATA-GATGTAATAGGTAGCGCTTATA-AATGTAATATGTATCGTTTATATAATGTAA
195 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAA
1504028 TAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATATTTTTTTCACTGT
260 TAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATA-TTTTTTCACTGT
*
1504093 GGAAACCATTAATTTAAGGTTATCTTTTGAGTGAG-TTTAAGATATTAATTTAGTAATTATAGGC
324 GGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
*
1504157 GTCTAATGATTTATTTTTTACGTTACGATATATTATTA
389 GTCTAATGATTTATTTTTTACGTTACTATATATTATTA
*
1504195 TTAAATAAAAATTCTAAATAAAATTTTAT-AAA-ATCAAAAAATCAAATAATTTTTTGTGCAAAT
1 TTAAATAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATTTTTTGTGCAAAT
*
1504258 GAAATTATTAAATTAA-ATTGTAGGTGGAAAACATGAAACGCTATTAAAAAAAATTGAAACATAA
66 GAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAA
1504322 ATTACATAAC-TTAAAAGAAGTATCAATCC-TTTTATAAAAAGTATGGACACTTTCAATATAATA
131 ATTACATAACTTTAAAAGAAGTATCAATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATA
1504385 GGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAAT
196 GGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAAT
*
1504450 AGGTAGTGGTTATATTGTAAAGTGTCTATCC-TTTTATAAAAGTGTCCATACTTTTTCACTGTGG
261 AGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATATTTTTTCACTGTGG
1504514 AAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGT
326 AAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGT
1504579 CTAATGATTTATTTTTTACGTTACGATATATATTATTA
391 CTAATGATTTATTTTTTACGTTAC--TATATATTATTA
*
1504617 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATTAAATAATTTTTTGTGCAAA
1 TTAAA-TAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATTTTTTGTGCAAA
*
1504682 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTTGAAACATA
65 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATA
*
1504747 AATTACATAACTTTAAAAGAAGTATCAATCATTTTTATAAAAAGTATGGACACTTTCAATATAAT
130 AATTACATAACTTTAAAAGAAGTATCAATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
1504812 A
195 A
1504813 TAATGTAATA
Statistics
Matches: 1011, Mismatches: 17, Indels: 27
0.96 0.02 0.03
Matches are distributed among these distances:
419 89 0.09
420 114 0.11
421 118 0.12
422 62 0.06
423 26 0.03
424 202 0.20
425 119 0.12
426 229 0.23
427 18 0.02
428 34 0.03
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (426 bp):
TTAAATAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATTTTTTGTGCAAAT
GAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAA
ATTACATAACTTTAAAAGAAGTATCAATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATA
GGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAAT
AGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATATTTTTTCACTGTGG
AAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGT
CTAATGATTTATTTTTTACGTTACTATATATTATTA
Found at i:1504423 original size:23 final size:23
Alignment explanation
Indices: 1504392--1504464 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
1504382 ATAGGTAAAA
*
1504392 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1504415 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1504438 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
1504461 ATAT
1 ATAT
1504465 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1509380 original size:37 final size:37
Alignment explanation
Indices: 1509330--1509401 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
1509320 CAGATCGGGT
* * * *
1509330 TCGGATCGGGTGAAGGGTATATATTTTTTGGGTCGAA
1 TCGGATCGAGTGAAGGATATAAACTTTTTGGGTCGAA
*
1509367 TCGGATCGAGTGAAGGATGTAAACTTTTTGGGTCG
1 TCGGATCGAGTGAAGGATATAAACTTTTTGGGTCG
1509402 GGTCGAGTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.22, C:0.10, G:0.35, T:0.33
Consensus pattern (37 bp):
TCGGATCGAGTGAAGGATATAAACTTTTTGGGTCGAA
Found at i:1519112 original size:17 final size:19
Alignment explanation
Indices: 1519072--1519112 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
1519062 TTGGAACATC
1519072 TAAAATCATGTAATTTTAA
1 TAAAATCATGTAATTTTAA
*
1519091 TAAAA-CATTTAATTTT-A
1 TAAAATCATGTAATTTTAA
1519108 TAAAA
1 TAAAA
1519113 AAATACCACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.29
18 10 0.48
19 5 0.24
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (19 bp):
TAAAATCATGTAATTTTAA
Found at i:1521572 original size:19 final size:18
Alignment explanation
Indices: 1521548--1521583 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1521538 TCTCGCCATG
