Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002872.1 Hibiscus syriacus cultivar Beakdansim tig00005923_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: 67935
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1902 original size:13 final size:14
Alignment explanation
Indices: 1877--1911 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
1867 ATTGTTTAAT
1877 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1891 TGATTTGT-AAAGT
1 TGATTTGTAAAAGG
1904 TGATTTGT
1 TGATTTGT
1912 TTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:2061 original size:33 final size:33
Alignment explanation
Indices: 2016--2079 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
2006 AAAAAGTACT
*
2016 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
2049 ATCGCAACGCGAAATGAAAATCGCAACGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGA
2080 AATTAAATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:2091 original size:19 final size:19
Alignment explanation
Indices: 2016--2082 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
2006 AAAAAGTACT
* *
2016 ATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAAATGAAA
2035 ATCGCAACGAG--A-G--A
1 ATCGCAACGAGAAATGAAA
*
2049 ATCGCAACGCGAAATGAAA
1 ATCGCAACGAGAAATGAAA
2068 ATCGCAACGAGAAAT
1 ATCGCAACGAGAAAT
2083 TAAATTCGCG
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
14 11 0.28
16 2 0.05
17 2 0.05
19 24 0.62
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
ATCGCAACGAGAAATGAAA
Found at i:2133 original size:33 final size:33
Alignment explanation
Indices: 2091--2217 Score: 200
Period size: 33 Copynumber: 3.8 Consensus size: 33
2081 ATTAAATTCG
* * *
2091 CGTTGCGATTTTCATTTTGCATTGTGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
2124 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* *
2157 CATTGCGATTTTTATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
2190 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2218 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 85 1.00
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:2146 original size:19 final size:19
Alignment explanation
Indices: 2124--2237 Score: 68
Period size: 19 Copynumber: 6.5 Consensus size: 19
2114 GTGATTCCCT
2124 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
2143 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
* *
2157 CATTGCGATTTTTATTTCG
1 CGTTGCGATTTTCATTTCG
* *
2176 CATTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
2190 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ** *
2209 CATTGCGATAGTAATTTCCG
1 CGTTGCGATTTTCATTT-CG
2229 CGTTGCGAT
1 CGTTGCGAT
2238 AGACATTAAG
Statistics
Matches: 71, Mismatches: 13, Indels: 21
0.68 0.12 0.20
Matches are distributed among these distances:
14 18 0.25
16 5 0.07
17 5 0.07
19 33 0.46
20 10 0.14
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:4608 original size:24 final size:24
Alignment explanation
Indices: 4574--4626 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
4564 CTTCTGAAAC
4574 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAT
* *
4598 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAT
4622 ATCAA
1 ATCAA
4627 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAT
Found at i:5526 original size:20 final size:20
Alignment explanation
Indices: 5437--5528 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
5427 TGCGAATTTG
* *
5437 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
5457 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
5477 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
5498 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
5518 GAAAATCGCAA
1 GAAAATCGCAA
5529 TCATCTTCAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:5767 original size:20 final size:20
Alignment explanation
Indices: 5742--5829 Score: 97
Period size: 20 Copynumber: 4.4 Consensus size: 20
5732 CAACGGGGAA
*
5742 ATCGCAAAGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
5762 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
5782 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
*
5802 ATCGCAACGCAAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
5822 ATCGCAAC
1 ATCGCAAC
5830 TAGAAAATTG
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
