Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000780.1 Hibiscus syriacus cultivar Beakdansim tig00001515_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: 63533
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Found at i:218 original size:55 final size:55
Alignment explanation
Indices: 1--453 Score: 552
Period size: 55 Copynumber: 8.4 Consensus size: 55
* *
1 GAAGGAATGGAGAGCGGACCCGTTAT-TGAAGATTG-TCGAGTTCTATACTCTC-
1 GAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCTCT
53 GAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCTCT
1 GAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCTCT
* * * * *
108 GAAAGAATAGAGAGCAGA-AC-TGTTGTGAAGATTGTTCGAGTTCTATACTCTCT
1 GAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCTCT
* * *
161 GAAGGAATAGAGAGCAGACCCGTTTTATGAAGATTTTTCGAGTTCTATACTCCCT
1 GAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCTCT
* * * *
216 GAATGAATAGGGAGCGGA-CC-TATTAGTTAAAGATTGTTCGAGTTCTATACTCTCT
1 GAAGGAATAGAGAGCGGACCCGTTTTA--TGAAGATTGTTCGAGTTCTATACTCTCT
* *
271 GAAGGAATAGAGAGCAGACCCGTTTGT-TGAAGATTGTTCGAGTTCTATCCTCTCT
1 GAAGGAATAGAGAGCGGACCCGTTT-TATGAAGATTGTTCGAGTTCTATACTCTCT
* * *
326 GAAGGAATAGAGAGCGGACCTG-TTTCTGAAGATTGTTCGAG-TCTTATACTCCCT
1 GAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTC-TATACTCTCT
* * * * *
380 GAACGAATAGGGAGCAGACACG-TTTACTGAAGATTGTTCGAGTT-TATACTCCCT
1 GAAGGAATAGAGAGCGGACCCGTTTTA-TGAAGATTGTTCGAGTTCTATACTCTCT
*
434 GAAGGAATAGGGAGCGGACC
1 GAAGGAATAGAGAGCGGACC
454 GTCATTTGAA
Statistics
Matches: 348, Mismatches: 39, Indels: 26
0.84 0.09 0.06
Matches are distributed among these distances:
52 24 0.07
53 64 0.18
54 93 0.27
55 161 0.46
56 3 0.01
57 2 0.01
58 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (55 bp):
GAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCTCT
Found at i:290 original size:110 final size:108
Alignment explanation
Indices: 1--477 Score: 626
Period size: 108 Copynumber: 4.4 Consensus size: 108
* *
1 GAAGGAATGGAGAGCGGACCCGTTATTGAAGATTG-TCGAGTTCTATACTCTC-GAAGGAATAGA
1 GAAGGAATAGAGAGCGGACCTGTT-TTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGA
* *
64 GAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCTCT
65 GAGCAGACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCCCT
* * * *
108 GAAAGAATAGAGAGCAGAACTGTTGTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAG
1 GAAGGAATAGAGAGCGGACCTGTTTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAG
*
173 AGCAGACCCGTTTTATGAAGATTTTTCGAGTTCTATACTCCCT
66 AGCAGACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCCCT
* * * *
216 GAATGAATAGGGAGCGGACCTATTAGTTAAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAG
1 GAAGGAATAGAGAGCGGACCTGTT--TTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAG
* *
281 AGAGCAGACCCGTTTGT-TGAAGATTGTTCGAGTTCTATCCTCTCT
64 AGAGCAGACCCGTTT-TATGAAGATTGTTCGAGTTCTATACTCCCT
* *
326 GAAGGAATAGAGAGCGGACCTGTTTCTGAAGATTGTTCGAG-TCTTATACTCCCTGAACGAATAG
1 GAAGGAATAGAGAGCGGACCTGTTT-TGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAG
* *
390 GGAGCAGACACG-TTTACTGAAGATTGTTCGAGTT-TATACTCCCT
64 AGAGCAGACCCGTTTTA-TGAAGATTGTTCGAGTTCTATACTCCCT
* * *
434 GAAGGAATAGGGAGCGGACC-GTCATTTGAAGATTTTTCAAGTTC
1 GAAGGAATAGAGAGCGGACCTGT--TTTGAAGATTGTTCGAGTTC
478 ATTTATCCCG
Statistics
Matches: 326, Mismatches: 32, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
106 9 0.03
107 39 0.12
108 116 0.36
109 63 0.19
110 98 0.30
111 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (108 bp):
GAAGGAATAGAGAGCGGACCTGTTTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAG
AGCAGACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCCCT
Found at i:431 original size:218 final size:215
Alignment explanation
Indices: 1--453 Score: 664
Period size: 218 Copynumber: 2.1 Consensus size: 215
* *
1 GAAGGAAT-GGAGAGCGGACCCGTTATTGAAGATTGTCGAGTTCTATACTCTCGAAGGAATAGAG
1 GAAGGAATAGG-GAGCGGACCCATTATTAAAGATTGTCGAGTTCTATACTCTCGAAGGAATAGAG
*
65 AGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAAGAATAGAGAGCAGAACTG
65 AGCAGACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAAGAATAGAGAGCAGAACTG
