Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003979.1 Hibiscus syriacus cultivar Beakdansim tig00008648_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: 55378
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:144 original size:11 final size:11
Alignment explanation
Indices: 128--152 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
118 CTAAAATGAA
128 AAATAATAATT
1 AAATAATAATT
139 AAATAATAATT
1 AAATAATAATT
150 AAA
1 AAA
153 GTACTAATTT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATAATAATT
Found at i:3415 original size:45 final size:45
Alignment explanation
Indices: 3288--3573 Score: 442
Period size: 45 Copynumber: 6.5 Consensus size: 45
3278 GTAACCATGC
* * **
3288 AAATAAACTTACAAGCTTATGGAA-T-AATGACAAGTATATTGGT-
1 AAATAAGCTTACGAGCTTAT-GAATTAAATGGTAAGTATATTGGTA
3331 AAATAAGCTTACGAGCTTAT--ATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGAATTAAATGGTAAGTATATTGGTA
*
3374 AAATAAGCTTACGAGCTTATGAATTAAATGGTAATTATATTGGTA
1 AAATAAGCTTACGAGCTTATGAATTAAATGGTAAGTATATTGGTA
3419 AAATAAGCTTACGAGCTTATGAATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGAATTAAATGGTAAGTATATTGGTA
* *
3464 AAATAAGCTTACGAGCTTATGAATTAAATGGTAAGTGTGTTGGTA
1 AAATAAGCTTACGAGCTTATGAATTAAATGGTAAGTATATTGGTA
3509 AAATAAGCTTACGAGCTTATGGAA-T-AATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTAT-GAATTAAATGGTAAGTATATTGGTA
3553 AAATAAGCTTACGAGCTTATG
1 AAATAAGCTTACGAGCTTATG
3574 GGATAAATGA
Statistics
Matches: 227, Mismatches: 10, Indels: 12
0.91 0.04 0.05
Matches are distributed among these distances:
40 1 0.00
41 1 0.00
42 16 0.07
43 39 0.17
44 37 0.16
45 130 0.57
46 3 0.01
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.33
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGAATTAAATGGTAAGTATATTGGTA
Found at i:4773 original size:27 final size:27
Alignment explanation
Indices: 4738--4791 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
4728 AAATCAGAAA
4738 TAAATCAGTGACCTAAACATAAAATAC
1 TAAATCAGTGACCTAAACATAAAATAC
* *
4765 TAAATCAGTGACCTAAATATGAAATAC
1 TAAATCAGTGACCTAAACATAAAATAC
4792 GTATAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.50, C:0.17, G:0.09, T:0.24
Consensus pattern (27 bp):
TAAATCAGTGACCTAAACATAAAATAC
Found at i:6232 original size:55 final size:55
Alignment explanation
Indices: 6168--6635 Score: 557
Period size: 55 Copynumber: 8.6 Consensus size: 55
6158 TGACGAGTCT
* * *
6168 GCTCCCTATTCCTTCAG-GAAGTATA-AGACTCGAACAATCTTCATAAAATGTGTCT
1 GCTCTCTATTCCTTCAGAG-AGTATAGA-ACTCGAACAATCTTCATAAAACGTGTCC
* * *
6223 GCTCTCTATTCATTCAGAGAGTATA-AGACTTGAACAATCTTCAATAAAACGGGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTC-ATAAAACGTGTCC
6279 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGGAA-AATCTTCA-ATAAACAG-GTCC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTC-GAACAATCTTCATA-AAAC-GTGTCC
* * * * *
6334 GCTCCCTATTCTTTCAGAGAGTATAGGACT----CAATCTTTA-ACAAACGTGTTC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGTGTCC
* * *
6385 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATAAAACGGGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGTGTCC
*
6440 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAAACGTGTTC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGTGTCC
* *
6495 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATGAAACGGGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGTGTCC
* * *
6550 ACTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACGAACTTGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGTGTCC
* *
6605 GCTCCCTATTCCTTCAGAGAGTATAGGACTC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTC
6636 AATCTTCAAC
Statistics
Matches: 363, Mismatches: 34, Indels: 32
0.85 0.08 0.07
Matches are distributed among these distances:
50 1 0.00
51 43 0.12
54 2 0.01
55 266 0.73
56 47 0.13
57 4 0.01
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (55 bp):
GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGTGTCC
Found at i:6455 original size:161 final size:162
Alignment explanation
Indices: 6168--6650 Score: 549
Period size: 161 Copynumber: 3.0 Consensus size: 162
6158 TGACGAGTCT
* * *
6168 GCTCCCTATTCCTTCAG-GAAGTATA-AGACTCGAACAATCTTCATA-AAATGTGTCTGCTCTCT
1 GCTCCCTATTCCTTCAGAG-AGTATAGA-ACT---ACAATCTTCA-ACAAACGGGTCCGCTCTCT
* *
6230 ATTCATTCAGAGAGTATA-AGACTTGAACAATCTTCAATAAAACGGGTCCGCTCTCTATTCCTTC
60 ATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTC-ATAAAACGGGTCCGCTCTCTATTCCTTC
*
6294 AGAGAGTATAGAACTCGGAA-AATCTTCAATAAACAG-GTCC
123 AGAGAGTATAGAACTC-GAACAATCTTCAACAAAC-GTGTCC
* * * * * *
6334 GCTCCCTATTCTTTCAGAGAGTATAGGACT-CAATCTTTAACAAACGTGTTCGCTCCCTATTCCT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTACAATCTTCAACAAACGGGTCCGCTCTCTATTCCT
*
6398 TCAGAGAGTATAGAACTCGAGCAATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTA
66 TCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTA
*
6463 TAGAACTCGAACAATCTTCAACAAACGTGTTC
131 TAGAACTCGAACAATCTTCAACAAACGTGTCC
* ** *
6495 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATGAAACGGGTCCACTCTCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACT---ACAATCTTCAACAAACGGGTCCGCTCTCTATT
* ** *
6560 CCTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACGAACTTGTCCGCTCCCTATTCCTTCAGAG
63 CCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGGGTCCGCTCTCTATTCCTTCAGAG
*
6624 AGTATAGGACT----CAATCTTCAACAAACG
127 AGTATAGAACTCGAACAATCTTCAACAAACG
6651 AGTTTGCTTC
Statistics
Matches: 278, Mismatches: 28, Indels: 27
0.83 0.08 0.08
Matches are distributed among these distances:
160 4 0.01
161 104 0.37
162 51 0.18
163 1 0.00
164 1 0.00