19 5 0.09
20 44 0.81
21 5 0.09
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:5897 original size:19 final size:19
Alignment explanation
Indices: 5856--5919 Score: 93
Period size: 19 Copynumber: 3.6 Consensus size: 19
5846 GAAATGAAAA
5856 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
5872 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5889 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5908 TCGCATTGCGAT
1 TCGCATTGCGAT
5920 AGCCATTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.26
16 3 0.07
17 3 0.07
19 26 0.60
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:5926 original size:19 final size:19
Alignment explanation
Indices: 5885--5941 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
5875 TTGCGATTTT
***
5885 CATTTCGCATTGCGATTTT
1 CATTTCGCATTGCGATAGC
5904 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
* *
5923 CATTTTTGCGTTGCGATAG
1 CA-TTTCGCATTGCGATAG
5942 TCTGTTTTGC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.40
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:6065 original size:14 final size:14
Alignment explanation
Indices: 6046--6082 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
6036 CATCAATTAA
6046 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
6060 ACAAATCATCTTTT
1 ACAAATCAACATTT
6074 ACAAATCAA
1 ACAAATCAA
6083 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:8005 original size:19 final size:20
Alignment explanation
Indices: 7950--8016 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
7940 GAAACTTAAA
* *
7950 ATCGTAACGCGAAAATGACT
1 ATCGCAACGCGGAAATGACT
*
7970 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGGAAATGACT
* **
7990 ATCGCAATGC-GAAATGAAA
1 ATCGCAACGCGGAAATGACT
8009 ATCGCAAC
1 ATCGCAAC
8017 AACAAAATCG
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 13 0.33
20 26 0.67
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:8059 original size:32 final size:33
Alignment explanation
Indices: 7990--8080 Score: 150
Period size: 32 Copynumber: 2.8 Consensus size: 33
7980 GGAAATGGCT
7990 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
* *
8023 ATCGCAATGCGAAATGAAAA-CGGAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
8055 ATCGCAATGCGAAATG-AAATCGCAAC
1 ATCGCAATGCGAAATGAAAATCGCAAC
8081 GCGAAACACA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
31 3 0.06
32 31 0.57
33 20 0.37
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACAACAAA
Found at i:8103 original size:19 final size:18
Alignment explanation
Indices: 8053--8103 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
8043 CGGAACGACA
**
8053 AAATCGCAATGCGAAATG
1 AAATCGCAATGCGAAAAC
*
8071 AAATCGCAACGCGAAACAC
1 AAATCGCAATGCGAAA-AC
*
8090 AAATCGCATTGCGA
1 AAATCGCAATGCGA
8104 TTTTCATTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.43, C:0.24, G:0.20, T:0.14
Consensus pattern (18 bp):
AAATCGCAATGCGAAAAC
Found at i:8115 original size:19 final size:18
Alignment explanation
Indices: 8093--8186 Score: 80
Period size: 14 Copynumber: 5.7 Consensus size: 18
8083 GAAACACAAA
8093 TCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
* *
8112 TCGCGTTGCGATTT--TG
1 TCGCATTGCGATTTCATT
8128 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTCATT
*
8144 TCGCATTGCGATTT--TG
1 TCGCATTGCGATTTCATT
*
8160 TCG--TTGCGATTT-TTT
1 TCGCATTGCGATTTCATT
8175 TCGCATTGCGAT
1 TCGCATTGCGAT
8187 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
14 18 0.29
15 4 0.06
16 12 0.19
17 7 0.11
18 12 0.19
19 10 0.16
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:8145 original size:32 final size:32
Alignment explanation
Indices: 8098--8186 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
8088 ACAAATCGCA
*
8098 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
8131 TTGCGATTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTCATTTCGCATTGCGATTTTGTCG
*
8163 TTGCGATTT-TTTTCGCATTGCGAT
1 TTGCGATTTCATTTCGCATTGCGAT
8187 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
31 14 0.26
32 34 0.63
33 6 0.11
ACGTcount: A:0.11, C:0.18, G:0.22, T:0.48
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCATTGCGATTTTGTCG
Found at i:8208 original size:20 final size:20
Alignment explanation
Indices: 8183--8225 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
