Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004357.1 Hibiscus syriacus cultivar Beakdansim tig00009545_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: 84337
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:667 original size:22 final size:22
Alignment explanation
Indices: 639--691 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
629 ACACACATTC
639 CATCTTACGTGTGGGGAATGCA
1 CATCTTACGTGTGGGGAATGCA
661 CATCTTACGTGTGGGGAATGCA
1 CATCTTACGTGTGGGGAATGCA
*
683 C-TATTACGT
1 CATCTTACGT
692 TGTAGGATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 7 0.23
22 23 0.77
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (22 bp):
CATCTTACGTGTGGGGAATGCA
Found at i:3575 original size:21 final size:21
Alignment explanation
Indices: 3549--3593 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3539 TGATTTCTGG
* *
3549 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
3570 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
3591 CAA
1 CAA
3594 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:4621 original size:31 final size:31
Alignment explanation
Indices: 4574--4756 Score: 277
Period size: 31 Copynumber: 6.0 Consensus size: 31
4564 GGTCGAGGGT
4574 TTTACCTAT-TTCTTCGGGACATATGGACTG
1 TTTACCTATGTTCTTCGGGACATATGGACTG
4604 TTTACCTATGTTCTTC-GGACATATGGACTG
1 TTTACCTATGTTCTTCGGGACATATGGACTG
**
4634 TTTACCTATGTTCTTTAGGACATATGGACTG
1 TTTACCTATGTTCTTCGGGACATATGGACTG
*
4665 TTTACCTATGTTATTCGGGACATATGGACTG
1 TTTACCTATGTTCTTCGGGACATATGGACTG
4696 TTTACCTATGTTCTTCGGGACATATGGAC--
1 TTTACCTATGTTCTTCGGGACATATGGACTG
* *
4725 TTTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTTACCTATGTTCTTCGGGA-CATATGGACTG
4756 T
1 T
4757 CCTTCGGGAC
Statistics
Matches: 141, Mismatches: 7, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
29 25 0.18
30 39 0.28
31 77 0.55
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (31 bp):
TTTACCTATGTTCTTCGGGACATATGGACTG
Found at i:4693 original size:92 final size:90
Alignment explanation
Indices: 4574--4739 Score: 280
Period size: 92 Copynumber: 1.8 Consensus size: 90
4564 GGTCGAGGGT
*
4574 TTTACCTATTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTC-GGACATATGGACTGTTTA
1 TTTACCTATTTATTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGAC--TTTA
*
4638 CCTATGTTCTTTAGGACATATGGACTG
64 CCTAGGTTCTTTAGGACATATGGACTG
4665 TTTACCTATGTTATTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACTTTAC
1 TTTACCTAT-TTATTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACTTTAC
4730 CTAGGTTCTT
65 CTAGGTTCTT
4740 CGGAATCTAT
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
91 23 0.32
92 36 0.51
93 12 0.17
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (90 bp):
TTTACCTATTTATTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACTTTACC
TAGGTTCTTTAGGACATATGGACTG
Found at i:16493 original size:31 final size:31
Alignment explanation
Indices: 16437--16518 Score: 89
Period size: 31 Copynumber: 2.6 Consensus size: 31
16427 TAAAATGTTA
* *
16437 AATTCAAGTATCTAATT-AGATATTAAAAT-G
1 AATTCAAGTATCAAATTGA-ACATTAAAATCG
*
16467 AAAATT-AAGTATCACATTGAACATTAAAATCG
1 --AATTCAAGTATCAAATTGAACATTAAAATCG
16499 AATTCAAGTATCAAATTGAA
1 AATTCAAGTATCAAATTGAA
16519 AAAAAAATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
30 4 0.09
31 33 0.77
32 6 0.14
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.32
Consensus pattern (31 bp):
AATTCAAGTATCAAATTGAACATTAAAATCG
Found at i:21889 original size:42 final size:43
Alignment explanation
Indices: 21834--21962 Score: 156
Period size: 42 Copynumber: 3.0 Consensus size: 43
21824 TATAATGGTG
* *
21834 TTTTGTCTACAAACGCCACTAATTATCTTGTCTTTAGTTA-CGT
1 TTTTG-CTACAAACGCCACTAATTCTCTTGTCTTTAGTTAGCAT
* *
21877 TTTTGCTACAAACGCCGCTAATTCTCTTGTATTTAG-TAGCAT
1 TTTTGCTACAAACGCCACTAATTCTCTTGTCTTTAGTTAGCAT
* * * *
21919 TTTTACCACAAACACCACTAGTTCTCTTGTCTTTAG-TAGCAT
1 TTTTGCTACAAACGCCACTAATTCTCTTGTCTTTAGTTAGCAT
21961 TT
1 TT
21963 GTAATACTAA
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
41 2 0.03
42 68 0.91
43 5 0.07
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.42
Consensus pattern (43 bp):
TTTTGCTACAAACGCCACTAATTCTCTTGTCTTTAGTTAGCAT
Found at i:27548 original size:55 final size:55
Alignment explanation
Indices: 27489--27637 Score: 282
Period size: 55 Copynumber: 2.7 Consensus size: 55
27479 ATATGTTCAC
*
27489 TCCCTATTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTTTGT
1 TCCCTATTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTATGT
27544 TCCCTATTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTATGT
1 TCCCTATTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTATGT
27599 TCCCTATTCTTTCAGAGAGTATGAGACTCGAAC-ATCTTC
1 TCCCTATTCTTTCAGAGAGTATGAGACTCGAACAATCTTC
27638 TTCTTACGGG
Statistics
Matches: 93, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
54 6 0.06
55 87 0.94
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (55 bp):
TCCCTATTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTATGT
Found at i:27667 original size:54 final size:54
Alignment explanation
Indices: 27483--27792 Score: 262
Period size: 55 Copynumber: 5.7 Consensus size: 54
27473 TGGAAAATAT
* * * * *
27483 GTTCACTCCCTATTCTTTCAGAGAGTATGAGACTCGAACAATCTTC-AATAATCGT
1 GTTCGCTCCCTTTTC-TTCAGAGAGTATGAGACTCGAACAATCTTCTTATTA-CGG
* * * * * *
27538 GTTTGTTCCCTATTCTTTCAGAGAGTATGAGACTCGAACAATCTTC-AATAATCGT
1 GTTCGCTCCCTTTTC-TTCAGAGAGTATGAGACTCGAACAATCTTCTTATTA-CGG
* * *
27593 GTAT-GTTCCCTATTCTTTCAGAGAGTATGAGACTCGAAC-ATCTTCTTCTTACGG
1 GT-TCGCTCCCTTTTC-TTCAGAGAGTATGAGACTCGAACAATCTTCTTATTACGG
* * *
27647 GTTCGCTCCCTCTTTCTTCAG-GAAGTAT-AGAACTC-AAAAATCGTCTTCTTACGG
1 GTTCGCTCCCT-TTTCTTCAGAG-AGTATGAG-ACTCGAACAATCTTCTTATTACGG
*
27701 GTTCGCTCCCTCTTTCTTCAGAGAGTAT-AGAACTCGAACAATCTTCTTTTTACGG
1 GTTCGCTCCCT-TTTCTTCAGAGAGTATGAG-ACTCGAACAATCTTCTTATTACGG
* *
27756 GTTCGCTCTCTATTTCTTCAGGGAGTA-GA-ACTCGAAC
1 GTTCGCTCCCT-TTTCTTCAGAGAGTATGAGACTCGAAC
27793 GATAATCTTC
Statistics
Matches: 228, Mismatches: 17, Indels: 22
0.85 0.06 0.08
Matches are distributed among these distances:
53 14 0.06
54 77 0.34
55 136 0.60
56 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.35
Consensus pattern (54 bp):
GTTCGCTCCCTTTTCTTCAGAGAGTATGAGACTCGAACAATCTTCTTATTACGG