* * * *
130 TTGTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACCCGTTTTATGAAGAT
130 TTCTGAAGATTGTTCGAGTTCTATACTCCCTGAACGAATAGAGAGCAGACACGTTTTATGAAGAT
*
195 TTTTCGAGTTCTATACTCCCT
195 TGTTCGAGTTCTATACTCCCT
* *
216 GAATGAATAGGGAGCGGACCTATTAGTTAAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAG
1 GAAGGAATAGGGAGCGGACCCATTA-TTAAAGATTG-TCGAGTTCTATACTCTC-GAAGGAATAG
* * * *
281 AGAGCAGACCCGTTTGT-TGAAGATTGTTCGAGTTCTATCCTCTCTGAAGGAATAGAGAGCGGAC
63 AGAGCAGACCCGTTT-TATGAAGATTGTTCGAGTTCTATACTCTCTGAAAGAATAGAGAGCAGAA
*
345 CTGTTTCTGAAGATTGTTCGAG-TCTTATACTCCCTGAACGAATAGGGAGCAGACACG-TTTACT
127 CTG-TTCTGAAGATTGTTCGAGTTC-TATACTCCCTGAACGAATAGAGAGCAGACACGTTTTA-T
408 GAAGATTGTTCGAGTT-TATACTCCCT
189 GAAGATTGTTCGAGTTCTATACTCCCT
434 GAAGGAATAGGGAGCGGACC
1 GAAGGAATAGGGAGCGGACC
454 GTCATTTGAA
Statistics
Matches: 214, Mismatches: 16, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
215 19 0.09
216 11 0.05
217 17 0.08
218 105 0.49
219 62 0.29
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (215 bp):
GAAGGAATAGGGAGCGGACCCATTATTAAAGATTGTCGAGTTCTATACTCTCGAAGGAATAGAGA
GCAGACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAAGAATAGAGAGCAGAACTGT
TCTGAAGATTGTTCGAGTTCTATACTCCCTGAACGAATAGAGAGCAGACACGTTTTATGAAGATT
GTTCGAGTTCTATACTCCCT
Found at i:5240 original size:20 final size:20
Alignment explanation
Indices: 5217--5270 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
5207 GTTTCGATAA
5217 TGTAAATCGCAACATGAATT
1 TGTAAATCGCAACATGAATT
5237 TGTAAATCGCAACATGAATT
1 TGTAAATCGCAACATGAATT
*
5257 TGTAATTCGCAACA
1 TGTAAATCGCAACA
5271 CAGAAGTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.30
Consensus pattern (20 bp):
TGTAAATCGCAACATGAATT
Found at i:5283 original size:20 final size:20
Alignment explanation
Indices: 5260--5308 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
5250 ATGAATTTGT
*
5260 AATTCGCAACACAGAAGTTA
1 AATTCGCAACACAGAAGTCA
5280 AATTCGCAACACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
5300 AATTCGCAA
1 AATTCGCAA
5309 AGCGCGTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.45, C:0.22, G:0.14, T:0.18
Consensus pattern (20 bp):
AATTCGCAACACAGAAGTCA
Found at i:5915 original size:20 final size:19
Alignment explanation
Indices: 5880--5933 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
5870 AAATCGCAAC
*
5880 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCATT
*
5899 GCGATTTTCATTTTCGCATT
1 GCGATTTT-AGTTTCGCATT
5919 GCGATTTTAAGTTTC
1 GCGATTTT-AGTTTC
5934 AGAAACTTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 8 0.27
20 22 0.73
ACGTcount: A:0.15, C:0.17, G:0.20, T:0.48
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCATT
Found at i:6852 original size:31 final size:31
Alignment explanation
Indices: 6804--6959 Score: 206
Period size: 31 Copynumber: 5.0 Consensus size: 31
6794 CCCGAAGGAC
* * * *
6804 CAGTCCATA-GATTCCGAAAAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
6835 TAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
6866 CAGTTCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
6897 CAGTCTATATGTCTCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
6928 CAGTCTATATGTCCCGAAAAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
6959 C
1 C
6960 CCTCGACCCT
Statistics
Matches: 112, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
31 111 0.99
32 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:7999 original size:21 final size:21
Alignment explanation
Indices: 7940--7999 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
7930 TTCGCTTGAG
*
7940 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
*
7962 GGTTACCGATT-CCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
7982 GGGTACCGATTCCCCTTG
1 GGGTACCGATTCCCCTTG
8000 CCCAGAAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 16 0.47
21 9 0.26
22 9 0.26
ACGTcount: A:0.18, C:0.27, G:0.23, T:0.32
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:11768 original size:31 final size:31
Alignment explanation
Indices: 11729--11885 Score: 244
Period size: 31 Copynumber: 5.1 Consensus size: 31