165 91 0.33
166 25 0.09
167 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.29
Consensus pattern (162 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTACAATCTTCAACAAACGGGTCCGCTCTCTATTCCT
TCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTA
TAGAACTCGAACAATCTTCAACAAACGTGTCC
Found at i:6522 original size:110 final size:110
Alignment explanation
Indices: 6168--6635 Score: 621
Period size: 110 Copynumber: 4.3 Consensus size: 110
6158 TGACGAGTCT
* * *
6168 GCTCCCTATTCCTTCAG-GAAGTATA-AGACTCGAACAATCTTCATAAAATGTGTCTGCTCTCTA
1 GCTCCCTATTCCTTCAGAG-AGTATAGA-ACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTA
* * * *
6231 TTCATTCAGAGAGTATA-AGACTTGAACAATCTTCAATAAAACGGGTCC
64 TTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAA-CAAACGTGTCC
* * *
6279 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGGAA-AATCTTCA-ATAAACAGGTCCGCTCCCTA
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTC-GAACAATCTTCATA-AAACGGGTCCGCTCTCTA
* * * *
6342 TTCTTTCAGAGAGTATAGGACT----CAATCTTTAACAAACGTGTTC
64 TTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
*
6385 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATAAAACGGGTCCGCTCTCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATT
*
6450 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTTC
66 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
* * *
6495 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATGAAACGGGTCCACTCTCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATT
* *
6560 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACGAACTTGTCC
66 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
*
6605 GCTCCCTATTCCTTCAGAGAGTATAGGACTC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTC
6636 AATCTTCAAC
Statistics
Matches: 318, Mismatches: 28, Indels: 23
0.86 0.08 0.06
Matches are distributed among these distances:
105 2 0.01
106 82 0.26
107 10 0.03
110 153 0.48
111 66 0.21
112 5 0.02
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (110 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATT
CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
Found at i:6977 original size:17 final size:17
Alignment explanation
Indices: 6945--6977 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
6935 TATCTTCATC
6945 TCAATGCTTCAATATCT
1 TCAATGCTTCAATATCT
6962 TCAAT-CTTCAACTATC
1 TCAATGCTTCAA-TATC
6978 ATTGGGAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.30, C:0.27, G:0.03, T:0.39
Consensus pattern (17 bp):
TCAATGCTTCAATATCT
Found at i:8034 original size:14 final size:14
Alignment explanation
Indices: 8017--8102 Score: 52
Period size: 14 Copynumber: 5.8 Consensus size: 14
8007 TCTCTTTTTT
8017 TTTTCATTTTTCTC
1 TTTTCATTTTTCTC
8031 TTTTTTCATTTTTCAT-
1 --TTTTCATTTTTC-TC
8047 TTTTCATTTTTTCTTC
1 TTTTCA-TTTTTC-TC
8063 TATTTTCCATTTTT-TC
1 --TTTT-CATTTTTCTC
* *
8079 TTCTC-TTTTTTTC
1 TTTTCATTTTTCTC
*
8092 TTTTCGTTTTT
1 TTTTCATTTTT
8103 TCCATCATTT
Statistics
Matches: 59, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
12 5 0.08
13 7 0.12
14 14 0.24
15 7 0.12
16 14 0.24
17 1 0.02
18 9 0.15
19 2 0.03
ACGTcount: A:0.07, C:0.17, G:0.01, T:0.74
Consensus pattern (14 bp):
TTTTCATTTTTCTC
Found at i:8034 original size:16 final size:15
Alignment explanation
Indices: 8011--8184 Score: 90
Period size: 16 Copynumber: 10.8 Consensus size: 15
8001 TTTATTTCTC
8011 TTTT-TTTTTTCATT
1 TTTTCTTTTTTCATT
8025 TTTCTCTTTTTTCA-T
1 TTT-TCTTTTTTCATT
*
8040 TTTTCATTTTTCATT
1 TTTTCTTTTTTCATT
8055 TTTTCTTCTATTTTCCATT
1 TTTTC-T-T-TTTT-CATT
**
8074 TTTTCTTCTCTTTTTTT
1 TTTTCTT-T-TTTCATT
8091 CTTTTCGTTTTTTCCATCAT
1 -TTTTC-TTTTTT-CAT--T
*
8111 TTTTCTTTTTTC-TCA
1 TTTTCTTTTTTCAT-T
8126 TTTTCTTTTCTTC--T
1 TTTTCTTTT-TTCATT
* *
8140 TTTTCTTCTTCTAATT
1 TTTTCTT-TTTTCATT
8156 TTTAT-TATTTTTCATT
1 TTT-TCT-TTTTTCATT
8172 TTTTCATTTTTTC
1 TTTTC-TTTTTTC
8185 TCTTTTATTT
Statistics
Matches: 125, Mismatches: 14, Indels: 40
0.70 0.08 0.22
Matches are distributed among these distances:
14 20 0.16
15 23 0.18
16 32 0.26
17 12 0.10
18 21 0.17
19 16 0.13
20 1 0.01
ACGTcount: A:0.09, C:0.17, G:0.01, T:0.74
Consensus pattern (15 bp):
TTTTCTTTTTTCATT
Found at i:8042 original size:6 final size:7
Alignment explanation
Indices: 8016--8057 Score: 57
Period size: 7 Copynumber: 5.7 Consensus size: 7
8006 TTCTCTTTTT
8016 TTTTTCA
1 TTTTTCA
*
8023 TTTTTCTCT
1 -TTTT-TCA
8032 TTTTTCA
1 TTTTTCA
8039 TTTTTCA
1 TTTTTCA
8046 TTTTTCA
1 TTTTTCA
8053 TTTTT
1 TTTTT
8058 TCTTCTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
7 21 0.68
8 8 0.26
9 2 0.06
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTCA
Found at i:8073 original size:19 final size:19
Alignment explanation
Indices: 8045--8087 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
8035 TTCATTTTTC
*
8045 ATTTTTCATTTTTTCTTCT
1 ATTTTCCATTTTTTCTTCT
8064 ATTTTCCATTTTTTCTTCT
1 ATTTTCCATTTTTTCTTCT
*
8083 CTTTT
1 ATTTT
8088 TTTCTTTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (19 bp):
ATTTTCCATTTTTTCTTCT
Found at i:17624 original size:45 final size:46
Alignment explanation
Indices: 17557--17661 Score: 176
Period size: 45 Copynumber: 2.3 Consensus size: 46
17547 CCATGCTTTG
17557 TTATTCACAAAAATAAATCCTAACCGCATGATATCTAATTCACATGC
1 TTATTCA-AAAAATAAATCCTAACCGCATGATATCTAATTCACATGC
* *
17604 TTATTCAAAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGC
1 TTATTCAAAAAATAAATCCTAACCGCATGATATCTAATTCACATGC
17649 TTATTCAAAAAAT
1 TTATTCAAAAAAT
17662 GAAAATAAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
45 40 0.71
46 9 0.16
47 7 0.12
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (46 bp):