Found at i:27831 original size:52 final size:52
Alignment explanation
Indices: 27768--28320 Score: 926
Period size: 52 Copynumber: 10.6 Consensus size: 52
27758 TCGCTCTCTA
* *
27768 TTTCTTCAGGGAGTAGAACTCGAACGATAATCTTCCTACGAGACTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
* * * *
27820 TTTCTTCAGGGACTAAAACTCGAACAATAATCTTCCTACGGGTCTGTCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
27872 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
*
27924 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGTCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
*
27976 TTTCTTCAGGGACTAGAACTAGAACAATAATCTTCCTACGAGACTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
* * *
28028 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCATACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
* * *
28080 TTTCTTCAGGGACTAGAACTCGAAAAATAATCTTCCTACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
* * *
28132 TTTCTTCAAGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
*
28184 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGAATGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
* *
28236 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
28288 TTTCTTCAGGGACTAGAACTCGAACAATAATCT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCT
28321 CCAACGATCG
Statistics
Matches: 473, Mismatches: 28, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 473 1.00
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.28
Consensus pattern (52 bp):
TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
Found at i:27929 original size:24 final size:24
Alignment explanation
Indices: 27902--28034 Score: 59
Period size: 24 Copynumber: 5.2 Consensus size: 24
27892 CGAACAATAA
*
27902 TCTTCCTACGAGACTGCCCAATTT
1 TCTTCCTACGAGACTGACCAATTT
** * * **
27926 TCTTCAGGGACTAGAACTCGAACAATAA
1 TCTTC--CTACGAG-ACT-GACCAATTT
*
27954 TCTTCCTACGAGACTGTCCAATTT
1 TCTTCCTACGAGACTGACCAATTT
** * * **
27978 TCTTCAGGGACTAGAACTAGAACAATAA
1 TCTTC--CTACGAG-ACT-GACCAATTT
*
28006 TCTTCCTACGAGACTGCCCAATTT
1 TCTTCCTACGAGACTGACCAATTT
28030 TCTTC
1 TCTTC
28035 AGGGACTAGA
Statistics
Matches: 73, Mismatches: 28, Indels: 16
0.62 0.24 0.14
Matches are distributed among these distances:
24 25 0.34
25 6 0.08
26 16 0.22
27 6 0.08
28 20 0.27
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (24 bp):
TCTTCCTACGAGACTGACCAATTT
Found at i:28269 original size:28 final size:28
Alignment explanation
Indices: 28186--28270 Score: 79
Period size: 28 Copynumber: 3.2 Consensus size: 28
28176 TGCCCAATTT
28186 TCTTCAGGGACTAGAACTCGAACAATAA
1 TCTTCAGGGACTAGAACTCGAACAATAA
** * ** **
28214 TCTTC--CTACGAGAA-T-GCCCAATTT
1 TCTTCAGGGACTAGAACTCGAACAATAA
28238 TCTTCAGGGACTAGAACTCGAACAATAA
1 TCTTCAGGGACTAGAACTCGAACAATAA
28266 TCTTC
1 TCTTC
28271 CTACGGGTCT
Statistics
Matches: 39, Mismatches: 14, Indels: 8
0.64 0.23 0.13
Matches are distributed among these distances:
24 10 0.26
25 1 0.03
26 12 0.31
27 1 0.03
28 15 0.38
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (28 bp):
TCTTCAGGGACTAGAACTCGAACAATAA
Found at i:28375 original size:55 final size:55
Alignment explanation
Indices: 28316--28704 Score: 606
Period size: 55 Copynumber: 7.1 Consensus size: 55
28306 CTCGAACAAT
*
28316 AATCTCCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * *
28371 AATCTTCAACAATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAATACTCGAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
*
28426 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGA-TC-CAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * * *
28479 AATCTTCATCAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAT
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* *
28534 AATCTTCAACGATCACGTCTGCCCCCTATTTCTTCAGAGAGTATAAGA-TC-CAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * *
28587 AATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAT
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
*
28642 AATCTTCAACGATCGCGTCTGCCCCCCTATTTCTTCAGAGAGTATAAGACTCAAAC
1 AATCTTCAACGATCGCGTCTG-CCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
28698 AATCTTC
1 AATCTTC
28705 TTTGCTTCAC
Statistics
Matches: 301, Mismatches: 28, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
53 93 0.31
54 8 0.03
55 161 0.53
56 39 0.13
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (55 bp):
AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
Found at i:28513 original size:163 final size:163
Alignment explanation
Indices: 28316--28704 Score: 593
Period size: 163 Copynumber: 2.4 Consensus size: 163
28306 CTCGAACAAT
* *
28316 AATCTCCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
1 AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
* * *
28381 AATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAATACTCGAACAATCTTCAACGATCGCGTCT
66 AATCACGTCTGCCCCCTATTTATTCAGAGAGTATAAGA-TC-AACAATCTTCAACAATCGCGTCT
*
28446 GCCCCCTATTTCTTCAGAGAGTATAAGA-TC-CAC
129 GCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * *
28479 AATCTTCATCAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAATAATCTTCAAC
1 AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
* * * *
28544 GATCACGTCTGCCCCCTATTTCTTCAGAGAGTATAAGATCCACAATCTTCATCAATCGCGTCTGC
66 AATCACGTCTGCCCCCTATTTATTCAGAGAGTATAAGATCAACAATCTTCAACAATCGCGTCTGC
*
28609 CCCCTATTTCTTCAGAGAGTATAAGACTCGAAT
131 CCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* *
28642 AATCTTCAACGATCGCGTCTGCCCCCCTATTTCTTCAGAGAGTATAAGACTCAAACAATCTTC
1 AATCTTCAACAATCGCGTCTG-CCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTC
28705 TTTGCTTCAC
Statistics
Matches: 204, Mismatches: 19, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
161 48 0.24
162 4 0.02
163 113 0.55
164 39 0.19
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (163 bp):
AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
AATCACGTCTGCCCCCTATTTATTCAGAGAGTATAAGATCAACAATCTTCAACAATCGCGTCTGC
CCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
Found at i:28530 original size:108 final size:110
Alignment explanation
Indices: 28313--28704 Score: 657
Period size: 108 Copynumber: 3.6 Consensus size: 110
28303 GAACTCGAAC
* *
28313 AATAATCTCCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTC
1 AATAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAAACAATCTTC
* * *
28378 AACAATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAATACTCG
66 ATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCG
* *
28423 AACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGA-TC-CACAATCTTC
1 AATAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAAACAATCTTC
*
28486 ATCAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCG
66 ATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCG
* *
28531 AATAATCTTCAACGATCACGTCTGCCCCCTATTTCTTCAGAGAGTATAAGA-TC-CACAATCTTC
1 AATAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAAACAATCTTC
28594 ATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCG
66 ATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCG
28639 AATAATCTTCAACGATCGCGTCTGCCCCCCTATTTCTTCAGAGAGTATAAGACTCAAACAATCTT
1 AATAATCTTCAACGATCGCGTCTG-CCCCCTATTTCTTCAGAGAGTATAAGACTCAAACAATCTT
28704 C
65 C
28705 TTTGCTTCAC
Statistics
Matches: 267, Mismatches: 12, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
108 178 0.67
109 29 0.11
110 51 0.19
111 9 0.03
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (110 bp):
AATAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAAACAATCTTC
ATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCG
Found at i:30033 original size:9 final size:9
Alignment explanation
Indices: 29975--30105 Score: 79
Period size: 9 Copynumber: 13.7 Consensus size: 9
29965 TGAACCCCCC
29975 TTTTATTTT
1 TTTTATTTT
*
29984 TTTTGGTTTT
1 TTTT-ATTTT
*
29994 TTCTTCTTTT
1 TT-TTATTTT
*
30004 TTCCTTCTTCTT
1 TT--TTATT-TT
30016 TTTTA-TTT
1 TTTTATTTT
30024 TTTTATTTT
1 TTTTATTTT
**
30033 TTCCATTTTT
1 TTTTA-TTTT
30043 ATATTTCATTTT
1 -T-TTT-ATTTT
*
30055 TTTCATTTT
1 TTTTATTTT
30064 TTTTATTTT
1 TTTTATTTT
30073 TTTTCATTTT
1 TTTT-ATTTT
30083 TTTTCA--TT
1 TTTT-ATTTT
*
30091 TTTCATTTT
1 TTTTATTTT
30100 TTTTAT
1 TTTTAT
30106 CTTTAAGCAA
Statistics
Matches: 99, Mismatches: 11, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
7 1 0.01
8 12 0.12
9 35 0.35
10 31 0.31
11 10 0.10
12 9 0.09
13 1 0.01
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.79
Consensus pattern (9 bp):
TTTTATTTT
Found at i:30092 original size:8 final size:8
Alignment explanation
Indices: 30014--30101 Score: 51
Period size: 10 Copynumber: 10.8 Consensus size: 8
30004 TTCCTTCTTC
30014 TTTTTT-A
1 TTTTTTCA
*
30021 TTTTTTTA
1 TTTTTTCA
30029 TTTTTTCCA
1 TTTTTT-CA
30038 -TTTTT-A
1 TTTTTTCA
*
30044 -TATTTCA
1 TTTTTTCA
30051 TTTTTTTCA
1 -TTTTTTCA
*
30060 TTTTTTTTA
1 -TTTTTTCA
30069 TTTTTTTTCA
1 --TTTTTTCA
30079 TTTTTTTTCA
1 --TTTTTTCA
30089 -TTTTTCA
1 TTTTTTCA
30096 TTTTTT
1 TTTTTT
30102 TTATCTTTAA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
6 5 0.07
7 14 0.20
8 17 0.25
9 15 0.22
10 18 0.26
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTCA
Found at i:40135 original size:16 final size:16
Alignment explanation
Indices: 40114--40148 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
40104 CTGATTGGTA
* *
40114 AAAAATATATTAAATT
1 AAAAATAAATTAAAAT
40130 AAAAATAAATTAAAAT
1 AAAAATAAATTAAAAT
40146 AAA
1 AAA
40149 TTAATCGTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAATAAATTAAAAT
Found at i:40140 original size:11 final size:11
Alignment explanation
Indices: 40124--40152 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
40114 AAAAATATAT
40124 TAAATTAAAAA
1 TAAATTAAAAA
40135 TAAATT-AAAA
1 TAAATTAAAAA
40145 TAAATTAA
1 TAAATTAA
40153 TCGTCCAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
TAAATTAAAAA
Found at i:40646 original size:89 final size:89
Alignment explanation
Indices: 40484--40647 Score: 256
Period size: 89 Copynumber: 1.8 Consensus size: 89
40474 AAATTTTAAC
*
40484 TAATTTATAATAATATGTTGAGTTCTTTAGAATTTTAATTTTTATAAATTAAATTAATGGCATTC
1 TAATTTATAATAATACGTTGAGTTCTTTAGAATTTTAATTTTTATAAATTAAATTAATGGCATTC
**
40549 GTCGTTAATGGTTCTCATCGCTGT
66 GTAATTAATGGTTCTCATCGCTGT
* * ** *
40573 TAATTTATAATTATACGTTGAGTTCTTTAGAATTTTAATTTTTATAAGTTAAATTAATGGTGTTG
1 TAATTTATAATAATACGTTGAGTTCTTTAGAATTTTAATTTTTATAAATTAAATTAATGGCATTC
40638 GTAATTAATG
66 GTAATTAATG
40648 ATGTCCATCA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
89 67 1.00
ACGTcount: A:0.32, C:0.06, G:0.14, T:0.48
Consensus pattern (89 bp):
TAATTTATAATAATACGTTGAGTTCTTTAGAATTTTAATTTTTATAAATTAAATTAATGGCATTC
GTAATTAATGGTTCTCATCGCTGT
Found at i:41009 original size:32 final size:32
Alignment explanation
Indices: 40973--41039 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
40963 TTAACTACTG
*
40973 TAAATCTAGAATTACTCCAATAGTTTTATCTA
1 TAAATCTAGAATTACTCCAAGAGTTTTATCTA
41005 TAAATCTAGAATTACTCCAAGAGTTTTATCTA
1 TAAATCTAGAATTACTCCAAGAGTTTTATCTA
41037 TAA
1 TAA
41040 TATTTAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (32 bp):
TAAATCTAGAATTACTCCAAGAGTTTTATCTA
Found at i:43089 original size:27 final size:27
Alignment explanation
Indices: 43039--43092 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
43029 AAAAATATTT
*
43039 TTAAAAAATCCTAAATTTTTCTAAAATA
1 TTAAAAAATCC-AAATTTTCCTAAAATA
43067 TTAAAAAATCC-AATTATTCCTAAAAT
1 TTAAAAAATCCAAATT-TTCCTAAAAT
43093 CTCTTATTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 9 0.38
28 11 0.46
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (27 bp):
TTAAAAAATCCAAATTTTCCTAAAATA
Found at i:45405 original size:22 final size:23
Alignment explanation
Indices: 45366--45420 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
45356 TACCATATAA
*
45366 ATTA-AAAATTATTTGATATGAT-
1 ATTATAAAATTATTGGATAT-ATG
45388 ATTATAAAATTA-TGGATATATG
1 ATTATAAAATTATTGGATATATG
*
45410 ATTTTAAAATT
1 ATTATAAAATT
45421 GCATTTTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 2 0.07
22 20 0.69
23 7 0.24
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (23 bp):
ATTATAAAATTATTGGATATATG
Found at i:46093 original size:14 final size:14
Alignment explanation
Indices: 46071--46109 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
46061 TTGTAAAATG
*
46071 AATTATATTTCTTGAA
1 AATTAT-TTTC-TAAA
46087 AATTATTTTCTAAA
1 AATTATTTTCTAAA
46101 AATTATTTT
1 AATTATTTT
46110 ACGGTGTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.55
15 4 0.18
16 6 0.27
