Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000233.1 Hibiscus syriacus cultivar Beakdansim tig00000403_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: 75305
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5626 original size:18 final size:18
Alignment explanation
Indices: 5603--5644 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
5593 TTTTTTCTTT
5603 AATATTAATTAATAA-ATA
1 AATATTAA-TAATAATATA
5621 AATATTAATAATAATATA
1 AATATTAATAATAATATA
*
5639 ATTATT
1 AATATT
5645 TTCCTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATATTAATAATAATATA
Found at i:8187 original size:18 final size:18
Alignment explanation
Indices: 8164--8209 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 18
8154 AGGCATTTGA
8164 TCCTCTGGCT-GTGCTTGT
1 TCCTCT-GCTCGTGCTTGT
8182 TCCTCTGCTCGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
8200 TCCTCGTGCT
1 TCCTC-TGCT
8210 GTTCTAGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.12
18 19 0.73
19 4 0.15
ACGTcount: A:0.00, C:0.33, G:0.24, T:0.43
Consensus pattern (18 bp):
TCCTCTGCTCGTGCTTGT
Found at i:8219 original size:18 final size:18
Alignment explanation
Indices: 8164--8219 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
8154 AGGCATTTGA
*
8164 TCCTCTGGCT-GTGCTTGT
1 TCCTCT-GCTCGTGCTAGT
*
8182 TCCTCTGCTCGTGCTTGT
1 TCCTCTGCTCGTGCTAGT
*
8200 TCCTCGTGCT-GTTCTAGT
1 TCCTC-TGCTCGTGCTAGT
8218 TC
1 TC
8220 ATCATCGGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 3 0.09
18 27 0.79
19 4 0.12
ACGTcount: A:0.02, C:0.30, G:0.23, T:0.45
Consensus pattern (18 bp):
TCCTCTGCTCGTGCTAGT
Found at i:9818 original size:23 final size:22
Alignment explanation
Indices: 9767--9848 Score: 85
Period size: 23 Copynumber: 3.7 Consensus size: 22
9757 AGAACCCCAG
* *
9767 GGGGGTATCGATTCCCCTACAA
1 GGGGGAATCGATTCCCCTTCAA
*
9789 -GGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATTCCCCTTC-AA
* * *
9811 GGGGGAATCGGTTCCCTTTCGA
1 GGGGGAATCGATTCCCCTTCAA
*
9833 GGGGGTATCGATTCCC
1 GGGGGAATCGATTCCC
9849 TCTGCACTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
21 16 0.31
22 17 0.33
23 18 0.35
ACGTcount: A:0.18, C:0.26, G:0.32, T:0.24
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:17033 original size:3 final size:3
Alignment explanation
Indices: 17025--17062 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
17015 GCCTTGTAAT
17025 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
17063 TGGTGAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:17978 original size:2 final size:2
Alignment explanation
Indices: 17971--17997 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17961 TTATATTGAT
17971 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 T
17998 TGCTTATTTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19131 original size:27 final size:27
Alignment explanation
Indices: 19087--19167 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
19077 ATTTATTTCC
19087 TTTT-ATTATTTGTATTATTAT-ATATATT
1 TTTTAATTATTT-T-TTATT-TCATATATT
*
19115 TTTTAATTATTTTTTATTTGAT-TATT
1 TTTTAATTATTTTTTATTTCATATATT
* *
19141 TTTTACTATATTTATTATTTCATATAT
1 TTTTAAT-TATTTTTTATTTCATATAT
19168 GTATATATAT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
26 11 0.24
27 20 0.43
28 8 0.17
29 7 0.15
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (27 bp):
TTTTAATTATTTTTTATTTCATATATT
Found at i:19373 original size:100 final size:102
Alignment explanation
Indices: 19099--19373 Score: 274
Period size: 100 Copynumber: 2.7 Consensus size: 102
19089 TTATTATTTG
* * * * ** *
19099 TATTATTATATATATTTTTTAATTATTTTTTATTTGATTATTTTTTACTATATTTATTATTTCAT
1 TATTATTATACATATATTCTAATTA-TCTTTAGCTGATTATTTTCTACTATATTTA-TA--TCAT
*
19164 ATATGTATATATATTTTTAAATATTTCATTTATAAACCTAT
62 ATATGTATATATACTTTTAAATATTTCATTTATAAACCTAT
* * **
19205 TATTATTATACGTATATTCTTATTATCTTTATTTGATTATTTTCTACTATATTT-TATCAT-TAT
1 TATTATTATACATATATTCTAATTATCTTTAGCTGATTATTTTCTACTATATTTATATCATATAT
* * ***
19268 ATATATATACTTTT-AATATTTTATTTATACGTCTAT
66 GTATATATACTTTTAAATATTTCATTTATAAACCTAT
* * *