8173 TTTCGCATTG
8183 CGATAGCCATTTCCGCGTTA
1 CGATAGCCATTTCCGCGTTA
* * *
8203 CGATAGTCATTTTCGTGTTA
1 CGATAGCCATTTCCGCGTTA
8223 CGA
1 CGA
8226 AAGTAAACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (20 bp):
CGATAGCCATTTCCGCGTTA
Found at i:8731 original size:18 final size:18
Alignment explanation
Indices: 8705--8749 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
8695 GTCGATCAGA
*
8705 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
8723 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
8741 TGATGGCTC
1 TGATGGCTC
8750 CCAAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:10110 original size:20 final size:20
Alignment explanation
Indices: 10068--10126 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
10058 AATAGTTTCT
* **
10068 GAAAATGAAAATCGCAAAAC
1 GAAAATGACAATCGCAACGC
*
10088 GAAAATGACTATCGCAACGC
1 GAAAATGACAATCGCAACGC
**
10108 GAATTTGACAATCGCAACG
1 GAAAATGACAATCGCAACG
10127 AGAGAATTGC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.46, C:0.20, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:10414 original size:21 final size:22
Alignment explanation
Indices: 10388--10430 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
10378 GATGGAGATA
10388 GACGGATTTCG-CGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
10409 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
10431 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.19, C:0.14, G:0.47, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:10643 original size:20 final size:20
Alignment explanation
Indices: 10618--10669 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
10608 ATTATGTATT
10618 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
*
10638 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
*
10658 ATCTCGTTGCGA
1 ATCGCGTTGCGA
10670 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:10729 original size:20 final size:20
Alignment explanation
Indices: 10597--10735 Score: 84
Period size: 20 Copynumber: 6.7 Consensus size: 20
10587 CGCTTTGAAA
*
10597 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
10618 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
10638 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
10658 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
10679 ATCGCATTGCGATAGTAAGTAAGT
1 ATCGCATTGCG--A-T-AGTCAGT
*
10703 ATAGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
10723 ATCGCATTGCGAT
1 ATCGCATTGCGAT
10736 TTTCCCAATT
Statistics
Matches: 94, Mismatches: 17, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
19 2 0.02
20 50 0.53
21 23 0.24
22 4 0.04
23 3 0.03
24 12 0.13
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:10733 original size:65 final size:61
Alignment explanation
Indices: 10597--10738 Score: 167
Period size: 65 Copynumber: 2.3 Consensus size: 61
10587 CGCTTTGAAA
* * * * *
10597 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATAGCATTGCGAAAGTCAGT
* * * *
10658 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTAAGTATAGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCG--A--AAGTAAGAATAGCATTGCGAAAGTCAGT
10723 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
10739 CCCAATTCGC
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
61 28 0.42
63 1 0.02
65 37 0.56
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATAGCATTGCGAAAGTCAGT
Found at i:11487 original size:5 final size:5
Alignment explanation
Indices: 11477--11511 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
11467 CGAAGAAGTC
11477 CAACT CAACT CAACT CAACT CAACT CAACT CAACT
1 CAACT CAACT CAACT CAACT CAACT CAACT CAACT
11512 AGGGCTTCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (5 bp):
CAACT
Found at i:15927 original size:45 final size:46
Alignment explanation
Indices: 15878--15968 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 46
15868 GAAAATCGAA
* *
15878 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
*
15923 TGCATTTGATGCATCGATGCACAAGACTATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
15969 ACTTTTTCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 21 0.50
46 21 0.50
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
Found at i:21824 original size:20 final size:21