11719 TCCCGAAGGG
* * *
11729 ACAGTCCATA-GATTCCGAAGAACCTAGGTAA
1 ACAGTCCATATG-TCCCAAAGAACATAGGTAA
*
11760 TCAGTCCATATGTCCCAAAGAACATAGGTAA
1 ACAGTCCATATGTCCCAAAGAACATAGGTAA
11791 ACAGTCCATATGTCCCAAAGAACATAGGTAA
1 ACAGTCCATATGTCCCAAAGAACATAGGTAA
*
11822 ACAGTTCATATGTCCCAAAGAACATAGGTAA
1 ACAGTCCATATGTCCCAAAGAACATAGGTAA
*
11853 ACAGTCCATATGTCCCGAAGAACATAGGTAA
1 ACAGTCCATATGTCCCAAAGAACATAGGTAA
11884 AC
1 AC
11886 CCTCAACCCT
Statistics
Matches: 117, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 116 0.99
32 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.20
Consensus pattern (31 bp):
ACAGTCCATATGTCCCAAAGAACATAGGTAA
Found at i:12825 original size:22 final size:22
Alignment explanation
Indices: 12800--12859 Score: 120
Period size: 22 Copynumber: 2.7 Consensus size: 22
12790 TTTTCCTTTA
12800 GGGGGAATCGATTCCCTCCTGT
1 GGGGGAATCGATTCCCTCCTGT
12822 GGGGGAATCGATTCCCTCCTGT
1 GGGGGAATCGATTCCCTCCTGT
12844 GGGGGAATCGATTCCC
1 GGGGGAATCGATTCCC
12860 CTATGAGATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.15, C:0.27, G:0.33, T:0.25
Consensus pattern (22 bp):
GGGGGAATCGATTCCCTCCTGT
Found at i:12918 original size:22 final size:21
Alignment explanation
Indices: 12893--12952 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
12883 TTCGCTTGAG
*
12893 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
12915 GGGTACCGATT-CCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
*
12935 GGGTACCGATTCTCCTTG
1 GGGTACCGATTCCCCTTG
12953 CCCAGAAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 17 0.49
21 8 0.23
22 10 0.29
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:13875 original size:16 final size:17
Alignment explanation
Indices: 13837--13878 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
13827 GCATCAGTTC
*
13837 TTATCACTCAAAATCAT
1 TTATCAATCAAAATCAT
* *
13854 TAATCAATCAAATTC-T
1 TTATCAATCAAAATCAT
13870 TTATCAATC
1 TTATCAATC
13879 TTTAATTACC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.38
Consensus pattern (17 bp):
TTATCAATCAAAATCAT
Found at i:16706 original size:31 final size:31
Alignment explanation
Indices: 16682--16823 Score: 257
Period size: 31 Copynumber: 4.6 Consensus size: 31
16672 CCATAGATTT
* *
16682 CGAAGAACCTAGGTAATCAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
16713 CGAAGAACATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
16744 CGAAGAACATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
16775 CGAAGAACATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
*
16806 CGAAGAACATATGTAAAC
1 CGAAGAACATAGGTAAAC
16824 CCTCGACCCT
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 108 1.00
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CGAAGAACATAGGTAAACAGTCCATATGTCC
Found at i:17835 original size:22 final size:21
Alignment explanation
Indices: 17810--17869 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
17800 TTCGCTTGAG
* *
17810 GGGTATCGTTTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
17832 GGGTACCGATT-CCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
17852 GGGTACCGATTCCCCTTG
1 GGGTACCGATTCCCCTTG
17870 CCCATAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 17 0.49
21 9 0.26
22 9 0.26
ACGTcount: A:0.17, C:0.27, G:0.25, T:0.32
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:20054 original size:21 final size:21
Alignment explanation
Indices: 20013--20056 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
20003 TAGTGCATGG
*
20013 CGTGATGAGGTACGGTATTTA
1 CGTGATGAGGTAAGGTATTTA
*
20034 CGTGGTGAGGTAGAGGT-TTTA
1 CGTGATGAGGTA-AGGTATTTA
20055 CG
1 CG
20057 CAATGAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.20, C:0.09, G:0.39, T:0.32
Consensus pattern (21 bp):
CGTGATGAGGTAAGGTATTTA
Found at i:20128 original size:21 final size:21
Alignment explanation
Indices: 20071--20129 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
20061 GAAAATGGTG
*
20071 CTTTACGTGGTGAGGCATCTA
1 CTTTACGTGGTGAGGTATCTA
20092 CTTTACGTGGTGAGGTATCTA
1 CTTTACGTGGTGAGGTATCTA
*
20113 CTTTACGTGATGAGGTA
1 CTTTACGTGGTGAGGTA