19304 TATTATTATTATATATATTCTAATTATTTTTAGCTGATT-TTTT-TA-TTTACTTTATATCATAT
1 TATTATTA-TACATATATTCTAATTATCTTTAGCTGATTATTTTCTACTATA-TTTATATCATAT
19366 ATGTATAT
64 ATGTATAT
19374 TTTTGTTTTC
Statistics
Matches: 144, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
97 3 0.02
98 5 0.03
99 36 0.25
100 47 0.33
101 4 0.03
103 2 0.01
105 27 0.19
106 20 0.14
ACGTcount: A:0.31, C:0.07, G:0.03, T:0.60
Consensus pattern (102 bp):
TATTATTATACATATATTCTAATTATCTTTAGCTGATTATTTTCTACTATATTTATATCATATAT
GTATATATACTTTTAAATATTTCATTTATAAACCTAT
Found at i:19429 original size:25 final size:25
Alignment explanation
Indices: 19401--19459 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
19391 CTTTATTTAT
19401 TTTTTTTATTCTATTTTT-TCTTT-TC
1 TTTTTTTATT-TATTTTTGT-TTTGTC
19426 TTTTTTTA-TTATTTTTGTTTTGTC
1 TTTTTTTATTTATTTTTGTTTTGTC
19450 TTTTATTTAT
1 TTTT-TTTAT
19460 GTCAGCATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
23 10 0.33
24 8 0.27
25 12 0.40
ACGTcount: A:0.10, C:0.07, G:0.03, T:0.80
Consensus pattern (25 bp):
TTTTTTTATTTATTTTTGTTTTGTC
Found at i:19492 original size:15 final size:16
Alignment explanation
Indices: 19472--19504 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
19462 CAGCATTTTA
*
19472 TTTATTTTGT-TTATT
1 TTTATTTTCTCTTATT
19487 TTTATTTTCTCTTATT
1 TTTATTTTCTCTTATT
19503 TT
1 TT
19505 ATCATTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.12, C:0.06, G:0.03, T:0.79
Consensus pattern (16 bp):
TTTATTTTCTCTTATT
Found at i:29925 original size:12 final size:12
Alignment explanation
Indices: 29908--29944 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
29898 TCGAAGAAGA
29908 AAAAGAAAAAAG
1 AAAAGAAAAAAG
29920 AAAAGAAAAAA-
1 AAAAGAAAAAAG
*
29931 ACAA-AAAAAAG
1 AAAAGAAAAAAG
29942 AAA
1 AAA
29945 CGTTTAGGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
10 6 0.27
11 5 0.23
12 11 0.50
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAG
Found at i:31047 original size:43 final size:43
Alignment explanation
Indices: 30926--31054 Score: 179
Period size: 43 Copynumber: 3.0 Consensus size: 43
30916 CGAAGGGGTC
* *
30926 ATCCACGATTTCAACTCCACGAC-AGAGGATATCGTACCCATAA
1 ATCCACGATTTCAACTCCACGACGA-AGGATATCGTGCCCACAA
** *
30969 ATCCATAATTTCAACTCCACGACGGAGGATATCGTGCCCACAA
1 ATCCACGATTTCAACTCCACGACGAAGGATATCGTGCCCACAA
* *
31012 ATCCACGATTTCAACTTCACGACGAAGGATATCGTGCACACAA
1 ATCCACGATTTCAACTCCACGACGAAGGATATCGTGCCCACAA
31055 GCAGCATCCA
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
43 75 1.00
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (43 bp):
ATCCACGATTTCAACTCCACGACGAAGGATATCGTGCCCACAA
Found at i:31626 original size:2 final size:2
Alignment explanation
Indices: 31619--31668 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
31609 TTTCTGTCAC
31619 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31661 AT AT AT AT
1 AT AT AT AT
31669 TGCTTATTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32783 original size:15 final size:15
Alignment explanation
Indices: 32756--32787 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
32746 ATATTATATA
*
32756 TTATTTTATTATTTT
1 TTATTTGATTATTTT
32771 TTATTTGATTATTTT
1 TTATTTGATTATTTT
32786 TT
1 TT
32788 TACTATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (15 bp):
TTATTTGATTATTTT
Found at i:32835 original size:108 final size:108
Alignment explanation
Indices: 32742--33001 Score: 300
Period size: 108 Copynumber: 2.4 Consensus size: 108
32732 TTATTATTTG
* * *
32742 TATTA-TATTATATAT-TATT-TTATTATTTTTTATTTGATTATTTTTTTACTATA-TTTATCAT
1 TATTATTATTATATATATATTCTGATTA-TCTTTATTTGATTA-TTTTCTACTATATTTTATCAT
*
32803 T-TCATATATGTATATATATATTTTTAAATATTTCATTTATAAACC
64 TAT-ATATATATATATATATATTTTTAAATATTTCATTTATAAACC
*
32848 TATTATTATTATATGTATATTCTGATTATCTTTATTTGATTATTTTCTACTATATTTTATCATTA
1 TATTATTATTATATATATATTCTGATTATCTTTATTTGATTATTTTCTACTATATTTTATCATTA
** * ***
32913 TATATATATATATATATACCTTT-AATATTTTATTTATACGTC
66 TATATATATATATATATATTTTTAAATATTTCATTTATAAACC
* * *
32955 TATTATTATTATTATATATATTCTAATTAT-TTGTATCTGATTTTTTT