Alignment explanation
Indices: 21799--21854 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
21789 TTGTGCTTCA
21799 TGCATCGATACACC-TAACAT-
1 TGCATCGATACACCTTAA-ATG
* *
21819 TGCATCGATGCATCCTTGAATG
1 TGCATCGATACA-CCTTAAATG
21841 TGCATCGATACACC
1 TGCATCGATACACC
21855 ATGAAGATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 11 0.37
21 6 0.20
22 13 0.43
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (21 bp):
TGCATCGATACACCTTAAATG
Found at i:21865 original size:21 final size:20
Alignment explanation
Indices: 21798--21865 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 20
21788 TTTGTGCTTC
*
21798 ATGCATCGATACACCT-AAC
1 ATGCATCGATACACCTGAAG
*
21817 ATTGCATCGATGCATCCTTGAATG
1 A-TGCATCGATACA-CC-TGAA-G
21841 -TGCATCGATACACCATGAAG
1 ATGCATCGATACACC-TGAAG
21861 ATGCA
1 ATGCA
21866 CTGATGCTCG
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
19 1 0.03
20 12 0.31
21 12 0.31
22 12 0.31
23 2 0.05
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATGCATCGATACACCTGAAG
Found at i:21894 original size:23 final size:22
Alignment explanation
Indices: 21819--21895 Score: 63
Period size: 23 Copynumber: 3.5 Consensus size: 22
21809 CACCTAACAT
21819 TGCATCGATGCAT-CCTTGAATG
1 TGCATCGATGC-TCCCTTGAATG
* * *
21841 TGCATCGATAC-ACCATGAA-G
1 TGCATCGATGCTCCCTTGAATG
21861 ATGCA-CTGATGCTCGCCTTGAATG
1 -TGCATC-GATGCTC-CCTTGAATG
21885 TGCATCGATGC
1 TGCATCGATGC
21896 ACAAGGCCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 13
0.70 0.08 0.21
Matches are distributed among these distances:
20 2 0.05
21 14 0.33
22 10 0.23
23 15 0.35
24 2 0.05
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (22 bp):
TGCATCGATGCTCCCTTGAATG
Found at i:24579 original size:20 final size:20
Alignment explanation
Indices: 24554--24592 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
24544 TTTTCAAGGG
24554 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
* *
24574 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
24593 TAATTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:24661 original size:45 final size:46
Alignment explanation
Indices: 24612--24702 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 46
24602 GAACATCGAA
* * * *
24612 TGCATTTTATGCATCGATGCAC-ATACCATGCATTGATGCACTCAG
1 TGCATTTGATGCATCAATGCACAAAACCATGCATCGATGCACTCAG
* *
24657 TGCATTTGATGCATCAATGCACAAAACTATGCATCGGTGCACTCAG
1 TGCATTTGATGCATCAATGCACAAAACCATGCATCGATGCACTCAG
24703 GCTTTTTCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
45 20 0.51
46 19 0.49
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (46 bp):
TGCATTTGATGCATCAATGCACAAAACCATGCATCGATGCACTCAG
Found at i:24677 original size:17 final size:17
Alignment explanation
Indices: 24620--24677 Score: 55
Period size: 19 Copynumber: 3.3 Consensus size: 17
24610 AATGCATTTT
* *
24620 ATGCATCGATGCACATACC
1 ATGCATTGATGCAC-T-CA
24639 ATGCATTGATGCACTCA
1 ATGCATTGATGCACTCA
*
24656 GTGCATTTGATGCA-TCA
1 ATGCA-TTGATGCACTCA
24673 ATGCA
1 ATGCA
24678 CAAAACTATG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
17 12 0.35
18 9 0.26
19 13 0.38
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (17 bp):
ATGCATTGATGCACTCA
Found at i:27012 original size:14 final size:14
Alignment explanation
Indices: 26989--27019 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
26979 AGGGCTTATC
*
26989 AAATCGAAATAAAT
1 AAATCAAAATAAAT
27003 AAATCAAAATAAAT
1 AAATCAAAATAAAT
27017 AAA
1 AAA
27020 GAAATAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.19
Consensus pattern (14 bp):
AAATCAAAATAAAT
Found at i:27018 original size:18 final size:17
Alignment explanation
Indices: 26995--27028 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
26985 TATCAAATCG
*
26995 AAATAAATAAATCAAAAT
1 AAATAAAGAAAT-AAAAT
27013 AAATAAAGAAATAAAA
1 AAATAAAGAAATAAAA
27029 CTTACCTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (17 bp):
AAATAAAGAAATAAAAT
Found at i:33869 original size:14 final size:14
Alignment explanation
Indices: 33847--33885 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
33837 TAATATTGTA
*
33847 AATATATATTAAAT
1 AATAAATATTAAAT
*
33861 AATAAATATTATAT
1 AATAAATATTAAAT
33875 AATGAAATATT
1 AAT-AAATATT
33886 TACAAAAGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (14 bp):
AATAAATATTAAAT
