Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001578.1 Hibiscus syriacus cultivar Beakdansim tig00003141_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: 104457
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:17 original size:12 final size:12
Alignment explanation
Indices: 1--76 Score: 73
Period size: 12 Copynumber: 6.3 Consensus size: 12
*
1 AAAAAAAT-TAA
1 AAAAAAATAAAA
*
12 AAAAAACTAAAA
1 AAAAAAATAAAA
24 AAAAAAATAAAA
1 AAAAAAATAAAA
* *
36 AAAAAAATATAT
1 AAAAAAATAAAA
* * *
48 ATATAAACAAAA
1 AAAAAAATAAAA
60 AAAAAAATATAAA
1 AAAAAAATA-AAA
73 AAAA
1 AAAA
77 CATATATTAT
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
11 7 0.14
12 36 0.72
13 7 0.14
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAAATAAAA
Found at i:60 original size:36 final size:36
Alignment explanation
Indices: 15--88 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 36
5 AAATTAAAAA
15 AAACTAAAAAAAAAAATAAAAAAAAAAATATATATAT
1 AAACTAAAAAAAAAAATAAAAAAAAAAATATAT-TAT
* *
52 AAAC-AAAAAAAAAAATATAAAAAAACATATATTAT
1 AAACTAAAAAAAAAAATAAAAAAAAAAATATATTAT
87 AA
1 AA
89 TATTTTTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 5 0.14
36 26 0.74
37 4 0.11
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (36 bp):
AAACTAAAAAAAAAAATAAAAAAAAAAATATATTAT
Found at i:76 original size:14 final size:13
Alignment explanation
Indices: 10--42 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1 AAAAAAATT
*
10 AAAAAAAACT-AA
1 AAAAAAAAATAAA
22 AAAAAAAAATAAA
1 AAAAAAAAATAAA
35 AAAAAAAA
1 AAAAAAAA
43 TATATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.91, C:0.03, G:0.00, T:0.06
Consensus pattern (13 bp):
AAAAAAAAATAAA
Found at i:5544 original size:24 final size:24
Alignment explanation
Indices: 5512--5557 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
5502 CCAACACAGC
*
5512 AAGCCCAACACTAAGCCCAAATAG
1 AAGCCCAACACCAAGCCCAAATAG
5536 AAGCCCAACACCAAGCCCAAAT
1 AAGCCCAACACCAAGCCCAAAT
5558 CCAGCCCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.37, G:0.11, T:0.07
Consensus pattern (24 bp):
AAGCCCAACACCAAGCCCAAATAG
Found at i:9761 original size:21 final size:21
Alignment explanation
Indices: 9719--9771 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
9709 ATTCTGACTA
9719 TCGCATTGCGATTTCACAAAT
1 TCGCATTGCGATTTCACAAAT
* *
9740 TCGCGTTGCGATTTTC-CTAAT
1 TCGCATTGCGA-TTTCACAAAT
*
9761 TCGCAATGCGA
1 TCGCATTGCGA
9772 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCACAAAT
Found at i:9786 original size:20 final size:20
Alignment explanation
Indices: 9761--9895 Score: 198
Period size: 20 Copynumber: 6.7 Consensus size: 20
9751 TTTTCCTAAT
9761 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
9781 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
9801 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
*
9821 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
9841 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
9862 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
9882 TCGCAATGTGAATA
1 TCGCAATGCGAATA
9896 TGACTATCGC
Statistics
Matches: 104, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
20 86 0.83
21 18 0.17
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:10499 original size:33 final size:33
Alignment explanation
Indices: 10441--10533 Score: 114
Period size: 33 Copynumber: 2.8 Consensus size: 33
10431 CGAGAATGAA
* **
10441 AATCGCAACGTGGAAATGACTATCGCAACGAGAG
1 AATCGCAACG-CGAAATGAAAATCGCAACGAGAG
*
10475 AATCGCAACGCGAAATGAAAATCGCAACGAGAT
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
* **
10508 AATCGCAACTCGAAACCAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
10534 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
33 42 0.81
34 10 0.19
ACGTcount: A:0.43, C:0.24, G:0.20, T:0.13
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:10618 original size:20 final size:19
Alignment explanation
Indices: 10529--10641 Score: 110
Period size: 19 Copynumber: 6.1 Consensus size: 19
10519 GAAACCAAAA
*
10529 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
10548 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
10567 TCGCGTTACGA--TT-A--
1 TCGCGTTGCGATTTTCATT
* **
10581 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
10600 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
* *
10620 CTCTCGTTGTGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
10640 TC
1 TC
10642 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
14 9 0.12
16 2 0.03
17 3 0.04
19 31 0.40
20 31 0.40
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:12515 original size:94 final size:93
Alignment explanation
Indices: 12328--12703 Score: 609
Period size: 94 Copynumber: 4.1 Consensus size: 93
12318 TAGATTGCTT
* *
12328 AGTAAATTTATTCGGTTGCTGCTAATACTGCTAAAC----TATT-TATTAACACTGTGAAGTTAG
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCT-TTAACACTGTGAAGTTAG
12388 TATTTGTCTTTTGTTTTGTCTTTTGGTTGA
65 TATTTGTC-TTTGTTTTGTCTTTTGGTTGA
12418 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
12483 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* *
12512 AGTAAATTTGTTCGGTTGCTGCCAATTCTGATAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
12577 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * *
12606 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
12671 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
12699 AGTAA
1 AGTAA