1 TATTATTATTA-TATATATATTCTGATTATCTT-TATTTGATTATTTT
33002 ATTTACTTTA
Statistics
Matches: 132, Mismatches: 15, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
106 5 0.04
107 48 0.36
108 73 0.55
109 6 0.05
ACGTcount: A:0.31, C:0.07, G:0.03, T:0.60
Consensus pattern (108 bp):
TATTATTATTATATATATATTCTGATTATCTTTATTTGATTATTTTCTACTATATTTTATCATTA
TATATATATATATATATATTTTTAAATATTTCATTTATAAACC
Found at i:33003 original size:54 final size:52
Alignment explanation
Indices: 32847--33003 Score: 124
Period size: 55 Copynumber: 2.9 Consensus size: 52
32837 ATTTATAAAC
* * * * *
32847 CTATTATTATTA-TATGTATATTCTGATTATCTTTATTTGATTATTTTCTACT
1 CTATTATTATTATTATATATATTCTAATTAT-TTTATATGATTTTTTTATACT
* * * *
32899 ATATT-TTATCATTATATATATATATATATATACCTTTA-AT-ATTTTATTTATACGT
1 CTATTATTATTATTATATATAT-TCTA-AT-TA-TTTTATATGATTTT-TTTATAC-T
*
32954 CTATTATTATTATTATATATATTCTAATTATTTGTATCTGATTTTTTTAT
1 CTATTATTATTATTATATATATTCTAATTATTT-TATATGATTTTTTTAT
33004 TTACTTTATA
Statistics
Matches: 80, Mismatches: 14, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
51 5 0.06
52 14 0.17
53 10 0.12
54 17 0.21
55 19 0.24
56 15 0.19
ACGTcount: A:0.30, C:0.08, G:0.04, T:0.59
Consensus pattern (52 bp):
CTATTATTATTATTATATATATTCTAATTATTTTATATGATTTTTTTATACT
Found at i:33115 original size:21 final size:22
Alignment explanation
Indices: 33069--33112 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
33059 TTATTTATTC
*
33069 TATTTTTTTTCTTTTCTCTTTT
1 TATTATTTTTCTTTTCTCTTTT
* *
33091 TATTATTTTTGTTTTGTCTTTT
1 TATTATTTTTCTTTTCTCTTTT
33113 ATTTATGTCA
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:0.07, C:0.09, G:0.05, T:0.80
Consensus pattern (22 bp):
TATTATTTTTCTTTTCTCTTTT
Found at i:33118 original size:22 final size:22
Alignment explanation
Indices: 33069--33118 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
33059 TTATTTATTC
33069 TATTT-TTTTTCTTTTCTCTTT
1 TATTTATTTTTCTTTTCTCTTT
* *
33090 T-TATTATTTTTGTTTTGTCTTT
1 TAT-TTATTTTTCTTTTCTCTTT
33112 TATTTAT
1 TATTTAT
33119 GTCATCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
20 1 0.04
21 3 0.12
22 19 0.79
23 1 0.04
ACGTcount: A:0.10, C:0.08, G:0.04, T:0.78
Consensus pattern (22 bp):
TATTTATTTTTCTTTTCTCTTT
Found at i:35591 original size:20 final size:20
Alignment explanation
Indices: 35566--35658 Score: 177
Period size: 20 Copynumber: 4.7 Consensus size: 20
35556 TTTTCCTAAT
35566 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
35586 TCGCAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
35606 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
35626 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
35646 TCGCAATGCGAAT
1 TCGCAATGCGAAT
35659 CTGACTATCG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 71 1.00
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:35669 original size:60 final size:61
Alignment explanation
Indices: 35525--35677 Score: 186
Period size: 60 Copynumber: 2.5 Consensus size: 61
35515 GTTTCCAGAT
* * * * * *
35525 TCGCAACGCGATTCTGACTATCGCATTGCGATTTTCCTAATTCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATCTGACTATCGCAATGCGATATACCTAAATCGCAATGCGAATACGTAAA
* * *
35586 TCGCAATACGAATAC-GTA-AATCGCAATGCGA-ATACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAAT-CTG-ACTATCGCAATGCGATATACCTAAATCGCAATGCGAATACGTAAA
35646 TCGCAATGCGAATCTGACTATCGCAATGCGAT
1 TCGCAATGCGAATCTGACTATCGCAATGCGAT
35678 TTACATAGCG
Statistics
Matches: 76, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
59 2 0.03
60 50 0.66
61 22 0.29
62 2 0.03
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (61 bp):
TCGCAATGCGAATCTGACTATCGCAATGCGATATACCTAAATCGCAATGCGAATACGTAAA
Found at i:35874 original size:22 final size:22
Alignment explanation
Indices: 35849--35924 Score: 107
Period size: 22 Copynumber: 3.5 Consensus size: 22
35839 CACTCTCTAA
* *
35849 GACGACATCCGTCCCCATCTCC
1 GACGAAATCAGTCCCCATCTCC
35871 GACGAAATCAGTCCCCATCTCC
1 GACGAAATCAGTCCCCATCTCC
* * *
35893 GACGATATCAGTCTCCATCTCT
1 GACGAAATCAGTCCCCATCTCC
35915 GACGAAATCA
1 GACGAAATCA