Found at i:34150 original size:22 final size:22
Alignment explanation
Indices: 34125--34166 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
34115 AACAATATTA
*
34125 TTTCTACCGGTTTTATTATTTT
1 TTTCTACCAGTTTTATTATTTT
*
34147 TTTCTACCAGTTTTGTTATT
1 TTTCTACCAGTTTTATTATT
34167 GTTTGACACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.14, G:0.10, T:0.62
Consensus pattern (22 bp):
TTTCTACCAGTTTTATTATTTT
Found at i:34278 original size:12 final size:12
Alignment explanation
Indices: 34261--34286 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
34251 TTATTTAAAT
34261 GATAACAAAACC
1 GATAACAAAACC
34273 GATAACAAAACC
1 GATAACAAAACC
34285 GA
1 GA
34287 CAACGTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.23, G:0.12, T:0.08
Consensus pattern (12 bp):
GATAACAAAACC
Found at i:37644 original size:11 final size:11
Alignment explanation
Indices: 37616--37645 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
37606 GAAAGTATCA
37616 TCATTTTTAAC
1 TCATTTTTAAC
37627 TCAATTTTTAAC
1 TC-ATTTTTAAC
37639 TCATTTT
1 TCATTTT
37646 GAACAAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.27, C:0.17, G:0.00, T:0.57
Consensus pattern (11 bp):
TCATTTTTAAC
Found at i:40243 original size:24 final size:24
Alignment explanation
Indices: 40209--40269 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
40199 TCTGACATGG
* **
40209 ATTATGATTTGATACCTGGCCTGA
1 ATTATGTTTTGATACCTGAACTGA
* *
40233 ATTCTGTTTTGATATCTGAACTGA
1 ATTATGTTTTGATACCTGAACTGA
40257 ATTATGTTTTGAT
1 ATTATGTTTTGAT
40270 TTTTTATATA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.25, C:0.11, G:0.18, T:0.46
Consensus pattern (24 bp):
ATTATGTTTTGATACCTGAACTGA
Found at i:40386 original size:35 final size:35
Alignment explanation
Indices: 40340--40440 Score: 202
Period size: 35 Copynumber: 2.9 Consensus size: 35
40330 TATACCTGAA
40340 GGCTCCTCGGCTTTGTGCTCAGGGCCTTACTTACT
1 GGCTCCTCGGCTTTGTGCTCAGGGCCTTACTTACT
40375 GGCTCCTCGGCTTTGTGCTCAGGGCCTTACTTACT
1 GGCTCCTCGGCTTTGTGCTCAGGGCCTTACTTACT
40410 GGCTCCTCGGCTTTGTGCTCAGGGCCTTACT
1 GGCTCCTCGGCTTTGTGCTCAGGGCCTTACT
40441 GGACTTGACG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 66 1.00
ACGTcount: A:0.08, C:0.32, G:0.27, T:0.34
Consensus pattern (35 bp):
GGCTCCTCGGCTTTGTGCTCAGGGCCTTACTTACT
Found at i:42423 original size:11 final size:10
Alignment explanation
Indices: 42395--42425 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
42385 CTGTTGGGGT
42395 AGTTTGACCC
1 AGTTTGACCC
42405 AGTTTGACCC
1 AGTTTGACCC
42415 AGTTTTGACCC
1 AG-TTTGACCC
42426 GACCCATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 12 0.60
11 8 0.40
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.32
Consensus pattern (10 bp):
AGTTTGACCC
Found at i:44713 original size:24 final size:24
Alignment explanation
Indices: 44686--44755 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
44676 ATTTCTAACC
*
44686 TGGATTCTGATCTGATACCTGACA
1 TGGATTCTGTTCTGATACCTGACA
* * *
44710 TGGATTCTGTTCTAATACTTGACC
1 TGGATTCTGTTCTGATACCTGACA
* *
44734 TGAATTCTGTTCTGATATCTGA
1 TGGATTCTGTTCTGATACCTGA
44756 ACTGAATTAT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.40
Consensus pattern (24 bp):
TGGATTCTGTTCTGATACCTGACA
Found at i:44760 original size:24 final size:23
Alignment explanation
Indices: 44689--44773 Score: 73
Period size: 24 Copynumber: 3.6 Consensus size: 23
44679 TCTAACCTGG
* *
44689 ATTCTGATCTGATACCTG-ACATGG
1 ATTCTGTTCTGATA-CTGAAC-TGA
* *
44713 ATTCTGTTCTAATACTTGACCTGA
1 ATTCTGTTCTGATAC-TGAACTGA
44737 ATTCTGTTCTGATATCTGAACTGA
1 ATTCTGTTCTGATA-CTGAACTGA
* *
44761 ATTATGTTTTGAT
1 ATTCTGTTCTGAT
44774 TTTTAATATA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
23 1 0.02
24 47 0.94
25 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.42
Consensus pattern (23 bp):
ATTCTGTTCTGATACTGAACTGA
Found at i:46863 original size:20 final size:20
Alignment explanation
Indices: 46840--47010 Score: 130
Period size: 20 Copynumber: 8.4 Consensus size: 20
46830 GTTTCTAGAT
*
46840 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTCTGACTA
** * **
46860 TCGCATTGCGATTTTAGAAAA
1 TCGCAACGCGATTCT-GACTA
* * * *
46881 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTCTG-ACTA
* *
46901 TCGCAACGAGATTCTAACTA
1 TCGCAACGCGATTCTGACTA