1521548 TTTTCTATTCTCTCTGCCT
1 TTTTCTATTCT-TCTGCCT
*
1521567 TTTTCTTTTCTTCTGCC
1 TTTTCTATTCTTCTGCC
1521584 GTGAAAATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.03, C:0.31, G:0.06, T:0.61
Consensus pattern (18 bp):
TTTTCTATTCTTCTGCCT
Found at i:1522061 original size:4 final size:4
Alignment explanation
Indices: 1522052--1522086 Score: 61
Period size: 4 Copynumber: 8.5 Consensus size: 4
1522042 TTCTTTGTTC
1522052 TTCT TTCT TTCT TTCT TTCT TTCT TTCTT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTC-T TTCT TT
1522087 TTCCGCTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:1529236 original size:2 final size:2
Alignment explanation
Indices: 1529229--1529255 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1529219 TTTTAAGGAT
1529229 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1529256 ATATCTGTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1530596 original size:126 final size:128
Alignment explanation
Indices: 1530219--1530817 Score: 980
Period size: 126 Copynumber: 4.9 Consensus size: 128
1530209 CTATAATCGG
1530219 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCC---ATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
*
1530281 TATCATTGCCCTATTATG-CATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
1530343 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCG-CTTCCATTATTTCGTCAGAGAATA---
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
*
1530404 TATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATA-CAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
1530466 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1530531 TATCATTG-CCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA-CTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
1530592 TTCACTATTCACATGAAGACGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
*
1530657 AATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG--AC-A-ATATATCAGTACC--TTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
1530714 TTCACTATTCACATGAAGGCGCGTTCCC--GGGCGCG----CC-TTATTTCGTCAGAGAATAT-T
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1530771 TATCATTGCCC-ATTATGTCACTCATGTCCCTCGGGGACACTAGATAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATAT
1530818 CAGTTTGAAT
Statistics
Matches: 455, Mismatches: 5, Indels: 37
0.92 0.01 0.07
Matches are distributed among these distances:
113 25 0.05
114 11 0.02
115 21 0.05
116 3 0.01
117 4 0.01
120 7 0.02
122 31 0.07
123 84 0.18
124 93 0.20
125 2 0.00
126 133 0.29
127 41 0.09
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.32
Consensus pattern (128 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:1530709 original size:250 final size:246
Alignment explanation
Indices: 1530219--1530817 Score: 981
Period size: 250 Copynumber: 2.5 Consensus size: 246
1530209 CTATAATCGG
1530219 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCC--ATTTCGTCAGAGAATATGTT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCTTATTTCGTCAGAGAATATGTT
*
1530282 ATCATTGCCCTATTATG-CATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 ATCATTG-CCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
1530346 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCTTCCATTATTTCGTCAGAGAATATATCATT
130 ACTATTCACATGAAGACGCGTTCCCGGGGGCGCGCTTCCATTATTTCGTCAGAGAATATATCATT
*
1530411 GCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATACAGTACCTATTAT
195 GCCCTATTATGTCACTCATGTCCCTCGGGGACAC-AGATATACAGTACC--TTAT
1530466 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCC-TTATTTCGTCAGAGAATATGT
1530531 TATCATTGCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA-CTATTATTTC
65 TATCATTGCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
1530595 ACTATTCACATGAAGACGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTAAT
130 ACTATTCACATGAAGACGCGTTCCCGGGGGCGCG-CTTCCATTATTTCGTCAGAGAATA--T-AT
*
1530660 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACA-ATATAT-CAGTACCTTAT
191 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACAGATATACAGTACCTTAT
1530714 TTCACTATTCACATGAAGGCGCGTTCCC--GGGCGCG----CCTTATTTCGTCAGAGAATAT-TT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCTTATTTCGTCAGAGAATATGTT
*
1530772 ATCATTGCCCATTATGTCACTCATGTCCCTCGGGGACACTAGATAT
66 ATCATTGCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATAT
1530818 CAGTTTGAAT
Statistics
Matches: 339, Mismatches: 5, Indels: 23