35925 TTCACGGTCA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.26, C:0.38, G:0.14, T:0.21
Consensus pattern (22 bp):
GACGAAATCAGTCCCCATCTCC
Found at i:36285 original size:19 final size:19
Alignment explanation
Indices: 36261--36342 Score: 59
Period size: 19 Copynumber: 4.5 Consensus size: 19
36251 GCGATTCTGT
36261 CGTTGCGATTTTCATTTCA
1 CGTTGCGATTTTCATTTCA
*
36280 CGTTGCGA--TTC--TT-G
1 CGTTGCGATTTTCATTTCA
** *
36294 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCA-TTTCA
*
36314 TGTTGCGATTTTCATTTCGA
1 CGTTGCGATTTTCATTTC-A
36334 -GTTGCGATT
1 CGTTGCGATT
36343 CTTGCGTTGC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 8 0.16
15 2 0.04
16 2 0.04
17 3 0.06
19 23 0.46
20 12 0.24
ACGTcount: A:0.13, C:0.18, G:0.23, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCA
Found at i:36320 original size:20 final size:20
Alignment explanation
Indices: 36295--36415 Score: 112
Period size: 20 Copynumber: 6.4 Consensus size: 20
36285 CGATTCTTGC
36295 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
** *
36315 GTTGCGATTTTCA-TTTCGA
1 GTTGCGATAGTCATTTTCGT
*
36334 GTTGCGAT--TC---TT-GC
1 GTTGCGATAGTCATTTTCGT
** *
36348 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCATTTTCGT
36368 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
36388 GTTGCGATTTTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
36408 GTTGCGAT
1 GTTGCGAT
36416 TTTAAGTTTC
Statistics
Matches: 86, Mismatches: 9, Indels: 12
0.80 0.08 0.11
Matches are distributed among these distances:
14 9 0.10
15 2 0.02
16 2 0.02
17 2 0.02
19 15 0.17
20 56 0.65
ACGTcount: A:0.15, C:0.17, G:0.25, T:0.44
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:36342 original size:53 final size:53
Alignment explanation
Indices: 36261--36396 Score: 193
Period size: 53 Copynumber: 2.5 Consensus size: 53
36251 GCGATTCTGT
**
36261 CGTTGCGATTTTCATTTC-ACGTTGCGATTCTTGCGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCATTTCGA-GTTGCGATTCTTGCGTTGCGATAGTCAAATTCG
*
36314 TGTTGCGATTTTCATTTCGAGTTGCGATTCTTGCGTTGCGATAGTCAAATTCG
1 CGTTGCGATTTTCATTTCGAGTTGCGATTCTTGCGTTGCGATAGTCAAATTCG
** *
36367 CGTTGCGATAGTCATTTTCGTGTTGCGATT
1 CGTTGCGATTTTCA-TTTCGAGTTGCGATT
36397 TTCATTTTCG
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
53 59 0.80
54 15 0.20
ACGTcount: A:0.15, C:0.18, G:0.24, T:0.43
Consensus pattern (53 bp):
CGTTGCGATTTTCATTTCGAGTTGCGATTCTTGCGTTGCGATAGTCAAATTCG
Found at i:36425 original size:20 final size:20
Alignment explanation
Indices: 36382--36425 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
36372 CGATAGTCAT
* *
36382 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
36402 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
36422 TTTC
1 TTTC
36426 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:38330 original size:20 final size:20
Alignment explanation
Indices: 38305--38461 Score: 110
Period size: 20 Copynumber: 8.5 Consensus size: 20
38295 AGAATAGTCT
38305 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
38325 ACTATCGCAACGTGAAAATG
1 ACTATCGCAATGCGAAAATG
*
38345 ACTATCGCAAT--G-AGA-G
1 ACTATCGCAATGCGAAAATG
38361 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
** **
38378 AAAATCATAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
*
38394 A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
38412 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
38432 ACTATCGCAATGC-AAATTTG
1 ACTATCGCAATGCGAAA-ATG
38452 ACTATCGCAA
1 ACTATCGCAA
38462 CGAAAGAATC
Statistics
Matches: 111, Mismatches: 11, Indels: 30
0.73 0.07 0.20
Matches are distributed among these distances:
14 13 0.12
16 9 0.08
17 8 0.07
18 4 0.04
19 8 0.07
20 69 0.62
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:38604 original size:20 final size:20
Alignment explanation
Indices: 38506--38594 Score: 142
Period size: 20 Copynumber: 4.5 Consensus size: 20
38496 GCGATTCTCT
**
38506 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
38526 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
38546 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