TTATTCAAAAAATAAATCCTAACCGCATGATATCTAATTCACATGC
Found at i:19413 original size:27 final size:27
Alignment explanation
Indices: 19375--19428 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
19365 AAATCAGAAA
*
19375 TAAATCAGTGACCTAAACATAAAATAC
1 TAAATCAATGACCTAAACATAAAATAC
* *
19402 TAAATCAATGACCTAAATATGAAATAC
1 TAAATCAATGACCTAAACATAAAATAC
19429 GTATAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.52, C:0.17, G:0.07, T:0.24
Consensus pattern (27 bp):
TAAATCAATGACCTAAACATAAAATAC
Found at i:21816 original size:3 final size:3
Alignment explanation
Indices: 21808--21846 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
21798 TGTAAAAGAT
*
21808 TAA TAA TAA TAA TAA TAC TAA TAA TAA TTAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
21847 ATAAACAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:21861 original size:16 final size:17
Alignment explanation
Indices: 21837--21872 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
21827 AATAATAATT
21837 AATATAATAAATAAACA
1 AATATAATAAATAAACA
21854 AATA-AATAAATAAACA
1 AATATAATAAATAAACA
21870 AAT
1 AAT
21873 GGGTAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (17 bp):
AATATAATAAATAAACA
Found at i:24308 original size:20 final size:20
Alignment explanation
Indices: 24283--24375 Score: 78
Period size: 21 Copynumber: 4.5 Consensus size: 20
24273 TTTTCCCAAT
*
24283 TCGCAATGTGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
24303 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
*
24323 TTCACAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
24344 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
24365 TCGCAATGCGA
1 TCGCAATGCGA
24376 TACTGACTAT
Statistics
Matches: 55, Mismatches: 16, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 25 0.45
21 30 0.55
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:24335 original size:21 final size:20
Alignment explanation
Indices: 24300--24375 Score: 80
Period size: 21 Copynumber: 3.7 Consensus size: 20
24290 GTGAATAAGT
*
24300 AAATCGCAACGCGAATTGGG
1 AAATCGCAATGCGAATTGGG
* ** *
24320 AAATTCACAATGCGAATAAGT
1 AAA-TCGCAATGCGAATTGGG
*
24341 AAATCGCAACGCGAATTGGG
1 AAATCGCAATGCGAATTGGG
24361 AAAATCGCAATGCGA
1 -AAATCGCAATGCGA
24376 TACTGACTAT
Statistics
Matches: 43, Mismatches: 11, Indels: 3
0.75 0.19 0.05
Matches are distributed among these distances:
20 15 0.35
21 28 0.65
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (20 bp):
AAATCGCAATGCGAATTGGG
Found at i:24337 original size:41 final size:41
Alignment explanation
Indices: 24280--24375 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
24270 CGATTTTCCC
*
24280 AATTCGCAATGTGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
24321 AATTCACAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
24362 AAATCGCAATGCGA
1 AATTCGCAATGCGA
24376 TACTGACTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.20
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:24388 original size:41 final size:41
Alignment explanation
Indices: 24302--24436 Score: 114
Period size: 41 Copynumber: 3.3 Consensus size: 41
24292 GAATAAGTAA
* * * *
24302 ATCGCAACGCGAATTGGGAAATTCACAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
24343 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
24384 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
24425 TTCGCAACGCGA
1 ATCGCAACGCGA
24437 TACTGACTTT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
40 4 0.05
41 72 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:24389 original size:20 final size:20
Alignment explanation
Indices: 24364--24457 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
24354 AATTGGGAAA
*
24364 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
24384 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
24405 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
24425 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
24445 TTCGCAACGCGAT
1 ATCGCAACGCGAT
24458 TTACTTAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:25040 original size:19 final size:19
Alignment explanation
Indices: 25016--25060 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
25006 GCAACGAGAT
*
25016 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
25035 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
25054 AATCGCA
1 AATCGCA
25061 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:25080 original size:19 final size:19
Alignment explanation
Indices: 25056--25164 Score: 155
Period size: 19 Copynumber: 5.7 Consensus size: 19
25046 GAAACCAAAA
25056 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
25075 TTGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
25094 TCGCATTGCGATTCTCATT
1 TCGCATTGCGATTTTCATT
* *
25113 TCGCGTTGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
25132 TCGCGGTTGCGATTTTCATT
1 TCGC-ATTGCGATTTTCATT
*
25152 TCGCGTTGCGATT
1 TCGCATTGCGATT
25165 GTCTGGTCGC
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
19 64 0.78
20 18 0.22
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:25152 original size:58 final size:57
Alignment explanation
Indices: 25056--25164 Score: 164
Period size: 58 Copynumber: 1.9 Consensus size: 57
25046 GAAACCAAAA
* *
25056 TCGCATTGCGATTTTCATTTTGCATTGCGATTTTCATTTCGCATTGCGATTCTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCATT
* * *
25113 TCGCGTTGCGATTTTAATTTCGCGGTTGCGATTTTCATTTCGCGTTGCGATT
1 TCGCATTGCGATTTTAATTTCGC-ATTGCGATTTTCATTTCGCATTGCGATT
25165 GTCTGGTCGC
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
57 20 0.43
58 26 0.57