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (14 bp):
AATTATTTTCTAAA
Found at i:46367 original size:22 final size:22
Alignment explanation
Indices: 46339--46435 Score: 76
Period size: 22 Copynumber: 4.5 Consensus size: 22
46329 TTTATTAAAA
*
46339 TAAAATTATATTAATCATTTAT
1 TAAAATTATATTAATAATTTAT
46361 TAAAATTA-A--AATAATTTAT
1 TAAAATTATATTAATAATTTAT
*
46380 TATTAATTATATTAATTAA-TTAT
1 TA-AAATTATATTAA-TAATTTAT
* * * **
46403 TATAATAATATTATTAAAATAT
1 TAAAATTATATTAATAATTTAT
46425 TAAAAATTATA
1 T-AAAATTATA
46436 ATAGTAAAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
19 11 0.18
20 5 0.08
21 5 0.08
22 22 0.36
23 15 0.25
24 3 0.05
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (22 bp):
TAAAATTATATTAATAATTTAT
Found at i:46384 original size:33 final size:36
Alignment explanation
Indices: 46332--46418 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 36
46322 ATTATATTTT
*
46332 ATTAAAATAAAATTA-TATTAATCAT-TT-ATTAA-A
1 ATTAAAAT-AATTTATTATTAATCATATTAATTAATA
* *
46365 ATTAAAATAATTTATTATTAATTATATTAATTAATT
1 ATTAAAATAATTTATTATTAATCATATTAATTAATA
*
46401 ATTATAATAATATTATTA
1 ATTAAAATAAT-TTATTA
46419 AAATATTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
32 5 0.11
33 17 0.38
34 2 0.04
35 5 0.11
36 10 0.22
37 6 0.13
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (36 bp):
ATTAAAATAATTTATTATTAATCATATTAATTAATA
Found at i:46397 original size:13 final size:12
Alignment explanation
Indices: 46372--46419 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
46362 AAAATTAAAA
46372 TAATT-TATTAT
1 TAATTATATTAT
46383 TAATTATATTAAT
1 TAATTATATT-AT
46396 TAA-T-TATTA-
1 TAATTATATTAT
*
46405 TAATAATATTAT
1 TAATTATATTAT
46417 TAA
1 TAA
46420 AATATTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
9 3 0.10
10 1 0.03
11 14 0.45
12 8 0.26
13 5 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TAATTATATTAT
Found at i:46426 original size:42 final size:43
Alignment explanation
Indices: 46330--46427 Score: 103
Period size: 42 Copynumber: 2.3 Consensus size: 43
46320 TAATTATATT
* *
46330 TTATTAAAATA-AAATTATATTAATCATTTATTAAAATTAAAA
1 TTATTAAAATATTAATTATATTAATCAATTATTAAAATTAAAA
* * * * * *
46372 TAATT-TATTATTAATTATATTAATTAATTATTATAA-TAATA
1 TTATTAAAATATTAATTATATTAATCAATTATTAAAATTAAAA
46413 TTATTAAAATATTAA
1 TTATTAAAATATTAA
46428 AAATTATAAT
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
41 11 0.26
42 32 0.74
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (43 bp):
TTATTAAAATATTAATTATATTAATCAATTATTAAAATTAAAA
Found at i:46603 original size:21 final size:21
Alignment explanation
Indices: 46508--46605 Score: 63
Period size: 21 Copynumber: 4.4 Consensus size: 21
46498 ATATTAATTA
*
46508 TATTAATAATTTATTATATATTAT
1 TATTAA-AATATATTAT-TA-TAT
* *
46532 TAAATAAAATTATAATATTATA-
1 T-ATTAAAA-TATATTATTATAT
* * *
46554 TATTATAATAATATAATTATAA
1 TATTAAAAT-ATATTATTATAT
* *
46576 CAATAAAATATATTATTATAT
1 TATTAAAATATATTATTATAT
46597 TATTAAAAT
1 TATTAAAAT
46606 TATCAATAAA
Statistics
Matches: 56, Mismatches: 14, Indels: 11
0.69 0.17 0.14
Matches are distributed among these distances:
20 1 0.02
21 31 0.55
22 7 0.12
23 2 0.04
24 5 0.09
25 10 0.18
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (21 bp):
TATTAAAATATATTATTATAT
Found at i:46617 original size:32 final size:31
Alignment explanation
Indices: 46522--46629 Score: 91
Period size: 35 Copynumber: 3.5 Consensus size: 31
46512 AATAATTTAT
* *
46522 TATATATTATTA-AATAAAATTAT-AAT-AT
1 TATATATTATAATAATAAAATTATCAATAAA
*
46550 TATATATTATAATAATATAATTATAACAATAAAA
1 TATATATTATAATAATAAAATTAT--CAAT-AAA
* *
46584 TATATTATTATATTATTAAAATTATCAATAAA
1 TATA-TATTATAATAATAAAATTATCAATAAA
*
46616 TACA-ATT-TAATAAT
1 TATATATTATAATAAT
46630 CAATATTTTT
Statistics
Matches: 64, Mismatches: 9, Indels: 13
0.74 0.10 0.15
Matches are distributed among these distances:
28 11 0.17
29 15 0.23
30 3 0.05
32 9 0.14
33 4 0.06
34 5 0.08
35 17 0.27
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (31 bp):
TATATATTATAATAATAAAATTATCAATAAA
Found at i:54248 original size:19 final size:19
Alignment explanation
Indices: 54210--54280 Score: 52
Period size: 20 Copynumber: 3.6 Consensus size: 19
54200 ACCAACAAAA
* * *
54210 TCGCAATGCGAACTCTAAT
1 TCGCAACGCGATCTCCAAT
54229 TCGCAACGCGATCTCCAATT
1 TCGCAACGCGATCTCCAA-T
* * * * *
54249 TCTCAACTCAATTTCCAAAA
1 TCGCAACGCGATCTCC-AAT
54269 TCGCAACGCGAT
1 TCGCAACGCGAT
54281 TCTCAAAAAT
Statistics
Matches: 39, Mismatches: 11, Indels: 3
0.74 0.21 0.06
Matches are distributed among these distances:
19 15 0.38
20 22 0.56
21 2 0.05
ACGTcount: A:0.31, C:0.31, G:0.13, T:0.25
Consensus pattern (19 bp):
TCGCAACGCGATCTCCAAT
Found at i:54275 original size:20 final size:21
Alignment explanation
Indices: 54252--54294 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
54242 TCCAATTTCT
* *
54252 CAACTCAATT-TCCAAAATCG
1 CAACGCAATTCTCAAAAATCG
*
54272 CAACGCGATTCTCAAAAATCG
1 CAACGCAATTCTCAAAAATCG
54293 CA
1 CA
54295 TTGCGATAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.40, C:0.30, G:0.09, T:0.21
Consensus pattern (21 bp):
CAACGCAATTCTCAAAAATCG
Found at i:54319 original size:21 final size:21
Alignment explanation
Indices: 54295--54587 Score: 221
Period size: 21 Copynumber: 14.0 Consensus size: 21
54285 AAAAATCGCA
54295 TTGCGATAGTACTGTTCACCG
1 TTGCGATAGTACTGTTCACCG
*
54316 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGTACTGTTCACCG
*
54337 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGTACTGTTCACCG
** *
54358 TTGCGATTTTACAT-TTC-GCG
1 TTGCGATAGTAC-TGTTCACCG
*
54378 TTGCGATAGTCTACAGTGT---CG
1 TTGCGATAG--TACTGT-TCACCG
** *
54399 TTGCGATTTTCCAT-TTCA-CG
1 TTGCGATAGTAC-TGTTCACCG
*
54419 TTGCGATAGTGTACAGTGT---CG
1 TTGCGATA--GTACTGT-TCACCG
** **** *
54440 TTGCGATTCTCAAAAATC-GCG
1 TTGCGATAGT-ACTGTTCACCG
* *
54461 TTGCGATAGCACTGTTCATCG
1 TTGCGATAGTACTGTTCACCG
*
54482 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGTACTGTTCACCG
54503 TTGCGATAGTACTGTTCACCG
1 TTGCGATAGTACTGTTCACCG
*
54524 TTGCGCTAGTACTGTTCACCG
1 TTGCGATAGTACTGTTCACCG
*
54545 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGTACTGTTCACCG
*
54566 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGTACTGTTCACCG
54587 T
1 T
54588 ATATATTTTG
Statistics