38566 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
38586 CGTTGCGAT
1 CGTTGCGAT
38595 TTTATGTTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:39148 original size:21 final size:21
Alignment explanation
Indices: 39074--39160 Score: 84
Period size: 21 Copynumber: 4.1 Consensus size: 21
39064 TATCGACTCA
39074 CCTGTCATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* ** *
39095 CCTATCATCCCTCAAGAGTCC
1 CCTGTCATCGTTCAAGAGGCC
** *
39116 CCTCCCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* * *
39137 ACTGTCATCGTTGAAGAGGTC
1 CCTGTCATCGTTCAAGAGGCC
39158 CCT
1 CCT
39161 CCCAATATTC
Statistics
Matches: 49, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.21, C:0.37, G:0.20, T:0.23
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:39154 original size:42 final size:42
Alignment explanation
Indices: 39082--39164 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
39072 CACCTGTCAT
*
39082 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCAC
* ** *
39124 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
39165 ATATTCTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.39, G:0.19, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:40565 original size:14 final size:14
Alignment explanation
Indices: 40546--40581 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
40536 ATTGTTTAAT
40546 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
40560 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
40574 TGATTTGT
1 TGATTTGT
40582 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:40737 original size:33 final size:33
Alignment explanation
Indices: 40687--40782 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
40677 AAAACAGACT
* ** *
40687 ATCGCAACGCGGAAATGACTATCGTAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
40721 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
40754 ATCGCAATACGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
40783 CGAAACTAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.54
34 26 0.46
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:40859 original size:33 final size:33
Alignment explanation
Indices: 40797--40881 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 33
40787 ACTAAATTCG
* *
40797 CGTTGCGCTTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCA-TTTCACATTGCGATTCTCT
40831 CGTTGCGATTTTCATTTCACATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCACATTGCGATTCTCT
**
40864 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
40882 CGCGTTGCGA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 34 0.72
34 13 0.28
ACGTcount: A:0.13, C:0.25, G:0.18, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCACATTGCGATTCTCT
Found at i:44229 original size:20 final size:20
Alignment explanation
Indices: 44204--44310 Score: 162
Period size: 20 Copynumber: 5.3 Consensus size: 20
44194 AAATTCAATA
44204 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
* *
44224 TTGCGATAATCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
44244 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
44264 TTGCGATAGTCATAATCGCG
1 TTGCGATAGTCAGAATCGCG
44284 TTGCGATAGTCA-AATTCGCG
1 TTGCGATAGTCAGAA-TCGCG
44304 TTGCGAT
1 TTGCGAT
44311 TTACATATTC
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
19 2 0.02
20 79 0.98
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:44320 original size:20 final size:20
Alignment explanation
Indices: 44297--44349 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
44287 CGATAGTCAA
*
44297 ATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACAT
*
44317 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACAT
44337 ATTCGCATTGCGA
1 ATTCGCATTGCGA
44350 ATTAGGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACAT
Found at i:44328 original size:40 final size:40
Alignment explanation
Indices: 44203--44330 Score: 136
Period size: 40 Copynumber: 3.2 Consensus size: 40
44193 GAAATTCAAT
* * *
44203 ATTGCGATAGTCAGAATCGCGTTGCGA-TAATCAGAATCTC
1 ATTGCGATAGTCAGAATCGCGTTGCGATTTA-CATAATCGC
* * *