**
46921 TCGCAACGCGATAAT-ACATAA
1 TCGCAACGCGATTCTGAC-T-A
*
46942 TCGCAACTCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
*
46962 TCGCAACGTGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
* *
46982 TTGCAACGCGATTCTGACTG
1 TCGCAACGCGATTCTGACTA
47002 TCGCAACGC
1 TCGCAACGC
47011 TGAATTTCAA
Statistics
Matches: 120, Mismatches: 25, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
19 3 0.03
20 85 0.71
21 30 0.25
22 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:46932 original size:61 final size:61
Alignment explanation
Indices: 46840--46994 Score: 152
Period size: 61 Copynumber: 2.5 Consensus size: 61
46830 GTTTCTAGAT
* * ** * *
46840 TCGCAACGCGATTTTGACTATCGCATTGCGATTTTAGAAAATCGCAA-TGCGAATATGTA-AA
1 TCGCAACGAGATTCTGACTATCGCAACGCGATTATACAAAATCGCAACT-CGAATATG-ACAA
* * * * * *
46901 TCGCAACGAGATTCTAACTATCGCAACGCGATAATACATAATCGCAACTCGATTCTGACTA
1 TCGCAACGAGATTCTGACTATCGCAACGCGATTATACAAAATCGCAACTCGAATATGACAA
* *
46962 TCGCAACGTGATTCTGACTATTGCAACGCGATT
1 TCGCAACGAGATTCTGACTATCGCAACGCGATT
46995 CTGACTGTCG
Statistics
Matches: 76, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
60 1 0.01
61 74 0.97
62 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.28
Consensus pattern (61 bp):
TCGCAACGAGATTCTGACTATCGCAACGCGATTATACAAAATCGCAACTCGAATATGACAA
Found at i:50176 original size:18 final size:17
Alignment explanation
Indices: 50145--50178 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
50135 AGAAAAAGGC
*
50145 AATCAAATCGCAATCAA
1 AATCAAATCCCAATCAA
50162 AATCAAAATCCCAATCA
1 AATC-AAATCCCAATCA
50179 CAACCGGCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.53, C:0.26, G:0.03, T:0.18
Consensus pattern (17 bp):
AATCAAATCCCAATCAA
Found at i:50490 original size:140 final size:140
Alignment explanation
Indices: 50238--50507 Score: 513
Period size: 140 Copynumber: 1.9 Consensus size: 140
50228 AAACGTTGTA
*
50238 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCTTGTATTAGTAACTTGAGCTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGCTTGAACATTGCTA
*
50303 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
50368 TATGTGTATT
131 TATGTGTATT
*
50378 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGCTTGAACATTGCTA
50443 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
50508 CTCAACGCGA
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 127 1.00
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGCTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:50503 original size:20 final size:20
Alignment explanation
Indices: 50478--50628 Score: 179
Period size: 20 Copynumber: 7.8 Consensus size: 20
50468 TTACACATTC
*
50478 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
50498 ATTTGACTATCTCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
50518 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
50538 ATTTGACTATCACAA--CGA
1 ATTTGACTATCGCAACGCGA
** *
50556 A----AAAATCGTAACGCGA
1 ATTTGACTATCGCAACGCGA
50572 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
50592 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
50612 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
50629 AGAAAATTGC
Statistics
Matches: 110, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
14 6 0.05
16 4 0.04
18 4 0.04
20 96 0.87
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:50614 original size:74 final size:74
Alignment explanation
Indices: 50486--50677 Score: 251
Period size: 74 Copynumber: 2.6 Consensus size: 74
50476 TCATTTGAAT
*
50486 ATCGCAACGCGAATTTGACTATCTCAACGCGAATTTGACTATCGCAACACGAATTTGACTATCAC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACACGAATTTGACTATCAC
50551 AACGAAAAA
66 AACGAAAAA
* * ** *
50560 ATCGTAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGGAATTTGACTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACACGAATTTGACTATCAC
*
50625 AACGAGAAA
66 AACGAAAAA
* * ** * * *
50634 ATTGCAAAGCTTATTAGACTATCGCAACACGAA-TTGACTTTCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGC
50678 GTTGCGATTT
Statistics
Matches: 102, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
73 9 0.09
74 93 0.91
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (74 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACACGAATTTGACTATCAC
AACGAAAAA