12704 TGCAATCCAT
Statistics
Matches: 272, Mismatches: 8, Indels: 9
0.94 0.03 0.03
Matches are distributed among these distances:
90 34 0.12
93 26 0.10
94 211 0.78
95 1 0.00
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:12838 original size:19 final size:19
Alignment explanation
Indices: 12792--12867 Score: 116
Period size: 19 Copynumber: 3.9 Consensus size: 19
12782 TCTTTTGGAT
* * *
12792 GAAATAAAAATCGTAACGA
1 GAAATGAAAATCGCAACGC
12811 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
12831 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
12850 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
12868 ACAAAATCGC
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
19 37 0.70
20 16 0.30
ACGTcount: A:0.50, C:0.17, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:12863 original size:38 final size:39
Alignment explanation
Indices: 12792--12867 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
12782 TCTTTTGGAT
*
12792 GAAATAAAAATCGTAACGAGAGAATGAAAATCGCAACGC
1 GAAATAAAAATCGCAACGAGAGAATGAAAATCGCAACGC
* *
12831 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAACG
1 GAAATAAAAATCGCAACGAGAGAATGAAAATCGCAACG
12868 ACAAAATCGC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 16 0.47
39 18 0.53
ACGTcount: A:0.50, C:0.17, G:0.21, T:0.12
Consensus pattern (39 bp):
GAAATAAAAATCGCAACGAGAGAATGAAAATCGCAACGC
Found at i:12918 original size:20 final size:19
Alignment explanation
Indices: 12893--12940 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
12883 GAAACTATAA
**
12893 TCGCGTTGCAATTTTTGGTT
1 TCGCGTTGCAA-TTTTCATT
*
12913 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCAATTTTCATT
12932 TCGCGTTGC
1 TCGCGTTGC
12941 GATTCTCTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.08, C:0.21, G:0.25, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCAATTTTCATT
Found at i:12933 original size:19 final size:19
Alignment explanation
Indices: 12911--12999 Score: 80
Period size: 19 Copynumber: 4.9 Consensus size: 19
12901 CAATTTTTGG
12911 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
12930 TTTCGCGTTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
*
12946 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* ** *
12963 TTTCGCATTGCGATAGTCTT
1 TTTCGCGTTGCGATTTTC-A
*
12983 TTTCACGTTGCGATTTT
1 TTTCGCGTTGCGATTTT
13000 AAGTTCCATT
Statistics
Matches: 54, Mismatches: 10, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
14 10 0.19
16 3 0.06
17 3 0.06
19 25 0.46
20 13 0.24
ACGTcount: A:0.11, C:0.21, G:0.20, T:0.47
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:13469 original size:21 final size:21
Alignment explanation
Indices: 13445--13511 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
13435 TCATTCCTCG
13445 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
13466 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
13487 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
13508 AGAG
1 AGAG
13512 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:13469 original size:42 final size:42
Alignment explanation
Indices: 13393--13511 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
13383 GACTCGCCTG
* * * * * * *
13393 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
13435 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
13477 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
13512 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:15044 original size:19 final size:19
Alignment explanation
Indices: 15022--15139 Score: 85
Period size: 19 Copynumber: 6.7 Consensus size: 19
15012 CGAAACTAAA
*
15022 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
15041 TTCGCTTTGCGA--TTC--
1 TTCGCATTGCGATTTTCAT
* *
15056 -CCTCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
15074 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
15090 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
**
15107 TTCGCATTGCGATAGTCAT
1 TTCGCATTGCGATTTTCAT
*
15126 TTCCGCGTTGCGAT
1 TT-CGCATTGCGAT
15140 AGACATTAAG
Statistics
Matches: 77, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
14 14 0.18
16 10 0.13
17 10 0.13
19 33 0.43
20 10 0.13
ACGTcount: A:0.13, C:0.25, G:0.19, T:0.43
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:15070 original size:33 final size:33
Alignment explanation
Indices: 15028--15119 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
15018 TAAATTCGCG
*
15028 TTGCGATTTTCATTTCGCTTTGCGATTCCCTCA
1 TTGCGATTTTCATTTCGCATTGCGATTCCCTCA
* *
15061 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCCCTCA
15094 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
15120 AGTCATTTCC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.13, C:0.24, G:0.17, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCCCTCA
Found at i:15138 original size:20 final size:20
Alignment explanation
Indices: 15092--15185 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
15082 GCGATTCTCT
**
15092 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
15111 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
15131 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
15150 ATGATTGCGA-ACGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
15172 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
15186 AATGATGCCT
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
19 17 0.29
20 26 0.45
21 12 0.21