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.46
Consensus pattern (57 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCATT
Found at i:25175 original size:39 final size:38
Alignment explanation
Indices: 25056--25259 Score: 146
Period size: 33 Copynumber: 5.6 Consensus size: 38
25046 GAAACCAAAA
* *
25056 TCGC-ATTGCGATTTTCATTTTGCATTGCGATTTTCATT
1 TCGCGATTGCGATTTTCATTTCGCGTTGCGATTTTC-TT
* *
25094 TCGC-ATTGCGATTCTCATTTCGCGTTGCGATTTTAATT
1 TCGCGATTGCGATTTTCATTTCGCGTTGCGATTTT-CTT
* *
25132 TCGCGGTTGCGATTTTCATTTCGCGTTGCGATTGTC--
1 TCGCGATTGCGATTTTCATTTCGCGTTGCGATTTTCTT
* **
25168 T-G-G-TCGCGATAGTCATTTCGCGTTGCGA--TTC--
1 TCGCGATTGCGATTTTCATTTCGCGTTGCGATTTTCTT
* ** *
25199 TCTCG-TTGCGATAGTCATTTCCGCGTTGCGATTCTCATT
1 TCGCGATTGCGATTTTCATTT-CGCGTTGCGATTTTC-TT
*
25238 ATCTCG-TTGCGATTTTCATTTC
1 -TCGCGATTGCGATTTTCATTTC
25260 AACCAAAAGA
Statistics
Matches: 138, Mismatches: 17, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
31 3 0.02
33 37 0.27
34 11 0.08
35 1 0.01
36 3 0.02
38 37 0.27
39 28 0.20
40 18 0.13
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (38 bp):
TCGCGATTGCGATTTTCATTTCGCGTTGCGATTTTCTT
Found at i:25236 original size:20 final size:20
Alignment explanation
Indices: 25202--25259 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
25192 GCGATTCTCT
**
25202 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
25222 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
25242 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
25260 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:27318 original size:42 final size:42
Alignment explanation
Indices: 27258--27380 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
27248 GCCCGACTCG
* * *
27258 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
27300 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
27342 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
27381 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:27338 original size:21 final size:21
Alignment explanation
Indices: 27314--27380 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
27304 TCATTCCTCG
27314 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
27335 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
27356 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
27377 AGAG
1 AGAG
27381 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:28755 original size:14 final size:14
Alignment explanation
Indices: 28736--28771 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
28726 ATTGTTTAAT
28736 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
28750 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
28764 TGATTTGT
1 TGATTTGT
28772 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:28940 original size:39 final size:38
Alignment explanation
Indices: 28878--28959 Score: 128
Period size: 39 Copynumber: 2.1 Consensus size: 38
28868 AAAAAGTACT
*
28878 ATCGCAATGCGAAATGAAAATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAA
*
28916 ATCGCAACGCGAAAATGAAAATCGCAACGCGAAATTAAA
1 ATCGCAACGCG-AAATGAAAATCGCAACGCGAAATGAAA
*
28955 TTCGC
1 ATCGC
28960 GTTGCGATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
38 10 0.25
39 30 0.75
ACGTcount: A:0.45, C:0.21, G:0.20, T:0.15
Consensus pattern (38 bp):
ATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAA
Found at i:28959 original size:19 final size:19
Alignment explanation
Indices: 28878--28950 Score: 128
Period size: 19 Copynumber: 3.8 Consensus size: 19
28868 AAAAAGTACT
*
28878 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
28897 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
28916 ATCGCAACGCGAAAATGAAA
1 ATCGCAACGCG-AAATGAAA
28936 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
28951 TAAATTCGCG
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
19 33 0.63
20 19 0.37
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:28977 original size:19 final size:19
Alignment explanation
Indices: 28955--29072 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
28945 CGAAATTAAA
28955 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
28974 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
28989 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
29007 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
29022 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
29040 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
29059 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
29073 GGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:29001 original size:33 final size:33
Alignment explanation
Indices: 28959--29052 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
28949 ATTAAATTCG
28959 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
28992 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
29025 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
29053 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:31357 original size:12 final size:12
Alignment explanation
Indices: 31340--31364 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31330 TCTTCGGGGA
31340 CTTTTTCTTCTT
1 CTTTTTCTTCTT
31352 CTTTTTCTTCTT
1 CTTTTTCTTCTT
31364 C
1 C
31365 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:32907 original size:14 final size:14
Alignment explanation
Indices: 32888--32924 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
32878 CATCAATTAA
32888 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
32902 ACAAATCATCTTTT
1 ACAAATCAACATTT
32916 ACAAATCAA
1 ACAAATCAA