Matches: 222, Mismatches: 34, Indels: 32
0.77 0.12 0.11
Matches are distributed among these distances:
18 1 0.00
19 5 0.02
20 23 0.10
21 183 0.82
22 8 0.04
23 2 0.01
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.33
Consensus pattern (21 bp):
TTGCGATAGTACTGTTCACCG
Found at i:54381 original size:20 final size:20
Alignment explanation
Indices: 54356--54425 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
54346 CACTGTTCAC
54356 CGTTGCGATTTTACATTTCG
1 CGTTGCGATTTTACATTTCG
* *
54376 CGTTGCGATAGTCTACA-GT-G
1 CGTTGCGAT--TTTACATTTCG
* *
54396 TCGTTGCGATTTTCCATTTCA
1 -CGTTGCGATTTTACATTTCG
54417 CGTTGCGAT
1 CGTTGCGAT
54426 AGTGTACAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
19 4 0.10
20 20 0.51
21 10 0.26
22 5 0.13
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTACATTTCG
Found at i:54401 original size:41 final size:41
Alignment explanation
Indices: 54356--54447 Score: 157
Period size: 41 Copynumber: 2.2 Consensus size: 41
54346 CACTGTTCAC
*
54356 CGTTGCGATTTTACATTTCGCGTTGCGATAGTCTACAGTGT
1 CGTTGCGATTTTACATTTCACGTTGCGATAGTCTACAGTGT
* *
54397 CGTTGCGATTTTCCATTTCACGTTGCGATAGTGTACAGTGT
1 CGTTGCGATTTTACATTTCACGTTGCGATAGTCTACAGTGT
54438 CGTTGCGATT
1 CGTTGCGATT
54448 CTCAAAAATC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTTACATTTCACGTTGCGATAGTCTACAGTGT
Found at i:55216 original size:21 final size:21
Alignment explanation
Indices: 55189--55276 Score: 131
Period size: 21 Copynumber: 4.1 Consensus size: 21
55179 CAAAATATAT
*
55189 ACGGTGAACAGTGCTATTGCA
1 ACGGTGAACAGTGCTATCGCA
* * *
55210 ACTGTGAATAGTGCTATCGTA
1 ACGGTGAACAGTGCTATCGCA
55231 ACGGTGAACAGTGCTTATCGCA
1 ACGGTGAACAGTGC-TATCGCA
55253 ACGGTGAACAGTGCTATCGCA
1 ACGGTGAACAGTGCTATCGCA
55274 ACG
1 ACG
55277 CGATTTTTGA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
21 39 0.66
22 20 0.34
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.24
Consensus pattern (21 bp):
ACGGTGAACAGTGCTATCGCA
Found at i:55266 original size:43 final size:42
Alignment explanation
Indices: 55189--55276 Score: 131
Period size: 43 Copynumber: 2.1 Consensus size: 42
55179 CAAAATATAT
* * * *
55189 ACGGTGAACAGTGCTATTGCAACTGTGAATAGTGCTATCGTA
1 ACGGTGAACAGTGCTATCGCAACGGTGAACAGTGCTATCGCA
55231 ACGGTGAACAGTGCTTATCGCAACGGTGAACAGTGCTATCGCA
1 ACGGTGAACAGTGC-TATCGCAACGGTGAACAGTGCTATCGCA
55274 ACG
1 ACG
55277 CGATTTTTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 14 0.34
43 27 0.66
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.24
Consensus pattern (42 bp):
ACGGTGAACAGTGCTATCGCAACGGTGAACAGTGCTATCGCA
Found at i:55339 original size:41 final size:41
Alignment explanation
Indices: 55288--55379 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 41
55278 GATTTTTGAG
* * *
55288 AATCACAACGACACTGTACACTATTGCAACGTAAAATGGAA
1 AATCGCAACGACACTGTACACTATCGCAACGCAAAATGGAA
* * * *
55329 AATCGCAACGATACTGTAGACTATCGCAACGCGAAATGTAA
1 AATCGCAACGACACTGTACACTATCGCAACGCAAAATGGAA
55370 AATCGCAACG
1 AATCGCAACG
55380 GTGAACAGTG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.18
Consensus pattern (41 bp):
AATCGCAACGACACTGTACACTATCGCAACGCAAAATGGAA
Found at i:55397 original size:21 final size:21
Alignment explanation
Indices: 55371--55440 Score: 131
Period size: 21 Copynumber: 3.3 Consensus size: 21
55361 GAAATGTAAA
55371 ATCGCAACGGTGAACAGTGCT
1 ATCGCAACGGTGAACAGTGCT
55392 ATCGCAACGGTGAACAGTGCT
1 ATCGCAACGGTGAACAGTGCT
*
55413 ATCGCAACGGTGAACAGTACT
1 ATCGCAACGGTGAACAGTGCT
55434 ATCGCAA
1 ATCGCAA
55441 TGCGATTTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (21 bp):
ATCGCAACGGTGAACAGTGCT
Found at i:55483 original size:20 final size:21
Alignment explanation
Indices: 55441--55506 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 21
55431 ACTATCGCAA
* *
55441 TGCGATTTTTGAGAATCGCGT
1 TGCGATTTTGGAGAATCGAGT
*
55462 TGCGATTTTGGA-AATTGAGT
1 TGCGATTTTGGAGAATCGAGT
* ** *
55482 TGAGAAATTGGAG-ATCGCGT
1 TGCGATTTTGGAGAATCGAGT
55502 TGCGA
1 TGCGA
55507 ATTAGAGTTC
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
20 24 0.69
21 11 0.31
ACGTcount: A:0.24, C:0.11, G:0.32, T:0.33
Consensus pattern (21 bp):
TGCGATTTTGGAGAATCGAGT
Found at i:57270 original size:21 final size:21
Alignment explanation
Indices: 57155--57312 Score: 67
Period size: 20 Copynumber: 7.7 Consensus size: 21
57145 GCGAAATAAA
*
57155 AATCGCAACGCGA-TCTCCAG
1 AATCGCAACGCGATTATCCAG
** *
57175 AATCGCAAATC-AGTT-CCCAG
1 AATCGCAACGCGA-TTATCCAG
* **
57195 AATCGTAACGCGATTATGAAG
1 AATCGCAACGCGATTATCCAG
* * *
57216 AATCGCAATGCGATAATACA-
1 AATCGCAACGCGATTATCCAG
* ** *
57236 AATTAGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTATCCAG
* * *
57258 AATCGCAACGCGAATAT-GAA
1 AATCGCAACGCGATTATCCAG
** **
57278 AATCGCAACGCGAACATATA-
1 AATCGCAACGCGATTATCCAG
57298 AATCGCAACGCGATT
1 AATCGCAACGCGATT
57313 CTAACTATCG
Statistics
Matches: 101, Mismatches: 30, Indels: 14
0.70 0.21 0.10
Matches are distributed among these distances:
19 1 0.01
20 55 0.54
21 43 0.43
22 2 0.02
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (21 bp):
AATCGCAACGCGATTATCCAG
Found at i:57283 original size:20 final size:20
Alignment explanation
Indices: 57258--57529 Score: 158
Period size: 20 Copynumber: 13.4 Consensus size: 20
57248 GATTTTCCAG
*
57258 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
57278 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* *
57298 AATCGCAACGCG-ATTCTAA
1 AATCGCAACGCGAATACGAA
* * * *
57317 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATACG-AA
* * *
57339 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
57359 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * * *
57380 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* * *
57400 AATCGCAATGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* *
57420 AATCGCAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GAA
* *
57440 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * * *
57460 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
57480 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * * *
57501 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
57521 AATCGCAAC
1 AATCGCAAC
57530 ACGATTTTTA
Statistics
Matches: 200, Mismatches: 39, Indels: 26
0.75 0.15 0.10
Matches are distributed among these distances:
19 4 0.02
20 144 0.72
21 50 0.25
22 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:57434 original size:40 final size:41
Alignment explanation
Indices: 57258--57529 Score: 331
Period size: 41 Copynumber: 6.7 Consensus size: 41
57248 GATTTTCCAG
* ** * * *
57258 AATCGCAACGCGAATATGAAAATCGCAACGCG-A-ACATATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA-A
* * *
57298 AATCGCAACGCG-ATTC-TAACTATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGTATCCGTAA--ATCGCAACGAGAATACGTAA
*
57339 AATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAA
* *
57380 AATCGCAATGCGTATCCGTAAATCGCAATGAGAATACGT-A
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAA
*
57420 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGT-A
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAA
* *
57460 AATCGCAATGCGTATCCGTAAATCGCAACGACAATACGTAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAA
*
57501 AATCGCAATGCGTATCCGTAAATCGCAAC
1 AATCGCAACGCGTATCCGTAAATCGCAAC
57530 ACGATTTTTA
Statistics
Matches: 206, Mismatches: 19, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
38 2 0.01
39 2 0.01
40 96 0.47
41 97 0.47
42 6 0.03
43 3 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (41 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAA
Found at i:58093 original size:20 final size:20
Alignment explanation
Indices: 58068--58158 Score: 105
Period size: 20 Copynumber: 4.5 Consensus size: 20
58058 TTCTAAACTT
*
58068 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
58088 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
58108 ACTACCGCAACGA-GAGAAATG
1 AAAATCGCAAC-ACGA-AAATG
*
58129 AAAATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
58148 AAAATCGCAAC
1 AAAATCGCAAC
58159 GAGATAATCG
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
19 16 0.27
20 29 0.48
21 15 0.25
ACGTcount: A:0.51, C:0.21, G:0.18, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:58129 original size:41 final size:40
Alignment explanation
Indices: 58083--58162 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 40
58073 CGCAACATGA
**
58083 AAATGAAAATCGCAACACGAAAATGACTACCGCAACGAGAG
1 AAATGAAAATCGCAACACG-AAATGAAAACCGCAACGAGAG
* *
58124 AAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGA
1 AAATGAAAATCGCAACACGAAATGAAAACCGCAACGAGA
58163 TAATCGCAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
40 17 0.49
41 18 0.51
ACGTcount: A:0.50, C:0.20, G:0.20, T:0.10
Consensus pattern (40 bp):
AAATGAAAATCGCAACACGAAATGAAAACCGCAACGAGAG
Found at i:58260 original size:20 final size:19
Alignment explanation
Indices: 58193--58263 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
58183 AATCGCATTT
*
58193 CGATTTTCATTT-TGCGTTA
1 CGATTTTCATTTCT-CGTTG
*
58212 CGATTTTCATTTCGCGTTG
1 CGATTTTCATTTCTCGTTG
**
58231 CGATAGTCATTCTCTCGTTG
1 CGATTTTCATT-TCTCGTTG
58251 CGATTTTCATTTC
1 CGATTTTCATTTC
58264 AACCTAAATA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 27 0.63
20 16 0.37
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.48
Consensus pattern (19 bp):
CGATTTTCATTTCTCGTTG
Found at i:60129 original size:94 final size:94
Alignment explanation
Indices: 59958--60338 Score: 642
Period size: 94 Copynumber: 4.1 Consensus size: 94
59948 TAGATTGCTT
* *
59958 AGTAAATTTATTCGGTTGCTAG-CAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAG
1 AGTAAATTTATTCGGTTGCT-GCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAG
*
60022 TATTTGTCTTTTGTTTTATCTTTTGGTTG-A
65 TATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
60052 AGTAAATTTATTCGGTTGCTGTCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAAGTTAG
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AAGTTAG
60117 TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
60147 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
60212 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
60241 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
60306 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
60334 AGTAA
1 AGTAA
60339 TGCAATCCAT
Statistics
Matches: 277, Mismatches: 7, Indels: 7
0.95 0.02 0.02
Matches are distributed among these distances:
93 7 0.03
94 199 0.72
95 71 0.26
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:60278 original size:189 final size:187
Alignment explanation
Indices: 59958--60338 Score: 640
Period size: 189 Copynumber: 2.0 Consensus size: 187
59948 TAGATTGCTT
*
59958 AGTAAATTTATTCGGTTGCTAGCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTAGCAATACTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
60023 ATTTGTCTTTTGTTTTATCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGTCAATTCTGCTAAAC
66 ATTTGTCTTTTGTTTTATCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAAC
*
60088 TGTGTATTCTTTAACACTGTGAAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TGTGTATTCTTTAACACTCTG-AAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* *
60147 AGTAAATTTGTTCGGTTGCT-GCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAG
1 AGTAAATTTATTCGGTTGCTAG-CAATACTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAG
* *
60211 TATTTGTC-TTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAA
65 TATTTGTCTTTTGTTTTATCTTTTGGTTG-AAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAA
*
60275 ACTGTGTATTCTTTAATACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
129 ACTGTGTATTCTTTAACACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
60334 AGTAA
1 AGTAA
60339 TGCAATCCAT
Statistics
Matches: 182, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
187 6 0.03
188 55 0.30
189 121 0.66
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (187 bp):
AGTAAATTTATTCGGTTGCTAGCAATACTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTTGTTTTATCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAAC
TGTGTATTCTTTAACACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:60478 original size:19 final size:19
Alignment explanation
Indices: 60454--60522 Score: 79
Period size: 17 Copynumber: 3.6 Consensus size: 19
60444 TGTTTTGTCT
*
60454 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCA
60473 CGTTGCGA--TTCATTTCA
1 CGTTGCGATTTTCATTTCA
**
60490 CGTTGCGATAGTCATTTTTCA
1 CGTTGCGATTTTCA--TTTCA
60511 CGTTGCGATTTT