0.92 0.01 0.06
Matches are distributed among these distances:
240 47 0.14
241 19 0.06
242 2 0.01
246 7 0.02
247 43 0.13
248 32 0.09
249 52 0.15
250 93 0.27
251 5 0.01
252 1 0.00
253 38 0.11
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.32
Consensus pattern (246 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCTTATTTCGTCAGAGAATATGTT
ATCATTGCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
CTATTCACATGAAGACGCGTTCCCGGGGGCGCGCTTCCATTATTTCGTCAGAGAATATATCATTG
CCCTATTATGTCACTCATGTCCCTCGGGGACACAGATATACAGTACCTTAT
Found at i:1531278 original size:34 final size:34
Alignment explanation
Indices: 1531202--1531296 Score: 104
Period size: 33 Copynumber: 2.9 Consensus size: 34
1531192 AAATTTAATG
* * *
1531202 TTAAATTTCGAATACTA-TAATTATATTTTAAAT
1 TTAAATTTTGAATAATATTATTTATATTTTAAAT
* * *
1531235 TTAAA-TTTGAATAATATTATTTTTATTTTTATT
1 TTAAATTTTGAATAATATTATTTATATTTTAAAT
* *
1531268 TTAAATTTTGAATAATATAATTTGTATTT
1 TTAAATTTTGAATAATATTATTTATATTT
1531297 AAAAACATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
32 9 0.17
33 22 0.42
34 21 0.40
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (34 bp):
TTAAATTTTGAATAATATTATTTATATTTTAAAT
Found at i:1531897 original size:21 final size:21
Alignment explanation
Indices: 1531809--1531902 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
1531799 TATGGTATAA
*
1531809 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
1531830 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
1531851 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
1531872 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
1531893 AACCCTGCGG
1 AACCCTGCGG
1531903 ATATGACATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:1533692 original size:17 final size:18
Alignment explanation
Indices: 1533666--1533700 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1533656 ATAATTATAT
*
1533666 AAATATTATTTA-ATAAA
1 AAATAATATTTACATAAA
1533683 AAATAATATTTACATAAA
1 AAATAATATTTACATAAA
1533701 TATATTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATAATATTTACATAAA
Found at i:1533700 original size:32 final size:32
Alignment explanation
Indices: 1533646--1533723 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 32
1533636 TTAATAATTC
* *
1533646 TAAATAAATAATAATTATATAAATATTATTTA-A
1 TAAA-AAATAATAATTACATAAATA-TATTAATA
*
1533679 TAAAAAATAATATTTACATAAATATATTAATA
1 TAAAAAATAATAATTACATAAATATATTAATA
1533711 TAAAAAATAATAA
1 TAAAAAATAATAA
1533724 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
31 5 0.12
32 31 0.77
33 4 0.10
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (32 bp):
TAAAAAATAATAATTACATAAATATATTAATA
Found at i:1533713 original size:14 final size:15
Alignment explanation
Indices: 1533649--1533719 Score: 56
Period size: 15 Copynumber: 4.7 Consensus size: 15
1533639 ATAATTCTAA
1533649 ATAAATAATAATT-AT
1 ATAAATAAT-ATTAAT
*
1533664 ATAAATATTATTTAAT
1 ATAAATAATA-TTAAT
* * *
1533680 AAAAAATAATATTTAC
1 -ATAAATAATATTAAT
1533696 ATAAAT-ATATTAAT
1 ATAAATAATATTAAT
*
1533710 ATAAAAAATA
1 ATAAATAATA
1533720 ATAACTATTT
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
14 12 0.28
15 18 0.42
16 5 0.12
17 8 0.19
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAAATAATATTAAT
Found at i:1534876 original size:11 final size:11
Alignment explanation
Indices: 1534860--1534885 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1534850 TAACAAGTTG
1534860 AATTCTACTAT
1 AATTCTACTAT
1534871 AATTCTACTAT
1 AATTCTACTAT
1534882 AATT
1 AATT
1534886 AATTTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (11 bp):
AATTCTACTAT
Found at i:1536356 original size:35 final size:35
Alignment explanation
Indices: 1536317--1536388 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
1536307 TCCTTTTATA
1536317 GAATTTGACCAAAGTTTTTTAATGAAGTTTTACTT
1 GAATTTGACCAAAGTTTTTTAATGAAGTTTTACTT
1536352 GAATTTGACCAAAGTTTTTTAATGAAGTTTTACTT
1 GAATTTGACCAAAGTTTTTTAATGAAGTTTTACTT
1536387 GA
1 GA
1536389 GGGGAAAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.44
Consensus pattern (35 bp):
GAATTTGACCAAAGTTTTTTAATGAAGTTTTACTT
Found at i:1542701 original size:94 final size:93
Alignment explanation
Indices: 1542403--1542720 Score: 447
Period size: 95 Copynumber: 3.4 Consensus size: 93
1542393 TCTTTAACCA
* * *
1542403 TTAATCGAATCGAAATTTATTTGGAAATTATTAACCGAATCAAATTAATCGATTTTTTTCTTTAA