20130 GCCGCTCTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.20, C:0.15, G:0.29, T:0.36
Consensus pattern (21 bp):
CTTTACGTGGTGAGGTATCTA
Found at i:20469 original size:42 final size:42
Alignment explanation
Indices: 20422--20515 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 42
20412 CCTCTCCTAT
*
20422 CGTTCAAGAGGCC-CTTATCATCCTTCCAGAGGCCCCTCCCAC
1 CGTTCAAGAGGCCTC-TATCATCCTTCAAGAGGCCCCTCCCAC
* * *
20464 CGTTCAAGAGGCCTCTGTCATCGTTCAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCTCTATCATCCTTCAAGAGGCCCCTCCCAC
*
20506 CGTTCGAGAG
1 CGTTCAAGAG
20516 CCCGATTCAC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 45 0.98
43 1 0.02
ACGTcount: A:0.19, C:0.37, G:0.21, T:0.22
Consensus pattern (42 bp):
CGTTCAAGAGGCCTCTATCATCCTTCAAGAGGCCCCTCCCAC
Found at i:20473 original size:21 final size:21
Alignment explanation
Indices: 20422--20515 Score: 82
Period size: 21 Copynumber: 4.5 Consensus size: 21
20412 CCTCTCCTAT
* **
20422 CGTTCAAGAGGCCCTTATCATC
1 CGTTCAAGAGGCCCCTCCCA-C
*
20444 C-TTCCAGAGGCCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
* ** *
20464 CGTTCAAGAGGCCTCTGTCAT
1 CGTTCAAGAGGCCCCTCCCAC
*
20485 CGTTCAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
*
20506 CGTTCGAGAG
1 CGTTCAAGAG
20516 CCCGATTCAC
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 2 0.04
21 53 0.95
22 1 0.02
ACGTcount: A:0.19, C:0.37, G:0.21, T:0.22
Consensus pattern (21 bp):
CGTTCAAGAGGCCCCTCCCAC
Found at i:21913 original size:64 final size:64
Alignment explanation
Indices: 21841--21989 Score: 244
Period size: 64 Copynumber: 2.3 Consensus size: 64
21831 AAATTGATGT
21841 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGATTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGATTGTTTAATTG
* * *** *
21905 ATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTGCTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGATTGTTTAATTG
21969 ATTTGTAAAAGTTGATTTGTT
1 ATTTGTAAAAGTTGATTTGTT
21990 GTTTTAAATT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 79 1.00
ACGTcount: A:0.30, C:0.01, G:0.17, T:0.52
Consensus pattern (64 bp):
ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGATTGTTTAATTG
Found at i:21927 original size:27 final size:26
Alignment explanation
Indices: 21890--21940 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
21880 GAATTATTTT
*
21890 TTGATTGTTTAATTGATTTGTAAAAG
1 TTGATTGTTTAATTGATGTGTAAAAG
21916 TTGATTTGTTTAATTGATGTGTAAA
1 TTGA-TTGTTTAATTGATGTGTAAA
21941 TAATTCTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (26 bp):
TTGATTGTTTAATTGATGTGTAAAAG
Found at i:23980 original size:25 final size:25
Alignment explanation
Indices: 23952--24001 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
23942 CATTATTTTC
*
23952 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
*
23977 CAAATAATGTATCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
24002 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:24433 original size:18 final size:18
Alignment explanation
Indices: 24410--24445 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
24400 AAGCCGGTTG
24410 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
24428 TGATTGCGATTTTGATTT
1 TGATTGAGATTTTGATTT
24446 CCTTTTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.56
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:26746 original size:24 final size:24
Alignment explanation
Indices: 26718--26771 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
26708 CTGAAACATC
* *
26718 ATCAAAATTCTAGTATTGACCAAG
1 ATCAAAATACGAGTATTGACCAAG
* * *
26742 ATCAAAGTACGGGTATTGACTAAG
1 ATCAAAATACGAGTATTGACCAAG
26766 ATCAAA
1 ATCAAA
26772 TTTCGAATAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.26
Consensus pattern (24 bp):
ATCAAAATACGAGTATTGACCAAG
Found at i:26919 original size:12 final size:12
Alignment explanation
Indices: 26898--26931 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
26888 AGATGTGGGT
*
26898 TTTGAGATTGTG
1 TTTGATATTGTG
26910 TTTGATATTGTG
1 TTTGATATTGTG
*
26922 TTTGGTATTG
1 TTTGATATTG