22 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:17464 original size:15 final size:14
Alignment explanation
Indices: 17428--17466 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
17418 CTCCCGTGGC
17428 ATTTTTCTTCGGGG
1 ATTTTTCTTCGGGG
* *
17442 ACTTTTCTTTGGGG
1 ATTTTTCTTCGGGG
17456 ATTTCTTCTTC
1 ATTT-TTCTTC
17467 TTCTTTTTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.08, C:0.18, G:0.21, T:0.54
Consensus pattern (14 bp):
ATTTTTCTTCGGGG
Found at i:17690 original size:24 final size:24
Alignment explanation
Indices: 17656--17709 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
17646 CTGAAAAATC
17656 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
17680 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
17704 ATCAAA
1 ATCAAA
17710 TTTCGAATAC
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:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:17723 original size:24 final size:24
Alignment explanation
Indices: 17656--17723 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
17646 CTGAAAAATC
* * *
17656 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
17680 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
17704 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
17724 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:18629 original size:21 final size:21
Alignment explanation
Indices: 18585--18824 Score: 294
Period size: 21 Copynumber: 11.7 Consensus size: 21
18575 GCGATTTACT
* *
18585 AAATCGCAATGCG-ATTACGT
1 AAATCGCAATGCGAATTAGGA
18605 AAATCG-AAGTGCGAATTAGGA
1 AAATCGCAA-TGCGAATTAGGA
*
18626 AAATCGCAATGCGAATTAGTA
1 AAATCGCAATGCGAATTAGGA
*
18647 AAATCGCAATGCGAATTAGAA
1 AAATCGCAATGCGAATTAGGA
*
18668 AAATCGCAATGCGAATTAGAA
1 AAATCGCAATGCGAATTAGGA
* * *
18689 AAATCGCAATACG-ATTACGT
1 AAATCGCAATGCGAATTAGGA
* *
18709 AAATCGCAATGCG-ATTACGT
1 AAATCGCAATGCGAATTAGGA
* *
18729 AAATCGCAATGCG-ATTACGT
1 AAATCGCAATGCGAATTAGGA
18749 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGA
* *
18770 AAATCGCAATGCG-ATTACGT
1 AAATCGCAATGCGAATTAGGA
*
18790 AAATCGTAATGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGA
18811 AAATCGCAATGCGA
1 AAATCGCAATGCGA
18825 TAGTCAGAAT
Statistics
Matches: 198, Mismatches: 17, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
19 2 0.01
20 83 0.42
21 111 0.56
22 2 0.01
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (21 bp):
AAATCGCAATGCGAATTAGGA
Found at i:18853 original size:41 final size:41
Alignment explanation
Indices: 18574--18825 Score: 325
Period size: 41 Copynumber: 6.1 Consensus size: 41
18564 AAAATCTCGT
* *
18574 TGCGATTTAC-TAAATCGCAATGCG-ATTACGTAAATCG-AA
1 TGCGA-TTACGTAAATCGCAATGCGAATTAGGAAAATCGCAA
* * *
18613 GTGCGAATTAGGAAAATCGCAATGCGAATTAGTAAAATCGCAA
1 -TGCG-ATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAA
* *
18656 TGCGAATTA-GAAAAATCGCAATGCGAATTAGAAAAATCGCAA
1 TGCG-ATTACG-TAAATCGCAATGCGAATTAGGAAAATCGCAA
* * *
18698 TACGATTACGTAAATCGCAATGCG-ATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAA
18738 TGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAA
*
18779 TGCGATTACGTAAATCGTAATGCGAATTAGGAAAATCGCAA
1 TGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAA
18820 TGCGAT
1 TGCGAT
18826 AGTCAGAATC
Statistics
Matches: 190, Mismatches: 15, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
40 43 0.23
41 92 0.48
42 53 0.28
43 2 0.01
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (41 bp):
TGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAA
Found at i:19250 original size:14 final size:14
Alignment explanation
Indices: 19232--19300 Score: 71
Period size: 14 Copynumber: 5.4 Consensus size: 14
19222 CAAAGGGCTC
*
19232 GTTCGTTCATTTAC
1 GTTCGTTCATTTAT
19246 GTTCG---ATTATAT
1 GTTCGTTCATT-TAT
19258 GTTCGTTCATTTA-
1 GTTCGTTCATTTAT
19271 --T-GTTCATTTAT
1 GTTCGTTCATTTAT
19282 GTTCGTTCATTTAT
1 GTTCGTTCATTTAT
19296 GTTCG
1 GTTCG
19301 AACGGAGGGC
Statistics
Matches: 46, Mismatches: 1, Indels: 16
0.73 0.02 0.25
Matches are distributed among these distances:
10 9 0.20
11 4 0.09
12 7 0.15
13 1 0.02
14 22 0.48
15 3 0.07
ACGTcount: A:0.16, C:0.14, G:0.16, T:0.54
Consensus pattern (14 bp):
GTTCGTTCATTTAT
Found at i:19287 original size:24 final size:26
Alignment explanation
Indices: 19232--19301 Score: 117
Period size: 24 Copynumber: 2.8 Consensus size: 26
19222 CAAAGGGCTC
*
19232 GTTCGTTCATTTACGTTCGATTATAT
1 GTTCGTTCATTTATGTTCGATTATAT
19258 GTTCGTTCATTTATGTTC-ATT-TAT
1 GTTCGTTCATTTATGTTCGATTATAT
19282 GTTCGTTCATTTATGTTCGA
1 GTTCGTTCATTTATGTTCGA
19302 ACGGAGGGCA
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
24 21 0.50
25 4 0.10
26 17 0.40
ACGTcount: A:0.17, C:0.14, G:0.16, T:0.53
Consensus pattern (26 bp):
GTTCGTTCATTTATGTTCGATTATAT
Found at i:19577 original size:10 final size:10
Alignment explanation
Indices: 19553--19602 Score: 57
Period size: 10 Copynumber: 4.8 Consensus size: 10
19543 TTTTTTTGTG
*
19553 TGTTTGTTT-
1 TGTTCGTTTA
19562 TGTTCGTTTA
1 TGTTCGTTTA
19572 TGTTCGTTTA
1 TGTTCGTTTA
19582 TTGTGTTCGTTTA
1 ---TGTTCGTTTA
19595 TGTTCGTT
1 TGTTCGTT
19603 CGTTAATGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
9 8 0.22
10 18 0.50
13 10 0.28
ACGTcount: A:0.06, C:0.08, G:0.22, T:0.64
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:19580 original size:23 final size:23
Alignment explanation
Indices: 19554--19619 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