1 TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAATCGATTTTTTTCTTTAA
1542468 CATTAATCGAACCGAAATTATTTGACCG
66 CATTAATCGAACCGAAATTATTTGACCG
* * * *
1542496 TTAATCGAACCGAGATTTATTTGAAAATTATTAATCTAACCAAATTAATTGAATTTTTTTTCTTT
1 TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAATCG-A-TTTTTTTCTTT
* * *
1542561 AACATTAAACGAACCGAAATTATTAGACAG
64 AACATTAATCGAACCGAAATTATTTGACCG
* * * *
1542591 TTAATCGAACCCAAATTTATTTGAAAATTATTAACCGAACCTAATCAACCGATTTTTTTCTTTAA
1 TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAATCGATTTTTTTCTTTAA
1542656 CTATTAATCGAACCGAAATTATTTGACCG
66 C-ATTAATCGAACCGAAATTATTTGACCG
* * * *
1542685 TTAATTGAATCTAAATTTATTTGAAAATAATTAACC
1 TTAATCGAACCGAAATTTATTTGAAAATTATTAACC
1542721 TAATTAACCG
Statistics
Matches: 197, Mismatches: 25, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
93 58 0.29
94 58 0.29
95 81 0.41
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.38
Consensus pattern (93 bp):
TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAATCGATTTTTTTCTTTAA
CATTAATCGAACCGAAATTATTTGACCG
Found at i:1544191 original size:16 final size:17
Alignment explanation
Indices: 1544170--1544201 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1544160 TACTATTCAT
1544170 GTGAATAGT-AAATTTC
1 GTGAATAGTGAAATTTC
1544186 GTGAATAGTGAAATTT
1 GTGAATAGTGAAATTT
1544202 TGTCGGCGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.38
Consensus pattern (17 bp):
GTGAATAGTGAAATTTC
Found at i:1545508 original size:25 final size:25
Alignment explanation
Indices: 1545451--1545508 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
1545441 GAACTGAGTA
*
1545451 AAACGGTTCGGTTTGGTTTGGCTTT
1 AAACGGTTCGGTTTGGTTCGGCTTT
1545476 AAACGGTTCGGTTTTTGGTTCGG-TTT
1 AAACGGTTCGG--TTTGGTTCGGCTTT
1545502 AAA-GGTT
1 AAACGGTT
1545509 TCATTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 15 0.50
26 6 0.20
27 9 0.30
ACGTcount: A:0.16, C:0.10, G:0.31, T:0.43
Consensus pattern (25 bp):
AAACGGTTCGGTTTGGTTCGGCTTT
Found at i:1553203 original size:32 final size:33
Alignment explanation
Indices: 1553162--1553243 Score: 114
Period size: 32 Copynumber: 2.5 Consensus size: 33
1553152 GTGATGCTGA
1553162 CTATACTATGCATTATCTGAATACAATACTGATT
1 CTAT-CTATGCATTATCTGAATACAATACTGATT
* *
1553196 CT-TCTATGCATTATCTGAATGCAATATTGATT
1 CTATCTATGCATTATCTGAATACAATACTGATT
*
1553228 CTAT-TGTGCATTATCT
1 CTATCTATGCATTATCT
1553244 AAAAGCAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
32 40 0.91
33 2 0.05
34 2 0.05
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.43
Consensus pattern (33 bp):
CTATCTATGCATTATCTGAATACAATACTGATT
Found at i:1553252 original size:32 final size:32
Alignment explanation
Indices: 1553167--1553255 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 32
1553157 GCTGACTATA
*
1553167 CTATGCATTATCTGAATA-CAATACTGATTCTT
1 CTATGCATTATCT-AAAAGCAATACTGATTCTT
* * *
1553199 CTATGCATTATCTGAATGCAATATTGATTCTAT
1 CTATGCATTATCTAAAAGCAATACTGATTCT-T
*
1553232 -TGTGCATTATCTAAAAGCAATACT
1 CTATGCATTATCTAAAAGCAATACT
1553256 AACTTTATTA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
31 1 0.02
32 45 0.96
33 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (32 bp):
CTATGCATTATCTAAAAGCAATACTGATTCTT
Found at i:1558703 original size:17 final size:17
Alignment explanation
Indices: 1558681--1558728 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
1558671 AAAAATAAAA
1558681 ATAAATATATAGGGACT
1 ATAAATATATAGGGACT
*
1558698 ATAAATATA-A---AAT
1 ATAAATATATAGGGACT
1558711 ATAAATATATAGGGACT
1 ATAAATATATAGGGACT
1558728 A
1 A
1558729 AAAAGGCAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
13 11 0.44
14 1 0.04
16 1 0.04
17 12 0.48
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.29
Consensus pattern (17 bp):
ATAAATATATAGGGACT
Found at i:1558730 original size:28 final size:28
Alignment explanation
Indices: 1558675--1558730 Score: 87
Period size: 30 Copynumber: 2.0 Consensus size: 28
1558665 AATATAAAAA
1558675 ATAAAAATAAATATATAGGGACTATAAAT
1 ATAAAAATAAATATATAGGGAC-ATAAAT
1558704 ATAAAATATAAATATATAGGGAC-TAAA
1 ATAAAA-ATAAATATATAGGGACATAAA
1558731 AAGGCAGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 4 0.15
29 6 0.23
30 16 0.62
ACGTcount: A:0.59, C:0.04, G:0.11, T:0.27
Consensus pattern (28 bp):
ATAAAAATAAATATATAGGGACATAAAT
Found at i:1560234 original size:13 final size:13
Alignment explanation