26932 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:27513 original size:14 final size:15
Alignment explanation
Indices: 27477--27514 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
27467 GAAATCATTG
27477 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
27492 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
27507 AAAAATTA
1 AAAAATTA
27515 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:27574 original size:22 final size:22
Alignment explanation
Indices: 27527--27574 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
27517 GATGGGGAAG
* * *
27527 GATGTCGTTGGATATAGGATCG
1 GATGTCGTCGGAGATAGGATCA
27549 GATGTCGTCGGAGATAGTGAT-A
1 GATGTCGTCGGAGATAG-GATCA
27571 GATG
1 GATG
27575 GAGATGGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.25, C:0.08, G:0.38, T:0.29
Consensus pattern (22 bp):
GATGTCGTCGGAGATAGGATCA
Found at i:27698 original size:20 final size:19
Alignment explanation
Indices: 27652--27779 Score: 73
Period size: 20 Copynumber: 6.5 Consensus size: 19
27642 AAAATATTTA
* *
27652 TGTTGCGAAAATAAAA-CT
1 TGTTGCGAAATTAAAATCG
*
27670 TGTTACGAAATTAAAATTCG
1 TGTTGCGAAATTAAAA-TCG
27690 TGTTGCG-AATTCGAAAATCG
1 TGTTGCGAAATT--AAAATCG
*
27710 AGTTGCG-AATTCAGAAATCG
1 TGTTGCGAAATT-A-AAATCG
* * *
27730 AGTTGCGAATTTGAAATTCAG
1 TGTTGCGAAATT-AAAATC-G
* *
27751 TGTTGCGAATTTGTAAATCG
1 TGTTGCGAAATT-AAAATCG
*
27771 CGTTGCGAA
1 TGTTGCGAA
27780 TTTGACTTAT
Statistics
Matches: 90, Mismatches: 13, Indels: 12
0.78 0.11 0.10
Matches are distributed among these distances:
18 14 0.16
19 5 0.06
20 46 0.51
21 25 0.28
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (19 bp):
TGTTGCGAAATTAAAATCG
Found at i:27780 original size:20 final size:19
Alignment explanation
Indices: 27691--27784 Score: 107
Period size: 20 Copynumber: 4.7 Consensus size: 19
27681 TAAAATTCGT
*
27691 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTTG-AAATCGA
*
27711 GTTGCGAATTCAGAAATCGA
1 GTTGCGAATT-TGAAATCGA
*
27731 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTGAAA-TC-GA
*
27752 GTTGCGAATTTGTAAATCGC
1 GTTGCGAATTTG-AAATCGA
27772 GTTGCGAATTTGA
1 GTTGCGAATTTGA
27785 CTTATGTGTT
Statistics
Matches: 66, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.08
20 42 0.64
21 16 0.24
22 3 0.05
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.32
Consensus pattern (19 bp):
GTTGCGAATTTGAAATCGA
Found at i:27815 original size:20 final size:20
Alignment explanation
Indices: 27792--27843 Score: 95
Period size: 20 Copynumber: 2.5 Consensus size: 20
27782 TGACTTATGT
27792 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAGATTCGC
27812 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAGATTCGC
27832 GTTGCGAATTTA
1 GTTGCG-ATTTA
27844 GAAACTGAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 26 0.84
21 5 0.16
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCGC
Found at i:31160 original size:13 final size:13
Alignment explanation
Indices: 31138--31169 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
31128 CATAGAACTA
*
31138 GTGGCGAATCCAT
1 GTGGCTAATCCAT
31151 GTGGCTAATCCAT
1 GTGGCTAATCCAT
31164 GTGGCT
1 GTGGCT
31170 CCGTAGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.28
Consensus pattern (13 bp):
GTGGCTAATCCAT
Found at i:32744 original size:24 final size:24
Alignment explanation
Indices: 32710--32763 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
32700 CATTTAAATG
*
32710 ATAAACGAACACAAATGAACGAAC
1 ATAAACAAACACAAATGAACGAAC
*
32734 ATAAACAAACATAAATGAACGAAC
1 ATAAACAAACACAAATGAACGAAC
32758 ATAAAC
1 ATAAAC
32764 GAACGGCTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.61, C:0.19, G:0.09, T:0.11
Consensus pattern (24 bp):
ATAAACAAACACAAATGAACGAAC
Found at i:32760 original size:14 final size:14
Alignment explanation
Indices: 32713--32768 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
32703 TTAAATGATA
*
32713 AACGAACACAAATG
1 AACGAACATAAATG
32727 AACGAACAT--A--
1 AACGAACATAAATG
*
32737 AACAAACATAAATG
1 AACGAACATAAATG
*
32751 AACGAACATAAACG
1 AACGAACATAAATG
32765 AACG
1 AACG
32769 GCTCACTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 8 0.24