19544 TTTTTTGTGT
*
19554 GTTTGTTTTGTTCGTTTATGTTC
1 GTTTGTTATGTTCGTTTATGTTC
* *
19577 GTTTATTGTGTTCGTTTATGTTC
1 GTTTGTTATGTTCGTTTATGTTC
*
19600 GTTCGTTAATGTTCGTTTAT
1 GTTTGTT-ATGTTCGTTTAT
19620 TTATTAAATG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 26 0.70
24 11 0.30
ACGTcount: A:0.09, C:0.09, G:0.21, T:0.61
Consensus pattern (23 bp):
GTTTGTTATGTTCGTTTATGTTC
Found at i:19605 original size:14 final size:14
Alignment explanation
Indices: 19573--19616 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
19563 GTTCGTTTAT
19573 GTTCGTTTAT-TGT-
1 GTTCGTTTATGT-TC
19586 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
*
19600 GTTCGTTAATGTTC
1 GTTCGTTTATGTTC
19614 GTT
1 GTT
19617 TATTTATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 11 0.39
14 17 0.61
ACGTcount: A:0.09, C:0.11, G:0.23, T:0.57
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:27629 original size:33 final size:33
Alignment explanation
Indices: 27565--27663 Score: 130
Period size: 33 Copynumber: 3.1 Consensus size: 33
27555 AAACATGAAA
*
27565 AATAAGTTGGTCACCTACCAA-A-GAATTTTCC
1 AATAAGTTGGTCACCAACCAAGATGAATTTTCC
* *
27596 ATTAAGTTGGCCACCAACCAAGATGAATTTTCC
1 AATAAGTTGGTCACCAACCAAGATGAATTTTCC
* * *
27629 AAAAAGTTGGTCACCAACAAAGATGAAATTTCC
1 AATAAGTTGGTCACCAACCAAGATGAATTTTCC
27662 AA
1 AA
27664 CTTGCCAACT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
31 18 0.31
32 1 0.02
33 39 0.67
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.25
Consensus pattern (33 bp):
AATAAGTTGGTCACCAACCAAGATGAATTTTCC
Found at i:29208 original size:21 final size:21
Alignment explanation
Indices: 29184--29235 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
29174 TTGTAGCGAA
29184 CATCTTTCTTGCTATGAGATC
1 CATCTTTCTTGCTATGAGATC
29205 CATCTTTCTTGCTATGAGATC
1 CATCTTTCTTGCTATGAGATC
29226 CATCTTTCTT
1 CATCTTTCTT
29236 TGCAAATACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.17, C:0.25, G:0.12, T:0.46
Consensus pattern (21 bp):
CATCTTTCTTGCTATGAGATC
Found at i:32343 original size:31 final size:30
Alignment explanation
Indices: 32298--32384 Score: 93
Period size: 33 Copynumber: 2.8 Consensus size: 30
32288 AAACATGAAA
*
32298 AATAAGTTGACCACCTACCAAAGAATTTTCC
1 AATAAGTTGGCCACC-ACCAAAGAATTTTCC
* *
32329 ATTAAGTTGGCCACCAACCAAGATAAATTTTCC
1 AATAAGTTGGCCACC-ACCAA-A-GAATTTTCC
* *
32362 AAAAAGTTGGCCACCAACAAAGA
1 AATAAGTTGGCCACCACCAAAGA
32385 TGAAATTTCC
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
30 1 0.02
31 19 0.41
32 5 0.11
33 21 0.46
ACGTcount: A:0.41, C:0.24, G:0.13, T:0.22
Consensus pattern (30 bp):
AATAAGTTGGCCACCACCAAAGAATTTTCC
Found at i:32369 original size:33 final size:34
Alignment explanation
Indices: 32321--32396 Score: 111
Period size: 33 Copynumber: 2.3 Consensus size: 34
32311 CCTACCAAAG
** *
32321 AATTTTCCATTAAGTTGGCCACCAACCAAGAT-A
1 AATTTTCCAAAAAGTTGGCCACCAACAAAGATGA
32354 AATTTTCCAAAAAGTTGGCCACCAACAAAGATGA
1 AATTTTCCAAAAAGTTGGCCACCAACAAAGATGA
32388 AA-TTTCCAA
1 AATTTTCCAA
32397 CTTGCCAACT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
33 36 0.92
34 3 0.08
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.25
Consensus pattern (34 bp):
AATTTTCCAAAAAGTTGGCCACCAACAAAGATGA
Found at i:33152 original size:15 final size:17
Alignment explanation
Indices: 33127--33158 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
33117 TATTAGTTTA
33127 TTGTCAAAAAT-TTATT
1 TTGTCAAAAATATTATT
33143 TTGT-AAAAATATTATT
1 TTGTCAAAAATATTATT
33159 AATAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (17 bp):
TTGTCAAAAATATTATT
Found at i:36951 original size:2 final size:2
Alignment explanation
Indices: 36879--36931 Score: 85
Period size: 2 Copynumber: 28.0 Consensus size: 2
36869 ACCCAAATTA
36879 AT AT AT AT A- 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
36920 AT -T AT A- AT AT AT
1 AT AT AT AT AT AT AT
36932 TTTTTATTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.06
2 45 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37659 original size:43 final size:43
Alignment explanation
Indices: 37596--37717 Score: 199
Period size: 43 Copynumber: 2.8 Consensus size: 43
37586 TTCAAATGGC
* * *
37596 ACGATATCCTCCATCATGGAGTTGAAATCGTGGATGTGTGGGT
1 ACGATATCCTCCGTCGTGGAGTTGAAATCGCGGATGTGTGGGT
*
37639 ACGATATCCTCCGTCGTGGAGTTGAAATCGCAGATGTGTGGGT
1 ACGATATCCTCCGTCGTGGAGTTGAAATCGCGGATGTGTGGGT
*
37682 ACAATATCCTCCGTCGTGGAGTTGAAATCGCGGATG
1 ACGATATCCTCCGTCGTGGAGTTGAAATCGCGGATG
37718 ACCCATTTGT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 73 1.00
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (43 bp):
ACGATATCCTCCGTCGTGGAGTTGAAATCGCGGATGTGTGGGT
Found at i:40186 original size:202 final size:199
Alignment explanation
Indices: 39794--40194 Score: 775
Period size: 202 Copynumber: 2.0 Consensus size: 199
39784 TGCATGTGCT
39794 CACAAACTCTTCATGTACTTCTTCCACTATCATTTTTGCCTCTTCAACATCGACGCACCTTAACA
1 CACAAACTCTTCATGTACTTCTTCCACTATCATTTTTGCCTCTTCAACATCGACGCACCTTAACA
39859 GGACTGATTATGGCTTTTCTTGTACAAGACCTCCCCGTAAAGGACGTATCCAGCTGCCATCCTTT
66 GGACTGATTATGGCTTTTCTTGTACAAGACCTCCCCGTAAAGGACGTATCCAGCTGCCATCCTTT
39924 AATGGTTCTTTTATCGGTTTCGGTGGCTTGTTCTGGATAACTTCGATGCTTGATGTATTGCAAAA
131 AATGGTTCTTTTATCGGTTTCGGTGGCTTGTTCTGGATAACTTCGATGCTTGATGTATTGCAAAA
39989 TGTC
196 TGTC
39993 CACAAACTCCTTCATGTACTTCTTCCACTATCATTTTTGCCTCTTCAACATCGACGCACCTTAAC