Found at i:50692 original size:20 final size:20
Alignment explanation
Indices: 50667--50744 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
50657 GCAACACGAA
*
50667 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCATTGCGATT
50687 TTGACTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
*
50707 TTGACTTTCACATTGCGATT
1 TTGACTTTCGCATTGCGATT
* * *
50727 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCATTGCGA
50745 AAGTGTACCT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.15, C:0.18, G:0.23, T:0.44
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:50914 original size:67 final size:67
Alignment explanation
Indices: 50796--50964 Score: 177
Period size: 67 Copynumber: 2.5 Consensus size: 67
50786 GATTGAAATC
*
50796 AACAAATCAACTTTTACATTTCAATCAATTAAACAAGCACAAATAAG-A-ATTATTTAC-ACATC
1 AACAAATCAACTTTTACA--T-AATCAATTAAACAAGCAAAAATAAGAATATTATTTACGACATC
50858 AATTA
63 AATTA
* * *
50863 AACAAATCAACTTTTACA-AATCAATTAAACAAGCAAAAAATACTAATAATTATTATTTTCGTCA
1 AACAAATCAACTTTTACATAATCAATTAAACAAGC--AAAA-A-TAAGAA-TATTATTTACGACA
50927 TCAATTA
61 TCAATTA
*
50934 AACAAATCAGACTTTTA-AGAATCAATTAAAC
1 AACAAATCA-ACTTTTACATAATCAATTAAAC
50965 GTTCAAAAAA
Statistics
Matches: 88, Mismatches: 4, Indels: 15
0.82 0.04 0.14
Matches are distributed among these distances:
63 16 0.18
65 3 0.03
66 1 0.01
67 21 0.24
68 1 0.01
70 8 0.09
71 19 0.22
72 19 0.22
ACGTcount: A:0.50, C:0.17, G:0.04, T:0.30
Consensus pattern (67 bp):
AACAAATCAACTTTTACATAATCAATTAAACAAGCAAAAATAAGAATATTATTTACGACATCAAT
TA
Found at i:52295 original size:21 final size:21
Alignment explanation
Indices: 52241--52359 Score: 87
Period size: 21 Copynumber: 5.7 Consensus size: 21
52231 TTGAATCGGG
* * *
52241 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAATGATGAGAGGGGC
* * *
52262 CTCTTCAACGATGACAGGGGC
1 CTCTTGAATGATGAGAGGGGC
* * *
52283 CTCTTGAATGATGGGATGGGA
1 CTCTTGAATGATGAGAGGGGC
** * *
52304 CTCTTGAGGGATGATAGGGTC
1 CTCTTGAATGATGAGAGGGGC
* *
52325 CTCTTGAACGAT-AGGAGAGGC
1 CTCTTGAATGATGA-GAGGGGC
52346 CTCTTGAATGATGA
1 CTCTTGAATGATGA
52360 CAGGTGAGTC
Statistics
Matches: 71, Mismatches: 25, Indels: 3
0.72 0.25 0.03
Matches are distributed among these distances:
20 1 0.01
21 69 0.97
22 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.25
Consensus pattern (21 bp):
CTCTTGAATGATGAGAGGGGC
Found at i:52308 original size:42 final size:41
Alignment explanation
Indices: 52241--52363 Score: 129
Period size: 42 Copynumber: 2.9 Consensus size: 41
52231 TTGAATCGGG
* *
52241 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
1 CTCTTGAATGATGGGAGGGA-CTCTTGAACGATGACAGGGGC
** * *
52283 CTCTTGAATGATGGGATGGGACTCTTGAGGGATGATAGGGTC
1 CTCTTGAATGATGGGA-GGGACTCTTGAACGATGACAGGGGC
* * * *
52325 CTCTTGAACGATAGGAGAGGCCTCTTGAATGATGACAGG
1 CTCTTGAATGATGGGAG-GGACTCTTGAACGATGACAGG
52364 TGAGTCGGGC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 1 0.01
42 62 0.93
43 4 0.06
ACGTcount: A:0.24, C:0.17, G:0.35, T:0.24
Consensus pattern (41 bp):
CTCTTGAATGATGGGAGGGACTCTTGAACGATGACAGGGGC
Found at i:52864 original size:20 final size:20
Alignment explanation
Indices: 52839--52901 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
52829 AATAGTTTCT
52839 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
*
52859 GAAACTTAAAATCGCAACGC
1 GAAACTTAAAATCGCAACAC
* * **
52879 GAAAATGACTATCGCAACAC
1 GAAACTTAAAATCGCAACAC
52899 GAA
1 GAA
52902 TTTGACTATC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.48, C:0.24, G:0.14, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:52907 original size:20 final size:20
Alignment explanation
Indices: 52849--52917 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
52839 GAAACTTAAA
* * **
52849 ATCGCAACACGAAACTTAAA
1 ATCGCAACACGAAAATGACT
*
52869 ATCGCAACGCGAAAATGACT
1 ATCGCAACACGAAAATGACT
**
52889 ATCGCAACACGAATTTGACT
1 ATCGCAACACGAAAATGACT
52909 ATCGCAACA
1 ATCGCAACA
52918 AGATAATCGC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.42, C:0.26, G:0.14, T:0.17
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:52946 original size:19 final size:20
Alignment explanation
Indices: 52922--52960 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
52912 GCAACAAGAT
*
52922 AATCGCAATGCGAAA-TAAA
1 AATCGCAACGCGAAACTAAA