32925 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:33369 original size:14 final size:16
Alignment explanation
Indices: 33349--33422 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
33339 TGAAAATCGC
33349 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
33364 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
33381 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
33400 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
33416 -TTGCGAT
1 ATTGCGAT
33423 AACCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:33386 original size:19 final size:19
Alignment explanation
Indices: 33345--33412 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
33335 GAAATGAAAA
33345 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
33361 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
33378 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
33397 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
33413 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:33548 original size:14 final size:14
Alignment explanation
Indices: 33529--33565 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
33519 CATCAATTAA
33529 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
33543 ACAAATCATCTTTT
1 ACAAATCAACATTT
33557 ACAAATCAA
1 ACAAATCAA
33566 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:33688 original size:641 final size:635
Alignment explanation
Indices: 32464--33814 Score: 2555
Period size: 641 Copynumber: 2.1 Consensus size: 635
32454 TTTAACAATT
32464 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
32529 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
32594 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
32659 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCGTTTTCATTGCG
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCGTTTTCATTGCG
32724 AAATGTTCAGTTTGAACATTGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAACCATT
261 -AATGTTCAGTTTG-ACATTGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAACCATT
32789 TCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAACAAATCAACTATT
324 TCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAACAAATCAACTATT
32854 ACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTACAAATCATCTTTTACA
389 ACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTACAAATCATCTTTTACA
32919 AATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCAATTATTGAATCAAGAAT
454 AATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCAATTATTGAATCAAGAAT
32984 CAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTAACCTCCAGAAACC
519 CAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTAACCTCCAGAAACC
33049 AAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAGCAA
584 AAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAGCAA
33101 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
33166 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
33231 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
33296 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAAT--C---GCG--TTT-
* *
33361 TCGTTGCG-ATTTTCA-TTTCG-CATTGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGAT
253 TCATTGCGAATGTTCAGTTT-GACATTGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGAT
33423 AACCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAACAAATC
317 AACCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAACAAATC
33488 AACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTACAAATCATC
382 AACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTACAAATCATC
33553 TTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCAATTATTGAAT
447 TTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCAATTATTGAAT
*
33618 CAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTAACCTGC
512 CAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTAACCTCC
33683 AGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAGCAA
577 AGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAGCAA
33742 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
33807 CTTGCATT
66 CTTGCATT
33815 TGACTTACCA
Statistics
Matches: 702, Mismatches: 3, Indels: 14
0.98 0.00 0.02
Matches are distributed among these distances:
637 245 0.35
639 1 0.00
641 433 0.62
642 6 0.01
643 7 0.01
644 3 0.00
645 7 0.01
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (635 bp):
ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCGTTTTCATTGCG
AATGTTCAGTTTGACATTGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAACCATTTC
GCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAACAAATCAACTATTAC
ATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTACAAATCATCTTTTACAAA
TCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCAATTATTGAATCAAGAATCA
ACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTAACCTCCAGAAACCAA
ACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAGCAA
Found at i:35461 original size:20 final size:19
Alignment explanation
Indices: 35426--35492 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
35416 GAAACTTAAA
35426 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
35445 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
35465 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
35484 ATCGCAACG
1 ATCGCAACG
35493 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:35500 original size:14 final size:14
Alignment explanation
Indices: 35481--35538 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
35471 ATGCGAAATG
35481 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
35495 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