Indices: 1560216--1560244 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1560206 TTCAAAGTAG
1560216 ACACGTTGTACGA
1 ACACGTTGTACGA
1560229 ACACGTTGTACGA
1 ACACGTTGTACGA
1560242 ACA
1 ACA
1560245 GAGCATGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (13 bp):
ACACGTTGTACGA
Found at i:1561804 original size:39 final size:39
Alignment explanation
Indices: 1561740--1561885 Score: 265
Period size: 39 Copynumber: 3.7 Consensus size: 39
1561730 GCTTGATATA
* *
1561740 TTTGCCAGGAATTGCGTAAGGTTGATCGAGTAGTGTTGC
1 TTTGACAGGAATTGCGTAAGCTTGATCGAGTAGTGTTGC
1561779 TTTGACAGGAATTGCGTAAGCTTGATCGAGTAGTGTTGC
1 TTTGACAGGAATTGCGTAAGCTTGATCGAGTAGTGTTGC
1561818 TTTGACAGGAATTGCGTAAGCTTGATCGAGTAGTGTTGC
1 TTTGACAGGAATTGCGTAAGCTTGATCGAGTAGTGTTGC
*
1561857 TTTGACAGGAATTGCGTAAGCTTGTTCGA
1 TTTGACAGGAATTGCGTAAGCTTGATCGA
1561886 AGAGTGCAAA
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 104 1.00
ACGTcount: A:0.23, C:0.13, G:0.31, T:0.34
Consensus pattern (39 bp):
TTTGACAGGAATTGCGTAAGCTTGATCGAGTAGTGTTGC
Found at i:1565110 original size:24 final size:24
Alignment explanation
Indices: 1565065--1565110 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
1565055 CTTTTCAGTG
**
1565065 TCTTCATCCTCGCCTTTTTCAGCA
1 TCTTCATCCTCGCCTTCCTCAGCA
* *
1565089 TCTTCATCTTCTCCTTCCTCAG
1 TCTTCATCCTCGCCTTCCTCAG
1565111 ATTTAGTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.11, C:0.39, G:0.07, T:0.43
Consensus pattern (24 bp):
TCTTCATCCTCGCCTTCCTCAGCA
Found at i:1566478 original size:35 final size:35
Alignment explanation
Indices: 1566439--1566520 Score: 110
Period size: 35 Copynumber: 2.3 Consensus size: 35
1566429 AAAAGAGAGT
1566439 TTTACATGCTTCAATACCGAAACAGAATTTCTACA
1 TTTACATGCTTCAATACCGAAACAGAATTTCTACA
* * * * * *
1566474 TTTACACGCTTCAGTTCTGAAACATAATTTCTACG
1 TTTACATGCTTCAATACCGAAACAGAATTTCTACA
1566509 TTTACATGCTTC
1 TTTACATGCTTC
1566521 TTGTATAACG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (35 bp):
TTTACATGCTTCAATACCGAAACAGAATTTCTACA
Found at i:1568421 original size:3 final size:3
Alignment explanation
Indices: 1568413--1568445 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1568403 AAAATATTAC
1568413 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1568446 TATTATTATT
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:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1569586 original size:18 final size:18
Alignment explanation
Indices: 1569563--1569606 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1569553 CATTATGGGT
*
1569563 TTTATTTTATTTTATTAC
1 TTTATTTTATTTTATGAC
*
1569581 TTTATTTTATTTTATGAT
1 TTTATTTTATTTTATGAC
1569599 TTTATTTT
1 TTTATTTT
1569607 TTTCCTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.75
Consensus pattern (18 bp):
TTTATTTTATTTTATGAC
Found at i:1575673 original size:24 final size:23
Alignment explanation
Indices: 1575641--1575718 Score: 84
Period size: 24 Copynumber: 3.3 Consensus size: 23
1575631 AATTGAGATA
*
1575641 AACATAAATGAACACATATAAACG
1 AACATAAATGAACA-ATATAAATG
* * * *
1575665 AACACAAATGAATGAACATAAATT
1 AACATAAATGAA-CAATATAAATG
1575689 AACATAAATGAACAAATATAAATG
1 AACATAAATGAAC-AATATAAATG
1575713 AACATA
1 AACATA
1575719 TTACCGAATG
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
24 42 0.98
25 1 0.02
ACGTcount: A:0.60, C:0.13, G:0.08, T:0.19
Consensus pattern (23 bp):
AACATAAATGAACAATATAAATG
Found at i:1575681 original size:14 final size:14
Alignment explanation
Indices: 1575644--1575687 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1575634 TGAGATAAAC
*
1575644 ATAAATGAACACAT
1 ATAAATGAACACAA
*
1575658 ATAAACGAACACAA
1 ATAAATGAACACAA
* *
1575672 ATGAATGAACATAA
1 ATAAATGAACACAA
1575686 AT
1 AT
1575688 TAACATAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.59, C:0.14, G:0.09, T:0.18
Consensus pattern (14 bp):
ATAAATGAACACAA
Found at i:1576878 original size:3 final size:3
Alignment explanation
Indices: 1576870--1576963 Score: 66
Period size: 3 Copynumber: 30.7 Consensus size: 3
1576860 TTAGCAATTT
**
1576870 GAA GAA GAA GAA GAA GAA GAA GCT GCAA GAA GAA GAA GAA -AA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA G-AA GAA GAA GAA GAA GAA GAA
** * ** *
1576915 GCT GCAA AAA GCAA GAA GAA GAA GCT GCAA GAA GAT GAA GAA -AA GAA
1 GAA G-AA GAA G-AA GAA GAA GAA GAA G-AA GAA GAA GAA GAA GAA GAA
1576962 GA
1 GA
1576964 TGTCACGTCA
Statistics
Matches: 69, Mismatches: 16, Indels: 12
0.71 0.16 0.12