52941 AATCGCAACGCGAAACTAAA
1 AATCGCAACGCGAAACTAAA
52961 TTCGCGTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.51, C:0.21, G:0.15, T:0.13
Consensus pattern (20 bp):
AATCGCAACGCGAAACTAAA
Found at i:53043 original size:20 final size:20
Alignment explanation
Indices: 52998--53063 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
52988 GCGATTATCC
*
52998 CGTTGCGATAGTCAAATT-CG
1 CGTTGCGATAGTC-ATTTCCG
*
53018 CTTTGCGATAGAT-ATTTCCG
1 CGTTGCGATAG-TCATTTCCG
*
53038 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
53058 CGTTGC
1 CGTTGC
53064 AATTTTTGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 4 0.10
20 34 0.87
21 1 0.03
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:54987 original size:20 final size:20
Alignment explanation
Indices: 54964--55014 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
54954 TCTGAAACTT
54964 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
54984 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
**
55004 ACTATCGCAAC
1 AAAATCGCAAC
55015 GCAAATTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.51, C:0.24, G:0.14, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:55444 original size:20 final size:21
Alignment explanation
Indices: 55419--55467 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
55409 TCTGAGAGAT
55419 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
*
55439 GGAGATGGGGACGGATTTCGCC
1 GGAGAT-GAGACGGATTTCGCC
*
55461 AGAGATG
1 GGAGATG
55468 GGGATGGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.24
21 1 0.04
22 18 0.72
ACGTcount: A:0.24, C:0.16, G:0.41, T:0.18
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:55453 original size:22 final size:22
Alignment explanation
Indices: 55426--55476 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
55416 GATGGAGATA
*
55426 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
55448 GACGGATTTCGCCAGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
*
55470 GATGGAT
1 GACGGAT
55477 GTCGTCGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:55673 original size:20 final size:20
Alignment explanation
Indices: 55650--55694 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
55640 TTATCGCAAC
55650 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
55670 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
55690 GCGAT
1 GCGAT
55695 TTTCTAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (20 bp):
GCGATAGTCAGAATCGCGTT
Found at i:63991 original size:64 final size:63
Alignment explanation
Indices: 63918--64101 Score: 217
Period size: 64 Copynumber: 2.9 Consensus size: 63
63908 ACTCTTTTAA
* * * **
63918 AATAA-AAACATTGAATGTAATTCATGCATCGATGCATAAGTAGTGCATCAATGCATCCCATT
1 AATAATAAACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGC
** *
63980 AATAATGAAACATCGAATGCAATTGGTGCATCGATGCATAAGGAGTGCATCGATGCATCCCAGC
1 AATAAT-AAACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGC
* ** * * *
64044 AATAATAATACATCGAATACCTTTTATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 AATAATAA-ACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCAT
64102 ACCTTCATTA
Statistics
Matches: 103, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
62 5 0.05
63 2 0.02
64 96 0.93
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (63 bp):
AATAATAAACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGC
Found at i:64427 original size:12 final size:12
Alignment explanation
Indices: 64409--64444 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
64399 TATATATGTT
64409 CATGTGATATGA
1 CATGTGATATGA
*
64421 TATGTGATATGA
1 CATGTGATATGA
64433 CATGTGATATGA
1 CATGTGATATGA
64445 GAACATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:64466 original size:23 final size:26
Alignment explanation
Indices: 64409--64477 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
64399 TATATATGTT
**
64409 CATGTGATAT--GATATGTGATATGA
1 CATGTGATATGAGATACATGATATGA
64433 CATGTGATATGAGA-ACATGATATGA
1 CATGTGATATGAGATACATGATATGA
64458 -A-GTGATATGAGATACATGAT
1 CATGTGATATGAGATACATGAT
64478 CACAAGAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 18 0.45
25 9 0.22
26 2 0.05
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.32
Consensus pattern (26 bp):
CATGTGATATGAGATACATGATATGA
Done.