44243 GTTGCGATAGTCAGAATCTCGTTGCGATAGT-CATAATCGC
1 ATTGCGATAGTCAGAATCGCGTTGCGAT-TTACATAATCGC
* *
44283 GTTGCGATAGTCA-AATTCGCGTTGCGATTTACATATTCGC
1 ATTGCGATAGTCAGAA-TCGCGTTGCGATTTACATAATCGC
44323 ATTGCGAT
1 ATTGCGAT
44331 TTACGTATTC
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
39 3 0.04
40 71 0.96
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (40 bp):
ATTGCGATAGTCAGAATCGCGTTGCGATTTACATAATCGC
Found at i:44370 original size:21 final size:21
Alignment explanation
Indices: 44346--44391 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
44336 TATTCGCATT
44346 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
44367 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
44388 GCGA
1 GCGA
44392 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:48668 original size:204 final size:204
Alignment explanation
Indices: 48318--49133 Score: 1524
Period size: 204 Copynumber: 4.0 Consensus size: 204
48308 GCTTAACAAT
* * * *
48318 ACTCGAGCTCGACTCGGTTTGTTTACATCCCAACGTCCAGGTTCCTTTCCCTCATTCGTTCTTCT
1 ACTCGAGCTCGACTTGGCTTGTTTACATCCCTACGTCCAGGTTCCTTTCCCTCATTCGATCTTCT
48383 CGAGTTCTCGTTCATTCGTTTACAATCGGTTGGTCTAGTGAGATGAGGCACTAGGTCCCTTAAGC
66 CGAGTTCTCGTTCATTCGTTTACAATCGGTTGGTCTAGTGAGATGAGGCACTAGGTCCCTTAAGC
48448 AAGGTCAAGGGTTCGACCCCTGACGTTTGTGAATGGAGCAAATTAACTTGGGAGAGTCACCCTCG
131 AAGGTCAAGGGTTCGACCCCTGACGTTTGTGAATGGAGCAAATTAACTTGGGAGAGTCACCCTCG
48513 CATCTACAG
196 CATCTACAG
48522 ACTCGAGCTCGACTTGGCTTGTTTACATCCCTACGTCCAGGTTCCTTTCCCTCATTCGATCTTCT
1 ACTCGAGCTCGACTTGGCTTGTTTACATCCCTACGTCCAGGTTCCTTTCCCTCATTCGATCTTCT
*
48587 CGAGTTCTCATTCATTCGTTTACAATCGGTTGGTCTAGTGAGATGAGGCACTAGGTCCCTTAAGC
66 CGAGTTCTCGTTCATTCGTTTACAATCGGTTGGTCTAGTGAGATGAGGCACTAGGTCCCTTAAGC
48652 AAGGTCAAGGGTTCGACCCCTGACGTTTGTGAATGGAGCAAATTAACTTGGGAGAGTCACCCTCG
131 AAGGTCAAGGGTTCGACCCCTGACGTTTGTGAATGGAGCAAATTAACTTGGGAGAGTCACCCTCG
48717 CATCTACAG
196 CATCTACAG
48726 ACTCGAGCTCGACTTGGCTTGTTTACATCCCTACGTCCAGGTTCCTTTCCCTCATTCGATCTTCT
1 ACTCGAGCTCGACTTGGCTTGTTTACATCCCTACGTCCAGGTTCCTTTCCCTCATTCGATCTTCT
*
48791 CGAGTTCTCGTTCATTCGTTTACAATCGGTTGGTCTAGTGGGATGAGGCACTAGGTCCCTTAAGC
66 CGAGTTCTCGTTCATTCGTTTACAATCGGTTGGTCTAGTGAGATGAGGCACTAGGTCCCTTAAGC
48856 AAGGTCAAGGGTTCGACCCCTGACGTTTGTGAATGGAGCAAATTAACTTGGGAGAGTCACCCTCG
131 AAGGTCAAGGGTTCGACCCCTGACGTTTGTGAATGGAGCAAATTAACTTGGGAGAGTCACCCTCG
48921 CATCTACAG
196 CATCTACAG
48930 ACTCGAGCTCGACTTGGCTTGTTTACATCCCTACGTCCAGGTTCCTTTCCCTCATTCGATCTTCT
1 ACTCGAGCTCGACTTGGCTTGTTTACATCCCTACGTCCAGGTTCCTTTCCCTCATTCGATCTTCT
* * *
48995 CGAGTTCTCGTTCATTCGTTTACAATCTGTTGGTCTAGTGGGATGAGGCACTAGGTCTCTTAAGC
66 CGAGTTCTCGTTCATTCGTTTACAATCGGTTGGTCTAGTGAGATGAGGCACTAGGTCCCTTAAGC
* *
49060 AAGGTCAAGGTTTCGACCCCTGGCGTTTGTGAATGGAGCAAATTAACTTGGGAGAGTCACCCTCG
131 AAGGTCAAGGGTTCGACCCCTGACGTTTGTGAATGGAGCAAATTAACTTGGGAGAGTCACCCTCG
*
49125 CCTCTACAG
196 CATCTACAG
49134 TACCTGATCT
Statistics
Matches: 600, Mismatches: 12, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
204 600 1.00
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (204 bp):
ACTCGAGCTCGACTTGGCTTGTTTACATCCCTACGTCCAGGTTCCTTTCCCTCATTCGATCTTCT
CGAGTTCTCGTTCATTCGTTTACAATCGGTTGGTCTAGTGAGATGAGGCACTAGGTCCCTTAAGC
AAGGTCAAGGGTTCGACCCCTGACGTTTGTGAATGGAGCAAATTAACTTGGGAGAGTCACCCTCG
CATCTACAG
Found at i:55535 original size:31 final size:30
Alignment explanation
Indices: 55500--55575 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 30
55490 ATAAAAGGGA
55500 AGTTTGATAAATTTAATAATGATTTTT-TAAT
1 AGTTTGATAAATTTAATAAT--TTTTTATAAT
* *
55531 AGTTTG-TCCAAATGTAATGATTTTTTATAAT
1 AGTTTGAT--AAATTTAATAATTTTTTATAAT
*
55562 AGTTTAATAAATTT
1 AGTTTGATAAATTT
55576 TTTAATTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
30 11 0.30
31 15 0.41
32 11 0.30
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.50
Consensus pattern (30 bp):
AGTTTGATAAATTTAATAATTTTTTATAAT
Found at i:59613 original size:20 final size:22
Alignment explanation
Indices: 59567--59618 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
59557 CCGTAAGGGG
* *
59567 GTATCGGTACCATAGTATGGTA