12 2 0.06
14 24 0.71
ACGTcount: A:0.59, C:0.20, G:0.12, T:0.09
Consensus pattern (14 bp):
AACGAACATAAATG
Found at i:34443 original size:29 final size:29
Alignment explanation
Indices: 34410--34472 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
34400 AATTTGAGAA
34410 AAAAT-AAAGAATAAATTGATTGGA-TTTTT
1 AAAATAAAAGAATAAATTGATT--ATTTTTT
* *
34439 AAAATAAAAGATTAAATTTATTATTTTTT
1 AAAATAAAAGAATAAATTGATTATTTTTT
34468 AAAAT
1 AAAAT
34473 TAGGATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 1 0.03
29 15 0.50
30 14 0.47
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (29 bp):
AAAATAAAAGAATAAATTGATTATTTTTT
Found at i:37330 original size:54 final size:54
Alignment explanation
Indices: 37262--37507 Score: 377
Period size: 54 Copynumber: 4.6 Consensus size: 54
37252 TAAACATACT
37262 ATGAA-TCTCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
1 ATGAATTC-CGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
* *
37316 ATGAATTCCATGAAATGCACACTTAGTGCCGAAACGGTTATTCATCTACATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
* * *
37370 ATGAATTCCGTGAAATTCACACTTAGTGTCGAAACGGTTATTCATCCACATAAG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
* * *
37424 ATGAATTTCGTGAAATGCACACCTAGTGCTGAAACGGTTATTCATCCACATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
** *
37478 ATGAATTTTGTGAAATGCACACTTAATGCC
1 ATGAATTCCGTGAAATGCACACTTAGTGCC
37508 TATTTGGTAA
Statistics
Matches: 174, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
54 172 0.99
55 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (54 bp):
ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
Found at i:38006 original size:94 final size:93
Alignment explanation
Indices: 37836--38006 Score: 247
Period size: 94 Copynumber: 1.8 Consensus size: 93
37826 TAGCTCCATA
* * *
37836 GTATCGATACCCTTACCATAGTATCGATACTACTATACTATGGTACCGATACCCCTTCTAGTATC
1 GTATAGATACCCTTACCATAGTATCGATACTACCATAATATGGTACCGATA-CCCTTCTAGTATC
*
37901 GATACCAATTTTAGATTCGATGTTACCTT
65 AATACCAATTTTAGATTCGATGTTACCTT
*
37930 GTATAGATACCCTTACCATGGTATCGATACTACCATAATATGGTACCGATA-CCTTCCTATGATA
1 GTATAGATACCCTTACCATAGTATCGATACTACCATAATATGGTACCGATACCCTT-CTA-G-TA
37994 TCAATACC-ATTTT
63 TCAATACCAATTTT
38007 GCATTCTGTT
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
92 4 0.06
93 3 0.04
94 53 0.77
95 9 0.13
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (93 bp):
GTATAGATACCCTTACCATAGTATCGATACTACCATAATATGGTACCGATACCCTTCTAGTATCA
ATACCAATTTTAGATTCGATGTTACCTT
Found at i:38053 original size:20 final size:21
Alignment explanation
Indices: 38024--38074 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
38014 GTTTCAAAAT
* *
38024 GGTATTGATACCT-TCCCTTC
1 GGTATCGATACCTCCCCCTTC
38044 GGTATCGATA-CTCCCCCTTC
1 GGTATCGATACCTCCCCCTTC
38064 GGTATCGATAC
1 GGTATCGATAC
38075 TGATTGAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.18, C:0.31, G:0.18, T:0.33
Consensus pattern (21 bp):
GGTATCGATACCTCCCCCTTC
Found at i:38075 original size:20 final size:20
Alignment explanation
Indices: 38038--38075 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
38028 TTGATACCTT
38038 CCCTTCGGTATCGATACTCC
1 CCCTTCGGTATCGATACTCC
38058 CCCTTCGGTATCGATACT
1 CCCTTCGGTATCGATACT
38076 GATTGAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.16, C:0.37, G:0.16, T:0.32
Consensus pattern (20 bp):
CCCTTCGGTATCGATACTCC
Found at i:38842 original size:17 final size:18
Alignment explanation
Indices: 38820--38855 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
38810 TTTAATAAGG
*
38820 TCCTTAAACAATTC-TCC
1 TCCTTAAAAAATTCATCC
38837 TCCTTAAAAAATTCATCC
1 TCCTTAAAAAATTCATCC
38855 T
1 T
38856 TAAATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.33, C:0.31, G:0.00, T:0.36
Consensus pattern (18 bp):
TCCTTAAAAAATTCATCC
Found at i:44194 original size:54 final size:54
Alignment explanation
Indices: 44129--44445 Score: 456
Period size: 54 Copynumber: 5.9 Consensus size: 54
44119 TAAACTTCTT
* * * * ** * *
44129 ATGAATCCCGTGAAATGTACCCTTAGTGTCGAAACAATTATTAATCTACATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