35511 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
35527 AAAATCGCAACG
1 AAAATCGCAACG
35539 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:35523 original size:32 final size:33
Alignment explanation
Indices: 35465--35543 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
35455 GGAAATGGCT
*
35465 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
35498 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
35530 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
35544 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:35591 original size:14 final size:14
Alignment explanation
Indices: 35572--35629 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
35562 TTTCATTTCG
35572 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
35586 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
35602 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
35618 CGTTCCGATTTT
1 CGTTGCGATTTT
35630 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.09, C:0.19, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:35602 original size:32 final size:33
Alignment explanation
Indices: 35555--35645 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
35545 ACAAATCGCA
35555 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
35588 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
* *
35620 TTCCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
35646 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:35664 original size:20 final size:19
Alignment explanation
Indices: 35630--35684 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
35620 TTCCGATTTT
*
35630 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
35649 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
35669 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
35685 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:36183 original size:18 final size:18
Alignment explanation
Indices: 36157--36201 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
36147 GTCGATCAGA
*
36157 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
36175 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
36193 TGATGGCTC
1 TGATGGCTC
36202 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:37546 original size:20 final size:20
Alignment explanation
Indices: 37521--37558 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
37511 AATAGTTTCT
37521 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
37541 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
37559 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:37846 original size:22 final size:22
Alignment explanation
Indices: 37821--37864 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
37811 GATTTAGATA
37821 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
37843 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
37865 TGAGAGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.45, T:0.18
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:38077 original size:20 final size:20
Alignment explanation
Indices: 38052--38145 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
38042 GATTATGTAT
38052 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
38072 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
38092 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
38113 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
38133 TATCGCATTGCGA
1 TATCGCGTTGCGA
38146 TTTTCTCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:38117 original size:41 final size:42
Alignment explanation
Indices: 38072--38207 Score: 118
Period size: 41 Copynumber: 3.3 Consensus size: 42
38062 CGAAAGTCAG
* * * *
38072 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTAT
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
* * *
38113 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAA
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
** ** * *
38155 T-TCGCGTTGCG-ATTTACTTATTCGCATTGCGAATTTCCCAA
1 TATCGCGTTGCGAAAGTAAGTA-TCGCATTGCGATTTTCTCAA
38196 T-TCGCGTTGCGA
1 TATCGCGTTGCGA
38208 TTTACTTATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
40 3 0.04
41 70 0.92
42 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (42 bp):
TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
Found at i:38146 original size:20 final size:20
Alignment explanation
Indices: 38032--38146 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
38022 CGCTTTGAAA
*
38032 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
38053 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
38073 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
38093 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
38114 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
38134 ATCGCATTGCGAT
1 ATCGCATTGCGAT
38147 TTTCTCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:38179 original size:20 final size:20
Alignment explanation
Indices: 38135--38227 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
38125 ATAGTCAGTA
*
38135 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
38156 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
38176 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
38197 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
38217 TCGCATTGCGA
1 TCGCATTGCGA
38228 ATTGGGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.47
21 31 0.53
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:38208 original size:41 final size:41
Alignment explanation
Indices: 38135--38230 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