1 CACAAACT-CTTCATGTACTTCTTCCACTATCATTTTTGCCTCTTCAACATCGACGCACCTTAAC
40058 AGGACTTGATTATGGCTTTTCTTGTACAAGACCTCCCCGTAAAGGACGTATCCAGCTGCCATCCT
65 AGGAC-TGATTATGGCTTTTCTTGTACAAGACCTCCCCGTAAAGGACGTATCCAGCTGCCATCCT
40123 TCTAATGGTTCTTTTATCGGTTTCGGTGGCTTGTTCTGGATAACTTCGATGCTTGATGTATTGCA
129 T-TAATGGTTCTTTTATCGGTTTCGGTGGCTTGTTCTGGATAACTTCGATGCTTGATGTATTGCA
40188 AAATGTC
193 AAATGTC
40195 GCAGTACCAA
Statistics
Matches: 199, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
199 8 0.04
200 61 0.31
201 60 0.30
202 70 0.35
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (199 bp):
CACAAACTCTTCATGTACTTCTTCCACTATCATTTTTGCCTCTTCAACATCGACGCACCTTAACA
GGACTGATTATGGCTTTTCTTGTACAAGACCTCCCCGTAAAGGACGTATCCAGCTGCCATCCTTT
AATGGTTCTTTTATCGGTTTCGGTGGCTTGTTCTGGATAACTTCGATGCTTGATGTATTGCAAAA
TGTC
Found at i:41842 original size:21 final size:21
Alignment explanation
Indices: 41816--41865 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
41806 TGGAATTATG
41816 TTGGCCACCCATTCCGGATAC
1 TTGGCCACCCATTCCGGATAC
41837 TTGGCCACCCATTCCGGATAC
1 TTGGCCACCCATTCCGGATAC
41858 TTGGCCAC
1 TTGGCCAC
41866 TTAAAGGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.38, G:0.20, T:0.24
Consensus pattern (21 bp):
TTGGCCACCCATTCCGGATAC
Found at i:58106 original size:15 final size:16
Alignment explanation
Indices: 58078--58109 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
58068 AAAATCTTTC
58078 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
58094 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
58109 T
1 T
58110 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:58884 original size:16 final size:16
Alignment explanation
Indices: 58860--58893 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
58850 TATCGCCGAC
*
58860 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
58876 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
58892 CG
1 CG
58894 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:61029 original size:29 final size:29
Alignment explanation
Indices: 60987--61073 Score: 113
Period size: 29 Copynumber: 3.0 Consensus size: 29
60977 GTCCCAGGGG
*
60987 TAGGTCGCCATGCACGCCCGGCGACCTAC
1 TAGGTCGCCATGCACGCCCAGCGACCTAC
* **
61016 TAGGTCGCCATGCACGCCCAGTGACCTGG
1 TAGGTCGCCATGCACGCCCAGCGACCTAC
*
61045 TAGGTCGCCATGCATG-CCATGCGACCTAC
1 TAGGTCGCCATGCACGCCCA-GCGACCTAC
61074 CAGCACCTCC
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
28 3 0.06
29 46 0.94
ACGTcount: A:0.18, C:0.37, G:0.28, T:0.17
Consensus pattern (29 bp):
TAGGTCGCCATGCACGCCCAGCGACCTAC
Found at i:61089 original size:10 final size:10
Alignment explanation
Indices: 61082--61134 Score: 65
Period size: 10 Copynumber: 5.3 Consensus size: 10
61072 ACCAGCACCT
61082 CCATGCACGC
1 CCATGCACGC
61092 CCATGCACGC
1 CCATGCACGC
*
61102 CCA-ACGAC-C
1 CCATGC-ACGC
61111 TCCATGCACGC
1 -CCATGCACGC
61122 CCATGCACGC
1 CCATGCACGC
61132 CCA
1 CCA
61135 ACGAGCTACT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 2 0.05
10 33 0.89
11 2 0.05
ACGTcount: A:0.23, C:0.51, G:0.17, T:0.09
Consensus pattern (10 bp):
CCATGCACGC
Found at i:61098 original size:40 final size:40
Alignment explanation
Indices: 61066--61292 Score: 164
Period size: 40 Copynumber: 5.5 Consensus size: 40
61056 GCATGCCATG
61066 CGACCTACCA-GCAC-CTCCATGCACGCCCATGCACGCCCAA
1 CGACCT-CCATGCACGC-CCATGCACGCCCATGCACGCCCAA
** *
61106 CGACCTCCATGCACGCCCATGCACGCCCA---ACGAGCTA
1 CGACCTCCATGCACGCCCATGCACGCCCATGCACGCCCAA
** * * **
61143 CTAGGTCGCCATGCACGCCCA-GCGACCTGGTAGGTCGCCATGCATGCCCTG
1 C--GACCTCCATGCACGCCCATGC-A-C------G-C-CCATGCACGCCCAA
61194 CGACCTACCA-GCAC-CTCCATGCACGCCCATGCACGCCCAA
1 CGACCT-CCATGCACGC-CCATGCACGCCCATGCACGCCCAA
*
61234 CGACCTCCATGCACGCCCATGCACGCCCAGGCACGCCCAA
1 CGACCTCCATGCACGCCCATGCACGCCCATGCACGCCCAA
61274 CGACCTCCATGCACGCCCA
1 CGACCTCCATGCACGCCCA
61293 ACGACCTCCA
Statistics
Matches: 148, Mismatches: 17, Indels: 44
0.71 0.08 0.21
Matches are distributed among these distances:
37 6 0.04
38 2 0.01
39 22 0.15
40 87 0.59
41 3 0.02
42 1 0.01
46 1 0.01
47 1 0.01
48 5 0.03
49 10 0.07
50 5 0.03
51 5 0.03
ACGTcount: A:0.22, C:0.47, G:0.20, T:0.11
Consensus pattern (40 bp):
CGACCTCCATGCACGCCCATGCACGCCCATGCACGCCCAA
Found at i:61112 original size:30 final size:30
Alignment explanation
Indices: 61078--61312 Score: 169
Period size: 30 Copynumber: 7.6 Consensus size: 30
61068 ACCTACCAGC
61078 ACCTCCATGCACGCCCATGCACGCCCAACG
1 ACCTCCATGCACGCCCATGCACGCCCAACG
61108 ACCTCCATGCACGCCCATGCACGCCCAACG
1 ACCTCCATGCACGCCCATGCACGCCCAACG
* * ** *
61138 AGCTAC-TAGGTCG-CCATGCACGCCCAGCG
1 ACCTCCAT-GCACGCCCATGCACGCCCAACG
** ** * *
61167 ACCT-GGTAGGTCGCCATGCATGCCCTGCGACCTACCAG
1 ACCTCCAT-GCACGCC---CATGCAC-GC--CC-AAC-G
61205 CACCTCCATGCACGCCCATGCACGCCCAACG
1 -ACCTCCATGCACGCCCATGCACGCCCAACG
*
61236 ACCTCCATGCACGCCCATGCACGCCC-AGG
1 ACCTCCATGCACGCCCATGCACGCCCAACG
*
61265 CACGC-CCA-ACGAC-CTCCATGCACGCCCAACG
1 -AC-CTCCATGC-ACGC-CCATGCACGCCCAACG
61296 ACCTCCATGCACGCCCA
1 ACCTCCATGCACGCCCA
61313 GCTCGCCAAA
Statistics
Matches: 165, Mismatches: 19, Indels: 42
0.73 0.08 0.19
Matches are distributed among these distances:
29 31 0.19
30 93 0.56
31 6 0.04
32 2 0.01
33 8 0.05
34 2 0.01
35 2 0.01
36 8 0.05
37 2 0.01
38 1 0.01
39 9 0.05
40 1 0.01
ACGTcount: A:0.22, C:0.47, G:0.20, T:0.11
Consensus pattern (30 bp):
ACCTCCATGCACGCCCATGCACGCCCAACG
Found at i:61176 original size:29 final size:29