Matches are distributed among these distances:
2 4 0.06
3 60 0.87
4 5 0.07
ACGTcount: A:0.59, C:0.07, G:0.30, T:0.04
Consensus pattern (3 bp):
GAA
Found at i:1576901 original size:13 final size:13
Alignment explanation
Indices: 1576883--1576949 Score: 56
Period size: 13 Copynumber: 5.5 Consensus size: 13
1576873 GAAGAAGAAG
1576883 AAGAAGAAGCTGC
1 AAGAAGAAGCTGC
**
1576896 AAGAAGAAGAAG-
1 AAGAAGAAGCTGC
1576908 AA-AAGAAGCTGC
1 AAGAAGAAGCTGC
*
1576920 -A-AA-AAGCAAG-
1 AAGAAGAAGC-TGC
1576930 AAGAAGAAGCTGC
1 AAGAAGAAGCTGC
1576943 AAGAAGA
1 AAGAAGA
1576950 TGAAGAAAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
10 4 0.10
11 12 0.29
12 5 0.12
13 21 0.50
ACGTcount: A:0.57, C:0.10, G:0.28, T:0.04
Consensus pattern (13 bp):
AAGAAGAAGCTGC
Found at i:1579580 original size:21 final size:22
Alignment explanation
Indices: 1579554--1579598 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
1579544 GTCTATGAAG
1579554 AGTCATAAGAGAAT-AAATATA
1 AGTCATAAGAGAATGAAATATA
* *
1579575 AGTCATATGATAATGAAATATA
1 AGTCATAAGAGAATGAAATATA
1579597 AG
1 AG
1579599 ATTATATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.53, C:0.04, G:0.16, T:0.27
Consensus pattern (22 bp):
AGTCATAAGAGAATGAAATATA
Found at i:1579753 original size:104 final size:104
Alignment explanation
Indices: 1579642--1579850 Score: 409
Period size: 104 Copynumber: 2.0 Consensus size: 104
1579632 AATAGAGTTT
1579642 TTTTGATTTAATGAGAGTTAAGGGAACTAAATAAGATTGAATTATAGAATGAAATGAGAATAGTA
1 TTTTGATTTAATGAGAGTTAAGGGAACTAAATAAGATTGAATTATAGAATGAAATGAGAATAGTA
1579707 TATCATTTAAGAAACTTGAATATAAAGGGATGATACGAA
66 TATCATTTAAGAAACTTGAATATAAAGGGATGATACGAA
1579746 TTTTGATTTAATGAGAGTTAAGGGAACTAAATAAGATTGAATTATAGAATGAAATGAGAATAGTA
1 TTTTGATTTAATGAGAGTTAAGGGAACTAAATAAGATTGAATTATAGAATGAAATGAGAATAGTA
*
1579811 TATCATTTAGGAAACTTGAATATAAAGGGATGATACGAA
66 TATCATTTAAGAAACTTGAATATAAAGGGATGATACGAA
1579850 T
1 T
1579851 ATATAAGATA
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 104 1.00
ACGTcount: A:0.44, C:0.04, G:0.21, T:0.31
Consensus pattern (104 bp):
TTTTGATTTAATGAGAGTTAAGGGAACTAAATAAGATTGAATTATAGAATGAAATGAGAATAGTA
TATCATTTAAGAAACTTGAATATAAAGGGATGATACGAA
Found at i:1583940 original size:24 final size:22
Alignment explanation
Indices: 1583908--1583969 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 22
1583898 GCACAGGTAG
1583908 TGCATCGATGCATATGTTAAGGAA
1 TGCATCGATGCATATGTT-A-GAA
* * *
1583932 TGCATCGATACA-CTG-TAGAG
1 TGCATCGATGCATATGTTAGAA
1583952 TGCATCGATGCATATGTT
1 TGCATCGATGCATATGTT
1583970 TATTAAAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
20 13 0.42
21 3 0.10
22 2 0.06
23 2 0.06
24 11 0.35
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (22 bp):
TGCATCGATGCATATGTTAGAA
Found at i:1584281 original size:9 final size:10
Alignment explanation
Indices: 1584266--1584311 Score: 53
Period size: 9 Copynumber: 4.9 Consensus size: 10
1584256 GTTTGTCATA
1584266 ATTATATGTG
1 ATTATATGTG
1584276 -TTATATGTG
1 ATTATATGTG
1584285 ATTATATGT-
1 ATTATATGTG
* *
1584294 ATTACAT-TA
1 ATTATATGTG
1584303 ATTATATGT
1 ATTATATGT
1584312 ATGTATGACT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
8 1 0.03
9 21 0.68
10 9 0.29
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (10 bp):
ATTATATGTG
Found at i:1584288 original size:19 final size:18
Alignment explanation
Indices: 1584264--1584313 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
1584254 GTGTTTGTCA
* *
1584264 TAATTATATGTGTTATAT
1 TAATTATATGTATTACAT
*
1584282 GTGATTATATGTATTACAT
1 -TAATTATATGTATTACAT
1584301 TAATTATATGTAT
1 TAATTATATGTAT
1584314 GTATGACTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.52
Consensus pattern (18 bp):
TAATTATATGTATTACAT
Found at i:1585565 original size:23 final size:23
Alignment explanation
Indices: 1585533--1585594 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
1585523 ACCTTATATA
1585533 GCACTTCGGTGCATTTCTA-AGCG
1 GCACTTCGGTGCATTTCTACA-CG
* * *
1585556 GCACTACGGTGCAATTCTACATG
1 GCACTTCGGTGCATTTCTACACG
1585579 GCACTTCGGTGCATTT
1 GCACTTCGGTGCATTT
1585595 ATACGAGCTG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
23 32 0.97
24 1 0.03
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (23 bp):
GCACTTCGGTGCATTTCTACACG
Found at i:1585767 original size:39 final size:37
Alignment explanation
Indices: 1585707--1585787 Score: 85
Period size: 39 Copynumber: 2.1 Consensus size: 37