1 GTATCGATACCATAGTATAGTA
59589 GTATCGATACCATAGTA-AG-A
1 GTATCGATACCATAGTATAGTA
59609 GTATCGATAC
1 GTATCGATAC
59619 TAGGCAACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 11 0.39
21 1 0.04
22 16 0.57
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (22 bp):
GTATCGATACCATAGTATAGTA
Found at i:59616 original size:95 final size:93
Alignment explanation
Indices: 59474--59707 Score: 255
Period size: 95 Copynumber: 2.5 Consensus size: 93
59464 AATTCAATCA
* * * *
59474 GTATCGATACC-GAAGAGGTAGTATCGATACCAT-GATAAGGGTATCGATACCAAGCAACATCGA
1 GTATCGATACCATAAGTGGTAGTATCGATACCATAG-TAAGAGTATCGATACCAAGCAACATCAA
* * *
59537 ATAAAAAAT-AGGTATCGATACCGTAAGGGG
65 ACAAAAAATCA-GTATCGATACC-AAAAGGG
* * *
59567 GTATCGGTACCAT-AGTATGGTAGTATCGATACCATAGTAAGAGTATCGATACTAGGCAACATCA
1 GTATCGATACCATAAG--TGGTAGTATCGATACCATAGTAAGAGTATCGATACCAAGCAACATCA
**
59631 AACCTAAAATCAGTATCGATACCAAAAGGG
64 AACAAAAAATCAGTATCGATACCAAAAGGG
59661 GTATCGATACCATAAGTGG--GTATCGATACCATAGTATAGAAGTATCG
1 GTATCGATACCATAAGTGGTAGTATCGATACCATAGTA-AG-AGTATCG
59708 GTACTAGGGT
Statistics
Matches: 120, Mismatches: 13, Indels: 16
0.81 0.09 0.11
Matches are distributed among these distances:
91 17 0.14
92 2 0.02
93 22 0.18
94 17 0.14
95 60 0.50
96 2 0.02
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.23
Consensus pattern (93 bp):
GTATCGATACCATAAGTGGTAGTATCGATACCATAGTAAGAGTATCGATACCAAGCAACATCAAA
CAAAAAATCAGTATCGATACCAAAAGGG
Found at i:59664 original size:18 final size:19
Alignment explanation
Indices: 59643--59691 Score: 82
Period size: 18 Copynumber: 2.6 Consensus size: 19
59633 CCTAAAATCA
59643 GTATCGATACCAAAAG-GG
1 GTATCGATACCAAAAGTGG
*
59661 GTATCGATACCATAAGTGG
1 GTATCGATACCAAAAGTGG
59680 GTATCGATACCA
1 GTATCGATACCA
59692 TAGTATAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 15 0.52
19 14 0.48
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.22
Consensus pattern (19 bp):
GTATCGATACCAAAAGTGG
Found at i:59683 original size:19 final size:18
Alignment explanation
Indices: 59643--59693 Score: 84
Period size: 19 Copynumber: 2.8 Consensus size: 18
59633 CCTAAAATCA
*
59643 GTATCGATACCAAAAGGG
1 GTATCGATACCATAAGGG
59661 GTATCGATACCATAAGTGG
1 GTATCGATACCATAAG-GG
59680 GTATCGATACCATA
1 GTATCGATACCATA
59694 GTATAGAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 15 0.48
19 16 0.52
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.24
Consensus pattern (18 bp):
GTATCGATACCATAAGGG
Found at i:60486 original size:68 final size:68
Alignment explanation
Indices: 60371--60626 Score: 352
Period size: 68 Copynumber: 3.8 Consensus size: 68
60361 AAACGATTAT
*
60371 AGGCCTAACTGTGTAAATGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCAAATGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
*
60436 TTA
66 TTG
* * * * *
60439 AAGCCTAATTGTGCAATTGACAGAAATGTGTCATTTATGCCACTTAGATGAAAGGCTAAATGCCT
1 AGGCCTAACTGTGCAAATGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
60504 TTG
66 TTG
* *
60507 AGGCCTAACTGTGCAAACGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCAAATGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
*
60572 CTG
66 TTG
* * * * * *
60575 AGGCCTAATTGTGCAATTGGCAGAAA-GATGTCAATTATGTCATTTAGATGAA
1 AGGCCTAACTGTGCAAATGACAGAAATG-TGTCATTTATGCCAGTTAGATGAA
60627 CGATTAAATA
Statistics
Matches: 165, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
67 1 0.01
68 164 0.99
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (68 bp):
AGGCCTAACTGTGCAAATGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:60622 original size:136 final size:136
Alignment explanation
Indices: 60371--60626 Score: 406
Period size: 136 Copynumber: 1.9 Consensus size: 136
60361 AAACGATTAT
* * *
60371 AGGCCTAACTGTGTAAATGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCAAACGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
* *
60436 TTAAAGCCTAATTGTGCAATTGACAGAAATGTGTCATTTATGCCACTTAGATGAAAGGCTAAATG
66 CTAAAGCCTAATTGTGCAATTGACAGAAATGTGTCAATTATGCCACTTAGATGAAAGGCTAAATG
60501 CCTTTG
131 CCTTTG
60507 AGGCCTAACTGTGCAAACGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCAAACGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
* * * * *
60572 CTGAGGCCTAATTGTGCAATTGGCAGAAA-GATGTCAATTATGTCATTTAGATGAA
66 CTAAAGCCTAATTGTGCAATTGACAGAAATG-TGTCAATTATGCCACTTAGATGAA
60627 CGATTAAATA
Statistics
Matches: 109, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
135 1 0.01
136 108 0.99
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (136 bp):
AGGCCTAACTGTGCAAACGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
CTAAAGCCTAATTGTGCAATTGACAGAAATGTGTCAATTATGCCACTTAGATGAAAGGCTAAATG
CCTTTG
Found at i:60679 original size:81 final size:81
Alignment explanation
Indices: 60578--60942 Score: 477
Period size: 81 Copynumber: 4.5 Consensus size: 81
60568 GCCTCTGAGG
* * * * *
60578 CCTAATTGTGCAATTGGCAGAAA-GATGTCAATTATGTCATTTAGATGAACGATTAAATACCATC
1 CCTAATTGTGCAATTGGCAGAAATG-TGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGTT
60642 GAGTAAAAGAATAATGA
65 GAGTAAAAGAATAATGA
*
60659 CCTAACTGTGCAATTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTG
1 CCTAATTGTGCAATTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTG
60724 AGTAAAAGAATAATG-
66 AGTAAAAGAATAATGA
* *
60739 CCTAATTGTGCAATTGGTAGAAAGGTGT-AATTATGCCAGTTAGATGAACGGTTAAATACCGTTG
1 CCTAATTGTGCAATTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTG
60803 AGTAAAAGAATAATGA
66 AGTAAAAGAATAATGA
** * * * **
60819 CCTAATTGTGCAATTGATAAAAATGTGTCAATTATGCCAGTTAGATGTACGGTTAAACAATGTTG
1 CCTAATTGTGCAATTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTG
60884 AGTAAAAGAATAATAGA
66 AGTAAAAGAATAAT-GA
* * * * * * * *
60901 -TTAGTTGTGCATTTGACATAAAAGTGTCAAATATGCAAGTTA
1 CCTAATTGTGCAATTGGCAGAAATGTGTCAATTATGCCAGTTA
60943 AGTAAAAAGA
Statistics
Matches: 256, Mismatches: 24, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
79 51 0.20
80 50 0.20
81 152 0.59
82 3 0.01
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (81 bp):
CCTAATTGTGCAATTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTG
AGTAAAAGAATAATGA
Found at i:60845 original size:160 final size:161
Alignment explanation
Indices: 60577--60897 Score: 500
Period size: 160 Copynumber: 2.0 Consensus size: 161
60567 TGCCTCTGAG
* *
60577 GCCTAATTGTGCAATTGGCAGAAAGATGTCAATTATGTCATTTAGATGAACGATTAAATACCATC
1 GCCTAATTGTGCAATTGGCAGAAAGATGTCAATTATGCCAGTTAGATGAACGATTAAATACCATC
* *
60642 GAGTAAAAGAATAATGACCTAACTGTGCAATTGGCAGAAATGTGTCAATTATGCCAGTTAGATGA
66 GAGTAAAAGAATAATGACCTAACTGTGCAATTGACAAAAATGTGTCAATTATGCCAGTTAGATGA
* *
60707 ACGGTTAAATACCGTTGAGTAAAAGAATAAT
131 ACGGTTAAACAACGTTGAGTAAAAGAATAAT
* * * * *
60738 GCCTAATTGTGCAATTGGTAGAAAGGTGT-AATTATGCCAGTTAGATGAACGGTTAAATACCGTT
1 GCCTAATTGTGCAATTGGCAGAAAGATGTCAATTATGCCAGTTAGATGAACGATTAAATACCATC
* * *
60802 GAGTAAAAGAATAATGACCTAATTGTGCAATTGATAAAAATGTGTCAATTATGCCAGTTAGATGT
66 GAGTAAAAGAATAATGACCTAACTGTGCAATTGACAAAAATGTGTCAATTATGCCAGTTAGATGA
*
60867 ACGGTTAAACAATGTTGAGTAAAAGAATAAT
131 ACGGTTAAACAACGTTGAGTAAAAGAATAAT
60898 AGATTAGTTG
Statistics
Matches: 145, Mismatches: 15, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
160 118 0.81
161 27 0.19
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (161 bp):
GCCTAATTGTGCAATTGGCAGAAAGATGTCAATTATGCCAGTTAGATGAACGATTAAATACCATC
GAGTAAAAGAATAATGACCTAACTGTGCAATTGACAAAAATGTGTCAATTATGCCAGTTAGATGA
ACGGTTAAACAACGTTGAGTAAAAGAATAAT
Found at i:62983 original size:18 final size:19
Alignment explanation
Indices: 62960--62996 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
62950 AAATAATATA
*
62960 TTTATT-AATAAAATTACT
1 TTTATTAAATAAAACTACT
62978 TTTATTAAATAAAACTACT
1 TTTATTAAATAAAACTACT
62997 CGATTCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTATTAAATAAAACTACT
Found at i:70951 original size:24 final size:24
Alignment explanation
Indices: 70916--70962 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
70906 CTGTAGTTTC
70916 AAAGAATGCTACAAATTTAGCGTT
1 AAAGAATGCTACAAATTTAGCGTT
*
70940 AAAGAATTCTACAAATTTAGCGT
1 AAAGAATGCTACAAATTTAGCGT
70963 CCATAGTGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (24 bp):
AAAGAATGCTACAAATTTAGCGTT
Done.