38125 ATAGTCAGTA
* *
38135 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
38176 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
38217 TCGCATTGCGAATT
1 TCGCATTGCGAATT
38231 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:44535 original size:17 final size:17
Alignment explanation
Indices: 44501--44534 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
44491 TTTCTTGCTA
*
44501 TGTTCTTTATTTTCTTT
1 TGTTCTTGATTTTCTTT
44518 TGTTCTTGATTTT-TTT
1 TGTTCTTGATTTTCTTT
44534 T
1 T
44535 TCAATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.06, C:0.09, G:0.09, T:0.76
Consensus pattern (17 bp):
TGTTCTTGATTTTCTTT
Found at i:44603 original size:24 final size:24
Alignment explanation
Indices: 44560--44618 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
44550 AATCGTTGTC
* *
44560 CTTGTGACATG-TTTTTCTCTGCT
1 CTTGTGGCATGCTTTTTCTCTACT
44583 CTTGTGGCATGCTTTTTCTCTACT
1 CTTGTGGCATGCTTTTTCTCTACT
*
44607 ATTGTGGCATGC
1 CTTGTGGCATGC
44619 CACTTGTGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 10 0.31
24 22 0.69
ACGTcount: A:0.10, C:0.22, G:0.20, T:0.47
Consensus pattern (24 bp):
CTTGTGGCATGCTTTTTCTCTACT
Found at i:45030 original size:11 final size:12
Alignment explanation
Indices: 45005--45033 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
44995 TGACTAACGC
45005 AAATAAAAAATA
1 AAATAAAAAATA
45017 AAATAAAAAA-A
1 AAATAAAAAATA
45028 AAATAA
1 AAATAA
45034 TATGATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (12 bp):
AAATAAAAAATA
Found at i:45589 original size:18 final size:18
Alignment explanation
Indices: 45562--45623 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
45552 ACAGTACCCG
*
45562 AAATTCATAAAATTCATA
1 AAATTTATAAAATTCATA
*
45580 AAATTTATAAAATTTTATA
1 AAATTTATAAAA-TTCATA
*
45599 AATATGTAT-AAATTCATA
1 AA-ATTTATAAAATTCATA
45617 AAATTTA
1 AAATTTA
45624 AAACGTTCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
17 4 0.11
18 18 0.49
19 10 0.27
20 5 0.14
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (18 bp):
AAATTTATAAAATTCATA
Found at i:45598 original size:10 final size:9
Alignment explanation
Indices: 45562--45623 Score: 63
Period size: 9 Copynumber: 6.8 Consensus size: 9
45552 ACAGTACCCG
*
45562 AAATTCATA
1 AAATTTATA
*
45571 AAATTCATA
1 AAATTTATA
45580 AAATTTATA
1 AAATTTATA
45589 AAATTTTATA
1 AAA-TTTATA
*
45599 AATATGTAT-
1 AA-ATTTATA
*
45608 AAATTCATA
1 AAATTTATA
45617 AAATTTA
1 AAATTTA
45624 AAACGTTCAT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
8 4 0.09
9 28 0.62
10 12 0.27
11 1 0.02
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (9 bp):
AAATTTATA
Found at i:46043 original size:15 final size:16
Alignment explanation
Indices: 46023--46056 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
46013 ACACCTATAC
*
46023 ATTTATCATTAA-CAT
1 ATTTATCAATAATCAT
46038 ATTTATCAATAATCAT
1 ATTTATCAATAATCAT
46054 ATT
1 ATT
46057 ATTATCACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTTATCAATAATCAT
Found at i:46371 original size:22 final size:21
Alignment explanation
Indices: 46346--46406 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 21
46336 CATATGAAAT
46346 TTGTCCCGAAGGACCTA-TGTA
1 TTGTCCCGAAGGACC-ACTGTA
46367 GTTGTCCCGAAGGACCACTGTA
1 -TTGTCCCGAAGGACCACTGTA
46389 TATGTCCCGAAGGACCAC
1 T-TGTCCCGAAGGACCAC
46407 GTAGACCCTC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
21 2 0.05
22 35 0.95
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.23
Consensus pattern (21 bp):
TTGTCCCGAAGGACCACTGTA
Found at i:46904 original size:2 final size:2
Alignment explanation
Indices: 46866--46891 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
46856 GCATATAAGA
46866 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
46892 CCATTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50422 original size:45 final size:45
Alignment explanation
Indices: 50373--50529 Score: 235
Period size: 45 Copynumber: 3.5 Consensus size: 45
50363 ACTATAACAT
* * *
50373 CTTTTTTGTTGATAATGCACCCATATCCATTTCAACTC-TAGTATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAAC-CATAGTATA
* *
50418 CTTTTCTGTTAATAATGTACCCGTATACATTTCAACCATAGTATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACCATAGTATA
*
50463 CATTTCTGTTGATAATGTACCCATATACATTTCAACCATAGTATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACCATAGTATA
*
50508 CTTTTCTGTTGATAATATACCC
1 CTTTTCTGTTGATAATGTACCC
50530 TAGTATACTT
Statistics
Matches: 101, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
44 1 0.01
45 100 0.99
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (45 bp):
CTTTTCTGTTGATAATGTACCCATATACATTTCAACCATAGTATA
Found at i:50558 original size:29 final size:29
Alignment explanation
Indices: 50501--50558 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
50491 ATTTCAACCA
*
50501 TAGTATACTTTTCTGTTGATAATATACCC
1 TAGTATACTTTTCTGTTGATAATACACCC
*
50530 TAGTATACTTTTCTGTTGATAATGCACCC
1 TAGTATACTTTTCTGTTGATAATACACCC
50559 ATATGCATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.43
Consensus pattern (29 bp):
TAGTATACTTTTCTGTTGATAATACACCC
Found at i:50583 original size:74 final size:74
Alignment explanation
Indices: 50456--50614 Score: 218
Period size: 74 Copynumber: 2.2 Consensus size: 74
50446 ATTTCAACCA
* **
50456 TAGTATACATTTCTGTTGATAATGTACCCATATACATTTCAACCATAGTATACTTTTC-TGTTGA
1 TAGTATACATTTCTGTTGATAATGCACCCATATACATTTCAACCATAACATAC-TTTCATGTTGA
50520 TAATATACCC
65 TAATATACCC
* *
50530 TAGTATACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTC-TAACATACTTTCATGTTGA
1 TAGTATACATTTCTGTTGATAATGCACCCATATACATTTCAAC-CATAACATACTTTCATGTTGA