1585697 AATGTATGTA
*
1585707 ATATATGTATATGATGTGTGATATGAAT-TGTATGACATG
1 ATATATGTATATGATGGGTGAT-TGAATCTGT-T-ACATG
* *
1585746 ATATATGTGTGAT-ATGGGTGATTGCATCTGTTACATG
1 ATATATGTAT-ATGATGGGTGATTGAATCTGTTACATG
1585783 ATATA
1 ATATA
1585788 CATGAATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
37 10 0.27
38 5 0.14
39 20 0.54
40 2 0.05
ACGTcount: A:0.31, C:0.05, G:0.23, T:0.41
Consensus pattern (37 bp):
ATATATGTATATGATGGGTGATTGAATCTGTTACATG
Found at i:1592556 original size:24 final size:24
Alignment explanation
Indices: 1592488--1592556 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
1592478 ATCTTATATA
*
1592488 GCACTACGGTGC-ATTTCTACGCG
1 GCACTTCGGTGCAATTTCTACGCG
* * *
1592511 GCACTTCAGTGCAAATTCTACGTG
1 GCACTTCGGTGCAATTTCTACGCG
* *
1592535 GCACTTTGGTGCAATTTATACG
1 GCACTTCGGTGCAATTTCTACG
1592557 AACTGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
23 10 0.27
24 27 0.73
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (24 bp):
GCACTTCGGTGCAATTTCTACGCG
Found at i:1592714 original size:19 final size:19
Alignment explanation
Indices: 1592690--1592729 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1592680 GATATGAAAT
1592690 ATGTTACATGAATTATATG
1 ATGTTACATGAATTATATG
** *
1592709 ATGTTATGTGTATTATATG
1 ATGTTACATGAATTATATG
1592728 AT
1 AT
1592730 ATACATAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47
Consensus pattern (19 bp):
ATGTTACATGAATTATATG
Found at i:1593216 original size:21 final size:21
Alignment explanation
Indices: 1593190--1593230 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1593180 GATACTTTAG
1593190 TGCATCGATGCACTATAGCAA
1 TGCATCGATGCACTATAGCAA
*
1593211 TGCATCGATGCACTGTAGCA
1 TGCATCGATGCACTATAGCA
1593231 CTATTCATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (21 bp):
TGCATCGATGCACTATAGCAA
Found at i:1597268 original size:14 final size:14
Alignment explanation
Indices: 1597251--1597277 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1597241 AAATCAAGTT
1597251 TTGAAATTAGAAAA
1 TTGAAATTAGAAAA
1597265 TTGAAATTAGAAA
1 TTGAAATTAGAAA
1597278 TTACTCCCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.30
Consensus pattern (14 bp):
TTGAAATTAGAAAA
Found at i:1599602 original size:19 final size:20
Alignment explanation
Indices: 1599556--1599615 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 20
1599546 TTCCCCTGTG
1599556 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TC-AA
1599579 GGGGGAATCGGTTCCCTC-A
1 GGGGGAATCGGTTCCCTCAA
* *
1599598 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
1599616 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.17, C:0.27, G:0.35, T:0.22
Consensus pattern (20 bp):
GGGGGAATCGGTTCCCTCAA
Found at i:1603450 original size:22 final size:21
Alignment explanation
Indices: 1603408--1603447 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1603398 GAGTTTGTTT
*
1603408 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1603429 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1603448 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1606947 original size:14 final size:13
Alignment explanation
Indices: 1606924--1606953 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
1606914 AACATATTAC
1606924 TCTTCTTTCTTCT
1 TCTTCTTTCTTCT
1606937 TCTTCCTTTCTTCT
1 TCTT-CTTTCTTCT
1606951 TCT
1 TCT
1606954 CCAACCGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (13 bp):
TCTTCTTTCTTCT
Found at i:1608466 original size:24 final size:24
Alignment explanation
Indices: 1608407--1608467 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 24
1608397 ATCTTATATA
* *
1608407 GCACTACGGTGC-ATTTCTACGCG
1 GCACTTCGGTGCAAATTCTACGCG
* * *
1608430 GTACTTCGTTGCAAATTCTACGTG
1 GCACTTCGGTGCAAATTCTACGCG
*
1608454 GCACTTTGGTGCAA
1 GCACTTCGGTGCAA
1608468 TTTATACGAG
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 9 0.31
24 20 0.69
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.31
Consensus pattern (24 bp):
GCACTTCGGTGCAAATTCTACGCG
Found at i:1610406 original size:18 final size:18
Alignment explanation
Indices: 1610383--1610424 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
1610373 TGACTAAAAT
1610383 AAAAACAAATAAAATTTG
1 AAAAACAAATAAAATTTG
1610401 AAAAACAAATAAAATTTG
1 AAAAACAAATAAAATTTG
*
1610419 AGAAAC
1 AAAAAC
1610425 GAATTAGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.19
Consensus pattern (18 bp):
AAAAACAAATAAAATTTG