Alignment explanation
Indices: 61122--61201 Score: 106
Period size: 29 Copynumber: 2.8 Consensus size: 29
61112 CCATGCACGC
* *
61122 CCATGCACGCCCAACGAGCTACTAGGTCG
1 CCATGCACGCCCAGCGACCTACTAGGTCG
**
61151 CCATGCACGCCCAGCGACCTGGTAGGTCG
1 CCATGCACGCCCAGCGACCTACTAGGTCG
* *
61180 CCATGCATGCCCTGCGACCTAC
1 CCATGCACGCCCAGCGACCTAC
61202 CAGCACCTCC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.20, C:0.40, G:0.25, T:0.15
Consensus pattern (29 bp):
CCATGCACGCCCAGCGACCTACTAGGTCG
Found at i:61217 original size:10 final size:10
Alignment explanation
Indices: 61210--61272 Score: 76
Period size: 10 Copynumber: 6.3 Consensus size: 10
61200 ACCAGCACCT
61210 CCATGCACGC
1 CCATGCACGC
61220 CCATGCACGC
1 CCATGCACGC
*
61230 CCA-ACGAC-C
1 CCATGC-ACGC
61239 TCCATGCACGC
1 -CCATGCACGC
61250 CCATGCACGC
1 CCATGCACGC
*
61260 CCAGGCACGC
1 CCATGCACGC
61270 CCA
1 CCA
61273 ACGACCTCCA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
9 2 0.04
10 42 0.91
11 2 0.04
ACGTcount: A:0.22, C:0.51, G:0.19, T:0.08
Consensus pattern (10 bp):
CCATGCACGC
Found at i:61222 original size:128 final size:128
Alignment explanation
Indices: 60994--61262 Score: 493
Period size: 128 Copynumber: 2.1 Consensus size: 128
60984 GGGTAGGTCG
** *
60994 CCATGCACGCCCGGCGACCTACTAGGTCGCCATGCACGCCCAGTGACCTGGTAGGTCGCCATGCA
1 CCATGCACGCCCAACGACCTACTAGGTCGCCATGCACGCCCAGCGACCTGGTAGGTCGCCATGCA
61059 TGCCATGCGACCTACCAGCACCTCCATGCACGCCCATGCACGCCCAACGACCTCCATGCACGC
66 TGCCATGCGACCTACCAGCACCTCCATGCACGCCCATGCACGCCCAACGACCTCCATGCACGC
*
61122 CCATGCACGCCCAACGAGCTACTAGGTCGCCATGCACGCCCAGCGACCTGGTAGGTCGCCATGCA
1 CCATGCACGCCCAACGACCTACTAGGTCGCCATGCACGCCCAGCGACCTGGTAGGTCGCCATGCA
*
61187 TGCCCTGCGACCTACCAGCACCTCCATGCACGCCCATGCACGCCCAACGACCTCCATGCACGC
66 TGCCATGCGACCTACCAGCACCTCCATGCACGCCCATGCACGCCCAACGACCTCCATGCACGC
61250 CCATGCACGCCCA
1 CCATGCACGCCCA
61263 GGCACGCCCA
Statistics
Matches: 136, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 136 1.00
ACGTcount: A:0.21, C:0.44, G:0.22, T:0.13
Consensus pattern (128 bp):
CCATGCACGCCCAACGACCTACTAGGTCGCCATGCACGCCCAGCGACCTGGTAGGTCGCCATGCA
TGCCATGCGACCTACCAGCACCTCCATGCACGCCCATGCACGCCCAACGACCTCCATGCACGC
Found at i:61243 original size:20 final size:20
Alignment explanation
Indices: 61220--61312 Score: 136
Period size: 20 Copynumber: 4.7 Consensus size: 20
61210 CCATGCACGC
61220 CCATGCACGCCCAACGACCT
1 CCATGCACGCCCAACGACCT
*
61240 CCATGCACGCCC-ATGCACGC-
1 CCATGCACGCCCAACG-AC-CT
*
61260 CCAGGCACGCCCAACGACCT
1 CCATGCACGCCCAACGACCT
61280 CCATGCACGCCCAACGACCT
1 CCATGCACGCCCAACGACCT
61300 CCATGCACGCCCA
1 CCATGCACGCCCA
61313 GCTCGCCAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
19 3 0.05
20 59 0.91
21 3 0.05
ACGTcount: A:0.24, C:0.51, G:0.17, T:0.09
Consensus pattern (20 bp):
CCATGCACGCCCAACGACCT
Found at i:61308 original size:40 final size:40
Alignment explanation
Indices: 61180--61312 Score: 148
Period size: 40 Copynumber: 3.3 Consensus size: 40
61170 TGGTAGGTCG
* ** *
61180 CCATGCATGCCCTGCGACCTACCA-GCAC-CTCCATGCACGC
1 CCATGCACGCCCAACGACCT-CCATGCACGC-CCACGCACGC
*
61220 CCATGCACGCCCAACGACCTCCATGCACGCCCATGCACGC
1 CCATGCACGCCCAACGACCTCCATGCACGCCCACGCACGC
*
61260 CCAGGCACGCCCAACGACCTCCATGCACGCCCAACG-AC-C
1 CCATGCACGCCCAACGACCTCCATGCACGCCC-ACGCACGC
61299 TCCATGCACGCCCA
1 -CCATGCACGCCCA
61313 GCTCGCCAAA
Statistics
Matches: 83, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
39 4 0.05
40 76 0.92
41 3 0.04
ACGTcount: A:0.23, C:0.50, G:0.17, T:0.11
Consensus pattern (40 bp):
CCATGCACGCCCAACGACCTCCATGCACGCCCACGCACGC
Found at i:61976 original size:21 final size:21
Alignment explanation
Indices: 61951--61994 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
61941 AATTTAGTTA
61951 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
61972 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
61993 AT
1 AT
61995 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:62290 original size:14 final size:14
Alignment explanation
Indices: 62273--62367 Score: 100
Period size: 14 Copynumber: 6.3 Consensus size: 14
62263 TTATTTATAA
62273 TAATGATTTAATAC
1 TAATGATTTAATAC
*
62287 TAATGATTTCATAATTTAG
1 TAATGA-TT--TAA--TAC
62306 TAATGATTTAATAC
1 TAATGATTTAATAC
*
62320 TAATGATTTAATAA
1 TAATGATTTAATAC
*
62334 TAATGATTTAAATATT
1 TAATGATTT-AATA-C
62350 TAATGATTTAATAC
1 TAATGATTTAATAC
62364 TAAT
1 TAAT
62368 AATAATGATT
Statistics
Matches: 69, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
14 34 0.49
15 10 0.14
16 12 0.17
17 3 0.04
18 2 0.03
19 8 0.12
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.45
Consensus pattern (14 bp):
TAATGATTTAATAC
Found at i:62324 original size:47 final size:44
Alignment explanation
Indices: 62265--62367 Score: 138
Period size: 47 Copynumber: 2.3 Consensus size: 44
62255 ATATTAGATT
* *
62265 ATTT-ATAATAATGATTTAATACTAATGATTTCATAAT-TTAGTAATG
1 ATTTAATACTAATGATTTAATAATAATGATTT-A-AATATT--TAATG
62311 ATTTAATACTAATGATTTAATAATAATGATTTAAATATTTAATG
1 ATTTAATACTAATGATTTAATAATAATGATTTAAATATTTAATG
62355 ATTTAATACTAAT
1 ATTTAATACTAAT
62368 AATAATGATT
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
44 18 0.34
45 3 0.06
46 7 0.13
47 25 0.47
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (44 bp):
ATTTAATACTAATGATTTAATAATAATGATTTAAATATTTAATG
Found at i:62351 original size:36 final size:36
Alignment explanation
Indices: 62273--62378 Score: 98