*
50594 TAATGTACCC
65 TAATATACCC
50604 -A-TATACATTTC
1 TAGTATACATTTC
50615 AACTAAAGTA
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
72 9 0.12
73 5 0.07
74 61 0.80
75 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.40
Consensus pattern (74 bp):
TAGTATACATTTCTGTTGATAATGCACCCATATACATTTCAACCATAACATACTTTCATGTTGAT
AATATACCC
Found at i:50625 original size:119 final size:119
Alignment explanation
Indices: 50410--50642 Score: 353
Period size: 119 Copynumber: 2.0 Consensus size: 119
50400 CATTTCAACT
* * **
50410 CTAGTATACTTTTCTGTTAATAATGTACCCGTATACATTTCAACCATAGTATACATTTCTGTTGA
1 CTAGTATACTTTTCTGTTAATAATGCACCCATATACATTTCAACCATAACATACATTTCTGTTGA
*
50475 TAATGTACCCATATACATTTCAACCATAGTATACTTTTCTGTTGATAATATACC
66 TAATGTACCCATATACATTTCAACCAAAGTATACTTTTCTGTTGATAATATACC
* *
50529 CTAGTATACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTC-TAACATAC-TTTCATGTT
1 CTAGTATACTTTTCTGTTAATAATGCACCCATATACATTTCAAC-CATAACATACATTTC-TGTT
* *
50592 GATAATGTACCCATATACATTTCAACTAAAGTATGCTTTTCTGTTGATAAT
64 GATAATGTACCCATATACATTTCAACCAAAGTATACTTTTCTGTTGATAAT
50643 GTACTCATAT
Statistics
Matches: 103, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
118 4 0.04
119 98 0.95
120 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.40
Consensus pattern (119 bp):
CTAGTATACTTTTCTGTTAATAATGCACCCATATACATTTCAACCATAACATACATTTCTGTTGA
TAATGTACCCATATACATTTCAACCAAAGTATACTTTTCTGTTGATAATATACC
Found at i:50664 original size:45 final size:45
Alignment explanation
Indices: 50531--50664 Score: 182
Period size: 45 Copynumber: 3.0 Consensus size: 45
50521 AATATACCCT
* * *
50531 AGTATACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTA
1 AGTATACTTTTCTGTTGATAATGTACCCATATACATTTCAACT-AA
*
50577 A-CATAC-TTTCATGTTGATAATGTACCCATATACATTTCAACTAA
1 AGTATACTTTTC-TGTTGATAATGTACCCATATACATTTCAACTAA
* *
50621 AGTATGCTTTTCTGTTGATAATGTACTCATATACATTTCAACTA
1 AGTATACTTTTCTGTTGATAATGTACCCATATACATTTCAACTA
50665 TGGCATCCTT
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
44 6 0.08
45 67 0.86
46 5 0.06
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (45 bp):
AGTATACTTTTCTGTTGATAATGTACCCATATACATTTCAACTAA
Found at i:50687 original size:45 final size:45
Alignment explanation
Indices: 50539--50703 Score: 172
Period size: 45 Copynumber: 3.7 Consensus size: 45
50529 CTAGTATACT
* * * *
50539 TTTC-TGTTGATAATGCACCCATATGCATTTCAACTCTAACATAC
1 TTTCATGTTGATAATGCACCCATATACATTTCAACTATAGCATCC
* * * *
50583 TTTCATGTTGATAATGTACCCATATACATTTCAACTAAAGTATGCT
1 TTTCATGTTGATAATGCACCCATATACATTTCAACTATAGCAT-CC
* * *
50629 TTTC-TGTTGATAATGTACTCATATACATTTCAACTATGGCATCC
1 TTTCATGTTGATAATGCACCCATATACATTTCAACTATAGCATCC
*** *
50673 TTTCATGCCAATAATGCACCCATATGCATTT
1 TTTCATGTTGATAATGCACCCATATACATTT
50704 TTCTTTTATA
Statistics
Matches: 99, Mismatches: 19, Indels: 5
0.80 0.15 0.04
Matches are distributed among these distances:
44 9 0.09
45 86 0.87
46 4 0.04
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (45 bp):
TTTCATGTTGATAATGCACCCATATACATTTCAACTATAGCATCC
Found at i:50687 original size:90 final size:90
Alignment explanation
Indices: 50531--50703 Score: 229
Period size: 90 Copynumber: 1.9 Consensus size: 90
50521 AATATACCCT
* * ***
50531 AGTATACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAACATACTTTCATGTTGATA
1 AGTATACTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAACATACTTTCATGCCAATA
*
50596 ATGTACCCATATACATTTCAACTAA
66 ATGCACCCATATACATTTCAACTAA
* * * ** *
50621 AGTATGCTTTTCTGTTGATAATGTACTCATATACATTTCAACTATGGCATCCTTTCATGCCAATA
1 AGTATACTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAACATACTTTCATGCCAATA
*
50686 ATGCACCCATATGCATTT
66 ATGCACCCATATACATTT
50704 TTCTTTTATA
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
90 70 1.00
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.38
Consensus pattern (90 bp):
AGTATACTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAACATACTTTCATGCCAATA
ATGCACCCATATACATTTCAACTAA
Found at i:50930 original size:33 final size:33
Alignment explanation
Indices: 50888--50953 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
50878 ACTTAGTGCC
50888 TATTTGGTAATCACCACATACATTTTTAAAACA
1 TATTTGGTAATCACCACATACATTTTTAAAACA
50921 TATTTGGTAATCACCACATACATTTTTAAAACA
1 TATTTGGTAATCACCACATACATTTTTAAAACA
50954 GACATGCATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.36
Consensus pattern (33 bp):
TATTTGGTAATCACCACATACATTTTTAAAACA
Found at i:51372 original size:54 final size:54
Alignment explanation
Indices: 51305--51424 Score: 213
Period size: 54 Copynumber: 2.2 Consensus size: 54
51295 CCCCCTTAAT
*
51305 GTATCGATACCTAAATTAGATTTGGTTTAGCCTGGTATCGATACCCTCACCATG
1 GTATCGATACCTAAATTAGATTTGGTTTAGCCCGGTATCGATACCCTCACCATG
* *
51359 GTATCGATGCCTAAATTAGCTTTGGTTTAGCCCGGTATCGATACCCTCACCATG
1 GTATCGATACCTAAATTAGATTTGGTTTAGCCCGGTATCGATACCCTCACCATG
51413 GTATCGATACCT
1 GTATCGATACCT
51425 CTATGTTATG
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (54 bp):
GTATCGATACCTAAATTAGATTTGGTTTAGCCCGGTATCGATACCCTCACCATG
Found at i:55073 original size:43 final size:43
Alignment explanation
Indices: 55007--55090 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 43
54997 AAGAATTGTT
* * *
55007 GTAATATGTTAATTTGGTATATTTGTGGATTGTTACTTTGGTG
1 GTAATATGCTAATTTGATATATTTGTAGATTGTTACTTTGGTG
* *
55050 GTAATATGCTAGTTTGATTTATTTGTAGATTGTTACTTTGG
1 GTAATATGCTAATTTGATATATTTGTAGATTGTTACTTTGG
55091 AGTTTAGATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.21, C:0.04, G:0.24, T:0.51
Consensus pattern (43 bp):
GTAATATGCTAATTTGATATATTTGTAGATTGTTACTTTGGTG
Done.