44183 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
* * *
44237 ATGAATTCCGTGAAATGTACACTTACTGCCGAAACGGTTATTCATCTACATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
* * **
44291 ATGAATTCCGTGAAATGTACACTTAGTACCGAAATAGTTATTCATCCACATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
* * *
44345 ATGAATTCCATGAAATGCACACTTAGTGCCAAAACGGTTATTAATCCA-ATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
*
44398 ATGAATTCTGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCA
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCA
44446 TGCACACTTA
Statistics
Matches: 236, Mismatches: 27, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
53 49 0.21
54 187 0.79
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (54 bp):
ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
Found at i:44454 original size:33 final size:33
Alignment explanation
Indices: 44412--44476 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
44402 ATTCTGTGAA
* *
44412 ATGCACACTTAGTGCCGAAACGGTTATTCATCC
1 ATGCACACTTAGTACCGAAACGATTATTCATCC
*
44445 ATGCACACTTAGTATCGAAACGATTATTCATC
1 ATGCACACTTAGTACCGAAACGATTATTCATC
44477 TACATAGGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (33 bp):
ATGCACACTTAGTACCGAAACGATTATTCATCC
Found at i:44506 original size:87 final size:86
Alignment explanation
Indices: 44359--44532 Score: 258
Period size: 87 Copynumber: 2.0 Consensus size: 86
44349 ATTCCATGAA
* * *
44359 ATGCACACTTAGTGCCAAAACGGTTATTAATCCAATAGGATGAATTCTGTGAAATGCACACTTAG
1 ATGCACACTTAGTACCAAAACGATTATTAATCCAATAGGATGAATTCCGTGAAATGCACACTTAG
44424 TGCCGAAACGGTTATTCATCC
66 TGCCGAAACGGTTATTCATCC
* * * * *
44445 ATGCACACTTAGTATCGAAACGATTATTCATCTACATAGGATGAATTCCGTGAAATTCACACTTA
1 ATGCACACTTAGTACCAAAACGATTATTAATCCA-ATAGGATGAATTCCGTGAAATGCACACTTA
*
44510 GTGTCGAAACGGTTATTCATCC
65 GTGCCGAAACGGTTATTCATCC
44532 A
1 A
44533 CATAAGATGA
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
86 28 0.36
87 50 0.64
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (86 bp):
ATGCACACTTAGTACCAAAACGATTATTAATCCAATAGGATGAATTCCGTGAAATGCACACTTAG
TGCCGAAACGGTTATTCATCC
Found at i:44530 original size:54 final size:54
Alignment explanation
Indices: 44445--44617 Score: 258
Period size: 54 Copynumber: 3.2 Consensus size: 54
44435 TTATTCATCC
* * * *
44445 ATGCACACTTAGTATCGAAACGATTATTCATCTACATAGGATGAATTCCGTGAA
1 ATGCACACTTAGTGTCGAAACGGTTATTCATCCACATAGGATGAATTTCGTGAA
* * *
44499 ATTCACACTTAGTGTCGAAACGGTTATTCATCCACATAAGATGAATTTTGTGAA
1 ATGCACACTTAGTGTCGAAACGGTTATTCATCCACATAGGATGAATTTCGTGAA
*
44553 ATGCACACCTAGTG-CTGAAACGGTTATTCATCCACATAGGATGAATTTCGTGAA
1 ATGCACACTTAGTGTC-GAAACGGTTATTCATCCACATAGGATGAATTTCGTGAA
44607 ATGCACACTTA
1 ATGCACACTTA
44618 ATGCCTATTT
Statistics
Matches: 106, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
53 1 0.01
54 105 0.99
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (54 bp):
ATGCACACTTAGTGTCGAAACGGTTATTCATCCACATAGGATGAATTTCGTGAA
Found at i:45171 original size:20 final size:20
Alignment explanation
Indices: 45148--45185 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
45138 TTGATACCTT
45148 CCCTTCGATATCGATACTCC
1 CCCTTCGATATCGATACTCC
*
45168 CCCTTCGGTATCGATACT
1 CCCTTCGATATCGATACT
45186 GATTGAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.37, G:0.13, T:0.32
Consensus pattern (20 bp):
CCCTTCGATATCGATACTCC
Found at i:51299 original size:54 final size:54
Alignment explanation
Indices: 51234--51585 Score: 496
Period size: 54 Copynumber: 6.6 Consensus size: 54
51224 TAAACTTCTT
* * * *
51234 ATGAATCCCGTGAAATGTACACTTAGTGCCGAAACGATTATTCATCTATATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGATTATTCATCCACATAGG
51288 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGATTATTCATCCACATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGATTATTCATCCACATAGG
* * *
51342 ATGAATTCCGTGAAATGTACACTTAGTGCCGAAACGGTTATTCATCTACATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGATTATTCATCCACATAGG
* * * *
51396 ATGAATTCCGTGAAATGTAAACTTAGTACCGAAAC-AGTTATTCGTCCACATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGA-TTATTCATCCACATAGG