Period size: 33 Copynumber: 3.0 Consensus size: 36
62263 TTATTTATAA
* * *
62273 TAATGATTTAATACTAATGATTTCATAAT--TTA-G
1 TAATGATTTAATACTAATGATTTAATAATAATGATT
62306 TAATGATTTAATACTAATGATTTAATAATAATGATT
1 TAATGATTTAATACTAATGATTTAATAATAATGATT
* *
62342 TAAAT-ATTTAATGATTTAAT-A-CTAATAATAATGATT
1 T-AATGATTTAAT-A-CTAATGATTTAATAATAATGATT
62378 T
1 T
62379 GATACTAAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
33 28 0.45
35 2 0.03
36 23 0.37
37 5 0.08
38 4 0.06
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (36 bp):
TAATGATTTAATACTAATGATTTAATAATAATGATT
Found at i:62375 original size:20 final size:20
Alignment explanation
Indices: 62328--62386 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
62318 ACTAATGATT
62328 TAATAATAATGATTTAA-A-
1 TAATAATAATGATTTAATAC
*
62346 T-AT-TTAATGATTTAATAC
1 TAATAATAATGATTTAATAC
*
62364 TAATAATAATGATTTGATAC
1 TAATAATAATGATTTAATAC
62384 TAA
1 TAA
62387 AAATCATTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 11 0.32
17 3 0.09
18 2 0.06
19 2 0.06
20 16 0.47
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (20 bp):
TAATAATAATGATTTAATAC
Found at i:64553 original size:15 final size:14
Alignment explanation
Indices: 64528--64558 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
64518 TTCAACACAA
64528 AACTTTAATATAAT
1 AACTTTAATATAAT
64542 AACTTATAATATAAT
1 AACTT-TAATATAAT
64557 AA
1 AA
64559 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:64566 original size:16 final size:16
Alignment explanation
Indices: 64533--64579 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
64523 CACAAAACTT
*
64533 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
64548 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
64564 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
64580 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:64694 original size:32 final size:33
Alignment explanation
Indices: 64620--64700 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 33
64610 CCAAACCCTT
*
64620 AAAC-AACTAATAAAATATTTTTTATATAACTA
1 AAACTAACTAATAAACTATTTTTTATATAACTA
64652 AAACTAACTAATAAACTATTTTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTTTTT-A-TATAACTA
*
64685 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
64701 TACTAACTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
32 15 0.34
33 22 0.50
34 2 0.05
35 5 0.11
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.38
Consensus pattern (33 bp):
AAACTAACTAATAAACTATTTTTTATATAACTA
Found at i:64830 original size:45 final size:48
Alignment explanation
Indices: 64740--64830 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 48
64730 CAACAAACAA
64740 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTT
1 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTT
*
64788 ATATAAC-TAACTA-TTAAC-AA-AACAAACTAATT-AATTATTTTTT
1 ATATAACTTAACTATTTAACTAACAA-AAACTAATTAAATAATTTTTT
64831 AACTATATAA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
44 12 0.29
45 11 0.27
46 5 0.12
47 6 0.15
48 7 0.17
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (48 bp):
ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTT
Found at i:64899 original size:41 final size:40
Alignment explanation
Indices: 64811--64899 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
64801 TTAACAAAAC
* *
64811 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
64852 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
64893 AAACTAA
1 AAACTAA
64900 CTAACAATCA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 29 0.74
42 5 0.13
43 5 0.13
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (40 bp):
AAACTAATTAAATAATTTTTAACTATATAACTATAAACAT
Found at i:64968 original size:16 final size:18
Alignment explanation
Indices: 64939--64977 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
64929 ACTAATTAAC
*
64939 ATTTATAATAATAAACTA
1 ATTTATAATAATAAACAA
64957 ATTTA-AAT-ATAAACAA
1 ATTTATAATAATAAACAA
64973 ATTTA
1 ATTTA
64978 CCTTATCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTATAATAATAAACAA
Found at i:65329 original size:29 final size:29
Alignment explanation
Indices: 65287--65352 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
65277 GTGACGCCGG
**
65287 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCCAGACTACAT
*
65316 GGCGACCTACAAGGTCGCCCAGACTGCAT
1 GGCGACCTACAAGGTCGCCCAGACTACAT
65345 GGCGACCT
1 GGCGACCT
65353 CTCCATTGGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.23, C:0.33, G:0.30, T:0.14
Consensus pattern (29 bp):
GGCGACCTACAAGGTCGCCCAGACTACAT
Found at i:65380 original size:32 final size:32
Alignment explanation
Indices: 65339--65420 Score: 164
Period size: 32 Copynumber: 2.6 Consensus size: 32
65329 GTCGCCCAGA
65339 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
65371 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
65403 CTGCATGGCGACCTCTCC
1 CTGCATGGCGACCTCTCC
65421 TCGTATAATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.10, C:0.37, G:0.27, T:0.27
Consensus pattern (32 bp):
CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
Found at i:65556 original size:29 final size:29
Alignment explanation
Indices: 65511--65571 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
65501 CGTATGGTAT
65511 ATCGCCTGGATTACATGGCGTCCTACAAG
1 ATCGCCTGGATTACATGGCGTCCTACAAG
* *
65540 ATCGCCTGGATTGCATGGCGTCCTACGAG
1 ATCGCCTGGATTACATGGCGTCCTACAAG
65569 ATC
1 ATC