Found at i:1610653 original size:24 final size:24
Alignment explanation
Indices: 1610626--1610701 Score: 143
Period size: 24 Copynumber: 3.2 Consensus size: 24
1610616 CTTATCTTCT
1610626 CTCTAAAGAGAGAAAAGCTCTCCC
1 CTCTAAAGAGAGAAAAGCTCTCCC
*
1610650 CTCTAAAGAGAGAAAAGCTTTCCC
1 CTCTAAAGAGAGAAAAGCTCTCCC
1610674 CTCTAAAGAGAGAAAAGCTCTCCC
1 CTCTAAAGAGAGAAAAGCTCTCCC
1610698 CTCT
1 CTCT
1610702 CTCTAGTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.36, C:0.29, G:0.16, T:0.20
Consensus pattern (24 bp):
CTCTAAAGAGAGAAAAGCTCTCCC
Found at i:1611562 original size:3 final size:3
Alignment explanation
Indices: 1611554--1611605 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
1611544 AAGTTTTGTA
1611554 AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1611600 ATAT AA
1 A-AT AA
1611606 GTCATGACGA
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 39 0.85
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:1611574 original size:14 final size:14
Alignment explanation
Indices: 1611555--1611597 Score: 86
Period size: 14 Copynumber: 3.1 Consensus size: 14
1611545 AGTTTTGTAA
1611555 ATAATAATAATAAT
1 ATAATAATAATAAT
1611569 ATAATAATAATAAT
1 ATAATAATAATAAT
1611583 ATAATAATAATAAT
1 ATAATAATAATAAT
1611597 A
1 A
1611598 ATATATAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:1611576 original size:17 final size:18
Alignment explanation
Indices: 1611554--1611604 Score: 88
Period size: 17 Copynumber: 2.9 Consensus size: 18
1611544 AAGTTTTGTA
1611554 AATAATAATAATA-ATAT
1 AATAATAATAATATATAT
1611571 AATAATAATAATATA-AT
1 AATAATAATAATATATAT
1611588 AATAATAATAATATATA
1 AATAATAATAATATATA
1611605 AGTCATGACG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 30 0.94
18 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AATAATAATAATATATAT
Found at i:1611958 original size:15 final size:15
Alignment explanation
Indices: 1611934--1611966 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1611924 ATTTACTCTG
1611934 TATATAATATTAAAT
1 TATATAATATTAAAT
*
1611949 TATATTATATTAAAT
1 TATATAATATTAAAT
1611964 TAT
1 TAT
1611967 TTGGCCTCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATATAATATTAAAT
Found at i:1615840 original size:7 final size:7
Alignment explanation
Indices: 1615827--1615866 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
1615817 CAGATTAAGA
1615827 ATTTAGG
1 ATTTAGG
*
1615834 GTTTAGG
1 ATTTAGG
1615841 ATTTAGG
1 ATTTAGG
*
1615848 ATTTAGT
1 ATTTAGG
*
1615855 ACTTAGG
1 ATTTAGG
1615862 ATTTA
1 ATTTA
1615867 TAGTTTATGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.28, C:0.03, G:0.25, T:0.45
Consensus pattern (7 bp):
ATTTAGG
Found at i:1617727 original size:24 final size:24
Alignment explanation
Indices: 1617698--1617751 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1617688 TGTTCGATAA
* *
1617698 TATGTTCGTTTATATTCGTTCATT
1 TATGTTCATTTATATGCGTTCATT
*
1617722 TATGTTCATTTATGTGCGTTCATT
1 TATGTTCATTTATATGCGTTCATT
1617746 TATGTT
1 TATGTT
1617752 TAGCCCAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.17, C:0.11, G:0.15, T:0.57
Consensus pattern (24 bp):
TATGTTCATTTATATGCGTTCATT
Found at i:1620459 original size:5 final size:5
Alignment explanation
Indices: 1620449--1620482 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
1620439 GGCGATGATG
1620449 GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA GAGA
1 GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA GAGA
1620483 TGGGAGATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (5 bp):
GAGAA
Found at i:1623139 original size:33 final size:33
Alignment explanation
Indices: 1623097--1623162 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1623087 GACTTCGCAG
*
1623097 ATTCTCCCAGTTGGCGTAGGAGTGATACTTTCT
1 ATTCTCCCAGTTGGAGTAGGAGTGATACTTTCT
*
1623130 ATTCTCCCAGTTGGAGTTGGAGTGATACTTTCT
1 ATTCTCCCAGTTGGAGTAGGAGTGATACTTTCT
1623163 CTATCAGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (33 bp):
ATTCTCCCAGTTGGAGTAGGAGTGATACTTTCT
Found at i:1627895 original size:21 final size:21
Alignment explanation
Indices: 1627871--1627913 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1627861 CAGAAGAAGA
1627871 AAGA-ATCAATGTCTACAATAG
1 AAGACATCAATGTCTA-AATAG
* *
1627892 AAGACATTAATGTTTAAATAG
1 AAGACATCAATGTCTAAATAG
1627913 A
1 A
1627914 GAAAAGGGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (21 bp):
AAGACATCAATGTCTAAATAG
Done.