1 CGTTGCGATTTT
60523 AAGTTCCAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
17 16 0.38
19 11 0.26
21 15 0.36
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCA
Found at i:61467 original size:14 final size:14
Alignment explanation
Indices: 61448--61483 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
61438 ATTGTTTAAT
61448 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
61462 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
61476 TGATTTGT
1 TGATTTGT
61484 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:61628 original size:19 final size:19
Alignment explanation
Indices: 61601--61650 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
61591 TCGCAATTCG
*
61601 CGTTGCGATTTTAGTTTCA
1 CGTTACGATTTTAGTTTCA
61620 CGTTACGATTTTAGTTTCA
1 CGTTACGATTTTAGTTTCA
61639 CGTTACGATTTT
1 CGTTACGATTTT
61651 GTCGTTGCGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.48
Consensus pattern (19 bp):
CGTTACGATTTTAGTTTCA
Found at i:61679 original size:19 final size:19
Alignment explanation
Indices: 61655--61713 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
61645 GATTTTGTCG
61655 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
61674 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
61688 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
61707 TTGCGAT
1 TTGCGAT
61714 AGTCATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 7 0.21
19 13 0.39
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:61721 original size:19 final size:17
Alignment explanation
Indices: 61663--61713 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
61653 CGTTGCGATT
61663 TTCATTTCGCATTGCGA
1 TTCATTTCGCATTGCGA
*
61680 TTC-TCTCG--TTGCGA
1 TTCATTTCGCATTGCGA
61694 TTTTCATTTCGCATTGCGA
1 --TTCATTTCGCATTGCGA
61713 T
1 T
61714 AGTCATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
14 6 0.22
16 7 0.26
17 8 0.30
19 6 0.22
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.45
Consensus pattern (17 bp):
TTCATTTCGCATTGCGA
Found at i:61839 original size:14 final size:14
Alignment explanation
Indices: 61820--61856 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
61810 CATCAATTAA
61820 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
61834 ACAAATCATCTTTT
1 ACAAATCAACTTTT
61848 ACAAATCAA
1 ACAAATCAA
61857 TTAAACATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:62366 original size:19 final size:18
Alignment explanation
Indices: 62338--62509 Score: 107
Period size: 19 Copynumber: 9.7 Consensus size: 18
62328 TGAAACTAAA
62338 TTCGCGTTGCGATTTTCAT
1 TTCGC-TTGCGATTTTCAT
*
62357 TTCGCTTTGCGA--TTC-C
1 TTCGC-TTGCGATTTTCAT
*
62373 CTCG-TTGCGATTTTCAT
1 TTCGCTTGCGATTTTCAT
62390 TTCGCATTGCGA--TTC-T
1 TTCGC-TTGCGATTTTCAT
*
62406 CTCG-TTGCGATTTTCAT
1 TTCGCTTGCGATTTTCAT
**
62423 TTCGCATTGCGATAGTCAT
1 TTCGC-TTGCGATTTTCAT
*
62442 TTCCGCGTTGCGATATTCAT
1 TT-CGC-TTGCGATTTTCAT
* *
62462 ATTTGCGTTACGATTTTCA-
1 -TTCGC-TTGCGATTTTCAT
62481 --CG-TTGCGATTTTCAT
1 TTCGCTTGCGATTTTCAT
62496 TTCGCATTGCGATT
1 TTCGC-TTGCGATT
62510 GTCTCGTTGC
Statistics
Matches: 120, Mismatches: 16, Indels: 34
0.71 0.09 0.20
Matches are distributed among these distances:
14 23 0.19
16 14 0.12
17 15 0.12
19 38 0.32
20 28 0.23
21 2 0.02
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (18 bp):
TTCGCTTGCGATTTTCAT
Found at i:62491 original size:106 final size:106
Alignment explanation
Indices: 62340--62549 Score: 287
Period size: 106 Copynumber: 2.0 Consensus size: 106
62330 AAACTAAATT
* * * *
62340 CGCGTTGCGATTTTCATTTCGCTTTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATTC
1 CGCGTTGCGATATTCATTTCGCGTTACGATTCCCACGTTGCGATTTTCATTTCGCATTGCGATTC
** * *
62405 TCTCGTTGCGATTTTCATTT-CGCATTGCGATAGTCATTTC
66 TCTCGTTGCGATAGTAATTTCCGCATTGCGATAGACATTTC
* **
62445 CGCGTTGCGATATTCATATTTGCGTTACGATTTTCACGTTGCGATTTTCATTTCGCATTGCGATT
1 CGCGTTGCGATATTCAT-TTCGCGTTACGATTCCCACGTTGCGATTTTCATTTCGCATTGCGATT
* *
62510 GTCTCGTTGCGATAGTAATTTCCGCGTTGCGATAGACATT
65 CTCTCGTTGCGATAGTAATTTCCGCATTGCGATAGACATT
62550 AAGATGATTG
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
105 16 0.18
106 58 0.64
107 16 0.18
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.42
Consensus pattern (106 bp):
CGCGTTGCGATATTCATTTCGCGTTACGATTCCCACGTTGCGATTTTCATTTCGCATTGCGATTC
TCTCGTTGCGATAGTAATTTCCGCATTGCGATAGACATTTC
Found at i:62493 original size:73 final size:66
Alignment explanation
Indices: 62342--62523 Score: 202
Period size: 73 Copynumber: 2.7 Consensus size: 66
62332 ACTAAATTCG
* * * *
62342 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATTCTC
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCGCGTTGCGATATTCATTTCGCATTACGATTCTC
*
62407 T
66 A
* *
62408 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCGCGTTGCGATATTCATATTTGCGTTAC
1 CGTTGCGATTTTCATTTCGCATTGCGAT--TC----CCGCGTTGCGATATTCAT-TTCGCATTAC
*
62473 GATTTTCA
59 GATTCTCA
** *
62481 CGTTGCGATTTTCATTTCGCATTGCGATTGTCTCGTTGCGATA
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCGCGTTGCGATA
62524 GTAATTTCCG
Statistics
Matches: 98, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
66 27 0.28
67 11 0.11
68 2 0.02
71 1 0.01
72 16 0.16
73 41 0.42
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (66 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCGCGTTGCGATATTCATTTCGCATTACGATTCTC
A
Found at i:62531 original size:33 final size:33
Alignment explanation
Indices: 62342--62522 Score: 209
Period size: 33 Copynumber: 5.3 Consensus size: 33
62332 ACTAAATTCG
* *
62342 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
62375 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
62408 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCGCATTGCGAT--TC---T-CT
* * * * * *
62447 CGTTGCGATATTCATATTTGCGTTACGATTTTCA
1 CGTTGCGATTTTCAT-TTCGCATTGCGATTCTCT
*
62481 CGTTGCGATTTTCATTTCGCATTGCGATTGTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
62514 CGTTGCGAT
1 CGTTGCGAT
62523 AGTAATTTCC
Statistics
Matches: 126, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
33 81 0.64
34 15 0.12
35 3 0.02
38 2 0.02
39 15 0.12
40 10 0.08
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:62588 original size:20 final size:20
Alignment explanation