* * * *
51450 ATGAATTCCATGAAATGCACACTTAGTGCC-ATAACGGTT-TTTAACCA-ATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGA-AACGATTATTCATCCACATAGG
* * *
51502 ATGAATTCTGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATATG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGATTATTCATCCACATAGG
51556 ATGAATTCCGTGAAATGCACACTTAGTGCC
1 ATGAATTCCGTGAAATGCACACTTAGTGCC
51586 TATTTGGTAA
Statistics
Matches: 266, Mismatches: 26, Indels: 12
0.88 0.09 0.04
Matches are distributed among these distances:
52 40 0.15
53 13 0.05
54 213 0.80
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (54 bp):
ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGATTATTCATCCACATAGG
Found at i:52047 original size:22 final size:20
Alignment explanation
Indices: 52002--52073 Score: 76
Period size: 22 Copynumber: 3.5 Consensus size: 20
51992 ATGTTACCTA
*
52002 GTATCGATACCCTTACCATG
1 GTATCGATACCCATACCATG
*
52022 GTATCGATACTACCATACTATG
1 GTATCGATAC--CCATACCATG
*
52044 GTATCGATA-CC-TTCCTATG
1 GTATCGATACCCATACC-ATG
52063 GTATCGATACC
1 GTATCGATACC
52074 ATTTTTGCAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.05
19 14 0.32
20 11 0.25
22 17 0.39
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (20 bp):
GTATCGATACCCATACCATG
Found at i:52061 original size:19 final size:19
Alignment explanation
Indices: 52002--52073 Score: 74
Period size: 19 Copynumber: 3.6 Consensus size: 19
51992 ATGTTACCTA
52002 GTATCGATACCCTTACC-ATG
1 GTATCGATA-CCTT-CCTATG
* *
52022 GTATCGATACTACCATACTATG
1 GTATCG--A-TACCTTCCTATG
52044 GTATCGATACCTTCCTATG
1 GTATCGATACCTTCCTATG
52063 GTATCGATACC
1 GTATCGATACC
52074 ATTTTTGCAT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
19 21 0.48
20 7 0.16
21 1 0.02
22 13 0.30
23 2 0.05
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (19 bp):
GTATCGATACCTTCCTATG
Found at i:52086 original size:95 final size:94
Alignment explanation
Indices: 51905--52086 Score: 251
Period size: 95 Copynumber: 1.9 Consensus size: 94
51895 TCTAGCTCCA
**
51905 TAGTATCGATACCCTTACCATGGTATCGATACTATTATACTATGGTACTGATACCCCCTTCCGGT
1 TAGTATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTACTGATACCCCCTT-CGGT
*
51970 ATCAATACCAATTTTATATTCTATGTTACC
65 ATCAATACCAATTTTACATTCTATGTTACC
*
52000 TAGTATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTA-TCGATACCTTCCTAT-G
1 TAGTATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTACT-GATACC-CCCT-TCG
* * *
52063 GTATCGATACCATTTTTGCATTCT
63 GTATCAATACCAATTTTACATTCT
52087 GTTTCAAAAT
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
94 1 0.01
95 72 0.94
96 3 0.04
97 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (94 bp):
TAGTATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTACTGATACCCCCTTCGGTA
TCAATACCAATTTTACATTCTATGTTACC
Found at i:55262 original size:6 final size:6
Alignment explanation
Indices: 55251--55292 Score: 57
Period size: 6 Copynumber: 6.5 Consensus size: 6
55241 ATATAAAGAA
55251 AAAAAT AAAAAT AAAAAT GAATAAAT AAAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT -AA-AAAT -AAAAAT AAAAAT AAA
55293 GTAAATAGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
6 21 0.64
7 6 0.18
8 6 0.18
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:55283 original size:21 final size:22
Alignment explanation
Indices: 55253--55299 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
55243 ATAAAGAAAA
*
55253 AAAT-AAAAATAAAAATGAA-T
1 AAATAAAAAATAAAAATAAAGT
55273 AAATAAAAAATAAAAATAAAGT
1 AAATAAAAAATAAAAATAAAGT
55295 AAATA
1 AAATA
55300 GTAAATAGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 4 0.17
21 14 0.58
22 6 0.25
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (22 bp):
AAATAAAAAATAAAAATAAAGT
Found at i:57403 original size:2 final size:2
Alignment explanation
Indices: 57342--57392 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
57332 AAGTAAATAA
* *
57342 AT AT AT -T AT TT AA AT AT A- 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
57382 AT AT AT AT AT A
1 AT AT AT AT AT A
57393 AATTAATATA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.