65572 ACTGTAGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (29 bp):
ATCGCCTGGATTACATGGCGTCCTACAAG
Found at i:69972 original size:21 final size:22
Alignment explanation
Indices: 69932--70002 Score: 108
Period size: 22 Copynumber: 3.3 Consensus size: 22
69922 AATTTGGAAA
69932 ATCGCAACAACAACTGTAGACT
1 ATCGCAACAACAACTGTAGACT
* **
69954 ATCGCAACGA-ATTTGTAGACT
1 ATCGCAACAACAACTGTAGACT
69975 ATCGCAACAACAACTGTAGACT
1 ATCGCAACAACAACTGTAGACT
69997 ATCGCA
1 ATCGCA
70003 TCCATATCGC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 18 0.43
22 24 0.57
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.21
Consensus pattern (22 bp):
ATCGCAACAACAACTGTAGACT
Found at i:69980 original size:43 final size:41
Alignment explanation
Indices: 69910--70002 Score: 141
Period size: 43 Copynumber: 2.2 Consensus size: 41
69900 TTTTTTTTTA
*
69910 ACTATCACAACGAATTTGGAAAATCGCAACAACAACTGTAG
1 ACTATCGCAACGAATTTGGAAAATCGCAACAACAACTGTAG
**
69951 ACTATCGCAACGAATTTGTAGACTATCGCAACAACAACTGTAG
1 ACTATCGCAACGAATTTG--GAAAATCGCAACAACAACTGTAG
69994 ACTATCGCA
1 ACTATCGCA
70003 TCCATATCGC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 17 0.36
43 30 0.64
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.22
Consensus pattern (41 bp):
ACTATCGCAACGAATTTGGAAAATCGCAACAACAACTGTAG
Found at i:70096 original size:21 final size:21
Alignment explanation
Indices: 70007--70099 Score: 89
Period size: 21 Copynumber: 4.5 Consensus size: 21
69997 ATCGCATCCA
70007 TATCGCAACGCGATTTTCAAC
1 TATCGCAACGCGATTTTCAAC
* * *
70028 TGTTGCAGCGCGATTTTCAAC
1 TATCGCAACGCGATTTTCAAC
* * ** **
70049 TGTCGCAACACGAAATGGAA-
1 TATCGCAACGCGATTTTCAAC
*
70069 AATCGCAACGCGATTTTCAAC
1 TATCGCAACGCGATTTTCAAC
70090 TATCGCAACG
1 TATCGCAACG
70100 TAAAATGCAA
Statistics
Matches: 53, Mismatches: 18, Indels: 2
0.73 0.25 0.03
Matches are distributed among these distances:
20 13 0.25
21 40 0.75
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (21 bp):
TATCGCAACGCGATTTTCAAC
Found at i:75713 original size:2 final size:2
Alignment explanation
Indices: 75706--75735 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
75696 CATAAATTTA
75706 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
75736 AAATAAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:76552 original size:35 final size:35
Alignment explanation
Indices: 76513--76580 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
76503 CCTCAATTTT
*
76513 ATTTTAAACCGAAAATTCTAAAACAATTCAATTAC
1 ATTTTAAACCCAAAATTCTAAAACAATTCAATTAC
* * *
76548 ATTTTGAACCCTAAATTCTAAAATAATTCAATT
1 ATTTTAAACCCAAAATTCTAAAACAATTCAATT
76581 TAGGGTTTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.35
Consensus pattern (35 bp):
ATTTTAAACCCAAAATTCTAAAACAATTCAATTAC
Found at i:79070 original size:21 final size:19
Alignment explanation
Indices: 79042--79087 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
79032 TCATTGAATC
79042 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
79062 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
79081 ACTTAGT
1 A-TTAGT
79088 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:80659 original size:21 final size:21
Alignment explanation
Indices: 80633--80672 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
80623 CTTGCAGGAA
80633 TTCATGGCCTCGACAAAAGAT
1 TTCATGGCCTCGACAAAAGAT
* *
80654 TTCATGGCGTCTACAAAAG
1 TTCATGGCCTCGACAAAAG
80673 CCTTGATGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (21 bp):
TTCATGGCCTCGACAAAAGAT
Found at i:88188 original size:21 final size:21
Alignment explanation
Indices: 88162--88202 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
88152 TTTTTCCTTT
88162 AGGGGGGAATCAATACCCCCC
1 AGGGGGGAATCAATACCCCCC
*
88183 AGGGGGGAATCGATACCCCC
1 AGGGGGGAATCAATACCCCC
88203 TGGACATACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.32, G:0.32, T:0.10
Consensus pattern (21 bp):
AGGGGGGAATCAATACCCCCC
Found at i:94298 original size:15 final size:15
Alignment explanation
Indices: 94278--94327 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
94268 CCGTAGGACC
94278 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
*
94293 ACTACGTCCCAAAGG
1 ACTACGTCCCGAAGG
*
94308 ACTACATCCCGAAGG
1 ACTACGTCCCGAAGG
94323 ACTAC
1 ACTAC
94328 AATACCCTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.32, C:0.34, G:0.20, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:97444 original size:22 final size:20
Alignment explanation
Indices: 97410--97456 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 20
97400 GTCACTAATT
97410 AAATAAAAAT-AAAAATAAA
1 AAATAAAAATAAAAAATAAA
97429 AGAATAAGAAGATAAAAAATAAA
1 A-AATAA-AA-ATAAAAAATAAA
97452 AAATA
1 AAATA
97457 TTGAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.04
20 5 0.21
21 2 0.08
22 6 0.25
23 10 0.42
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (20 bp):
AAATAAAAATAAAAAATAAA
Found at i:97452 original size:7 final size:7
Alignment explanation
Indices: 97410--97456 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
97400 GTCACTAATT
97410 AAAT-AA
1 AAATAAA
97416 AAAT-AA
1 AAATAAA
97422 AAATAAA
1 AAATAAA
97429 AGAATAAGA
1 A-AATAA-A
*
97438 AGATAAA
1 AAATAAA
97445 AAATAAA
1 AAATAAA
97452 AAATA
1 AAATA
97457 TTGAAAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
6 10 0.28
7 15 0.42
8 9 0.25
9 2 0.06
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (7 bp):
AAATAAA
Done.