Indices: 62515--62588 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
62505 CGATTGTCTC
* *
62515 GTTGCGATAGTAATTTCCGC
1 GTTGCGATAGTCATTTCCGT
* **
62535 GTTGCGATAGACA-TTAAGAT
1 GTTGCGATAGTCATTTCCG-T
62555 GATTGCGA-ACGTCATTTCCGT
1 G-TTGCGATA-GTCATTTCCGT
62576 GTTGCGATAGTCA
1 GTTGCGATAGTCA
62589 AATGAATGCC
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.07
20 23 0.56
21 12 0.29
22 3 0.07
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGT
Found at i:65084 original size:24 final size:24
Alignment explanation
Indices: 65050--65103 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
65040 CTGAAAAATC
65050 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
65074 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
65098 ATCAAA
1 ATCAAA
65104 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:65117 original size:24 final size:24
Alignment explanation
Indices: 65050--65117 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
65040 CTGAAAAATC
* * *
65050 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
65074 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
65098 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
65118 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:65990 original size:20 final size:20
Alignment explanation
Indices: 65967--66012 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
65957 CAGAATCTCG
65967 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
65987 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
66007 TTGCGA
1 TTGCGA
66013 ATTAGGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:66033 original size:21 final size:21
Alignment explanation
Indices: 66009--66054 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
65999 TATTCGCATT
66009 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
66030 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
66051 GCGA
1 GCGA
66055 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:75054 original size:54 final size:54
Alignment explanation
Indices: 74821--75029 Score: 337
Period size: 54 Copynumber: 3.9 Consensus size: 54
74811 TATGTGTACA
* * * *
74821 ATCGACACTAAGTATGTAACCCACGGAATTCATAATATGTTTATGAACGACCGT
1 ATCGACACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCAT
*
74875 ATCGACACTAAGTGTGCTACCCACAGAATTCATAATATGTTTATGAACGACCAT
1 ATCGACACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCAT
* *
74929 ATCGACACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGTCCAT
1 ATCGACACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCAT
* *
74983 ATCGACACTAAGTGTGCAACCCACAAAATTCATATTATGTTTATGAA
1 ATCGACACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAA
75030 TGACTGTATC
Statistics
Matches: 144, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 144 1.00
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.28
Consensus pattern (54 bp):
ATCGACACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCAT
Found at i:75072 original size:108 final size:108
Alignment explanation
Indices: 74821--75072 Score: 326
Period size: 108 Copynumber: 2.3 Consensus size: 108
74811 TATGTGTACA
* * ** *
74821 ATCGACACTAAGTATGTAACCCACGGAATTCATAATATGTTTATGAACGACCGTATCGACACTAA
1 ATCGACACTAAGTGTGCAACCCAAAGAATTCATAATATGTTTATGAACGACCATATCGACACTAA
* *
74886 GTGTGCTACCCACAGAATTCATAATATGTTTATGAACGACCAT
66 GTGTGCAACCCACAAAATTCATAATATGTTTATGAACGACCAT
** *
74929 ATCGACACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGTCCATATCGACACTAA
1 ATCGACACTAAGTGTGCAACCCAAAGAATTCATAATATGTTTATGAACGACCATATCGACACTAA
* * **
74994 GTGTGCAACCCACAAAATTCATATTATGTTTATGAATGACTGT
66 GTGTGCAACCCACAAAATTCATAATATGTTTATGAACGACCAT
* * * *
75037 ATCGGCTCTACGTGTGCACCCCAAAGAACTT-ATAAT
1 ATCGACACTAAGTGTGCAACCCAAAGAA-TTCATAAT
75073 GATTTGAAAA
Statistics
Matches: 127, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
108 125 0.98
109 2 0.02
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (108 bp):
ATCGACACTAAGTGTGCAACCCAAAGAATTCATAATATGTTTATGAACGACCATATCGACACTAA
GTGTGCAACCCACAAAATTCATAATATGTTTATGAACGACCAT
Found at i:77507 original size:30 final size:30
Alignment explanation
Indices: 77435--77496 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
77425 CCCGAAGGAC
77435 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
77465 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
77495 CT
1 CT
77497 GTTCATAGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:77738 original size:14 final size:14
Alignment explanation
Indices: 77721--77765 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
77711 TGTAACCATG
77721 TATTTTATATCATA
1 TATTTTATATCATA
77735 TATTTTATA--ATA
1 TATTTTATATCATA
*
77747 GATTCTTATATCAT-
1 TATT-TTATATCATA
77761 TATTT
1 TATTT
77766 GTTTCCTTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
12 6 0.23
13 6 0.23
14 12 0.46
15 2 0.08
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (14 bp):
TATTTTATATCATA
Found at i:82432 original size:28 final size:30
Alignment explanation
Indices: 82366--82463 Score: 110
Period size: 28 Copynumber: 3.3 Consensus size: 30
82356 CCCGAAGGAC
*
82366 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCATAGGTCATAAAGATCCTCGGTAA
82396 CTATCCATAGGTCAT-AAGATCCTC-GTAA
1 CTATCCATAGGTCATAAAGATCCTCGGTAA
* *** * *
82424 CTGTCCATAGGTCCCGAAGAACCTAGGTAAA
1 CTATCCATAGGTCATAAAGATCCTCGGT-AA
82455 CTATCCATA
1 CTATCCATA
82464 TGTTCCCTTA
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
28 16 0.28
29 16 0.28
30 16 0.28
31 10 0.17
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (30 bp):
CTATCCATAGGTCATAAAGATCCTCGGTAA
Found at i:82443 original size:29 final size:29
Alignment explanation
Indices: 82366--82463 Score: 99
Period size: 29 Copynumber: 3.3 Consensus size: 29
82356 CCCGAAGGAC
* *
82366 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCATAGGTCA-GAAGATCCTCGGTAA
*
82396 CTATCCATAGGTCATAAGATCCTC-GTAA
1 CTATCCATAGGTCAGAAGATCCTCGGTAA
* * * *
82424 CTGTCCATAGGTCCCGAAGAACCTAGGTAAA
1 CTATCCATAGGT-CAGAAGATCCTCGGT-AA
82455 CTATCCATA
1 CTATCCATA
82464 TGTTCCCTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
28 15 0.26
29 17 0.30
30 15 0.26
31 10 0.18
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (29 bp):
CTATCCATAGGTCAGAAGATCCTCGGTAA
Done.