Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007289.1 Hibiscus syriacus cultivar Beakdansim tig00019362_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: 118031
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:35 original size:21 final size:21
Alignment explanation
Indices: 9--117 Score: 77
Period size: 21 Copynumber: 5.3 Consensus size: 21
1 TTGGAATG
9 CGCAACGCGAACTTCGCCTAT
1 CGCAACGCGAACTTCGCCTAT
* **
30 CGCAA--CGAA-TTGGAATGAAT
1 CGCAACGCGAACTTCGCCT--AT
50 CGCAACGCGAACTTCGCCTAT
1 CGCAACGCGAACTTCGCCTAT
* * **
71 CGCAA--CG-ATTTGGAATGAAT
1 CGCAACGCGAACTTCGCCT--AT
91 CGCAACGCGAACTTCGCCTAT
1 CGCAACGCGAACTTCGCCTAT
112 CGCAAC
1 CGCAAC
118 AATTGGAATG
Statistics
Matches: 64, Mismatches: 14, Indels: 20
0.65 0.14 0.20
Matches are distributed among these distances:
18 9 0.14
19 6 0.09
20 14 0.22
21 20 0.31
22 6 0.09
23 9 0.14
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.19
Consensus pattern (21 bp):
CGCAACGCGAACTTCGCCTAT
Found at i:57 original size:41 final size:41
Alignment explanation
Indices: 4--192 Score: 301
Period size: 41 Copynumber: 4.6 Consensus size: 41
1 TTG
4 GAATGCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAAT
1 GAAT-CGCAACGCGAACTTCGCCTATCGCAACGAATTGGAAT
*
46 GAATCGCAACGCGAACTTCGCCTATCGCAACGATTTGGAAT
1 GAATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAAT
87 GAATCGCAACGCGAACTTCGCCTATCGCAAC-AATTGGAAT
1 GAATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAAT
* * *
127 GAATCGCAACGC-AACTTCGACTATCTCAACGAATTTGAAAT
1 GAATCGCAACGCGAACTTCGCCTATCGCAACGAA-TTGGAAT
*
168 GAATCGCAACGCGAACTTCGACTAT
1 GAATCGCAACGCGAACTTCGCCTAT
193 TGCGTTGCGA
Statistics
Matches: 139, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
39 16 0.12
40 22 0.16
41 85 0.61
42 16 0.12
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.21
Consensus pattern (41 bp):
GAATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAAT
Found at i:169 original size:81 final size:82
Alignment explanation
Indices: 4--192 Score: 310
Period size: 81 Copynumber: 2.3 Consensus size: 82
1 TTG
*
4 GAATGCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGCCT
1 GAAT-CGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGACT
*
69 ATCGCAACGATTTGGAAT
65 ATCGCAACGATTTGAAAT
87 GAATCGCAACGCGAACTTCGCCTATCGCAAC-AATTGGAATGAATCGCAACGC-AACTTCGACTA
1 GAATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGACTA
*
150 TCTCAACGAATTTGAAAT
66 TCGCAACG-ATTTGAAAT
*
168 GAATCGCAACGCGAACTTCGACTAT
1 GAATCGCAACGCGAACTTCGCCTAT
193 TGCGTTGCGA
Statistics
Matches: 101, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
80 17 0.17
81 53 0.52
82 27 0.27
83 4 0.04
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.21
Consensus pattern (82 bp):
GAATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGACTA
TCGCAACGATTTGAAAT
Found at i:4389 original size:38 final size:38
Alignment explanation
Indices: 4329--4426 Score: 130
Period size: 39 Copynumber: 2.6 Consensus size: 38
4319 AGAAATAATC
*
4329 TAGAATGTT-AGGGAAATAATTT-AGAAATT-AGAAATT
1 TAGAATGTTAAGGTAAATAATTTAAGAAATTAAG-AATT
4365 TAGAATGTTAAGGTAAAATAATTTAAGAAATTAAGAATT
1 TAGAATGTTAAGGT-AAATAATTTAAGAAATTAAGAATT
* *
4404 TAGAAGGTTAAGATAAATAATTT
1 TAGAATGTTAAGGTAAATAATTT
4427 GAGATTCATG
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
36 9 0.16
37 3 0.05
38 18 0.33
39 23 0.42
40 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (38 bp):
TAGAATGTTAAGGTAAATAATTTAAGAAATTAAGAATT
Found at i:6173 original size:2 final size:2
Alignment explanation
Indices: 6166--6190 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6156 ATATTTCATA
6166 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6191 CTATTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6678 original size:21 final size:21
Alignment explanation
Indices: 6651--6733 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
6641 TTACGATTTA
*
6651 CAAGTTCGCATTGCGATAGTC
1 CAAGTTCGCGTTGCGATAGTC
* *
6672 GAAGTTCGCGTTGCGATTTATTC
1 CAAGTTCGCGTTGCGA--TAGTC
* *
6695 CAAATT--CGTTGCGATAATC
1 CAAGTTCGCGTTGCGATAGTC
6714 CAAGTTCGCGTTGCGATAGT
1 CAAGTTCGCGTTGCGATAGT
6734 TCGACTATCG
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
19 9 0.18
21 33 0.66
23 8 0.16
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (21 bp):
CAAGTTCGCGTTGCGATAGTC
Found at i:6792 original size:42 final size:42
Alignment explanation
Indices: 6733--6900 Score: 218
Period size: 42 Copynumber: 4.0 Consensus size: 42
6723 GTTGCGATAG
*
6733 TTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
6775 TTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
* * * *
6817 TTGGACTATCACAACTAATTTGG-A-AAATCGCAACGCGAAC
1 TTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
* * *
6857 TTCGACTATTGTAACGCGAACTTGGACT--ATCGCAACGCGAAC
1 TTCGACTATCGCAA--CGAACTTGGAATAAATCGCAACGCGAAC
6899 TT
1 TT
6901 GTAAATCGCA
Statistics
Matches: 110, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
40 26 0.24
41 1 0.01
42 83 0.75
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (42 bp):
TTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
Found at i:6831 original size:21 final size:21
Alignment explanation
Indices: 6736--6901 Score: 146
Period size: 21 Copynumber: 8.0 Consensus size: 21
6726 GCGATAGTTC
*
6736 GACTATCGCAA--CGAATTTG
1 GACTATCGCAACGCGAACTTG
* *
6755 GAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAACGCGAACTTG
6778 GACTATCGCAA--CGAACTTG
1 GACTATCGCAACGCGAACTTG
*
6797 GAATAAATCGCAACGCGAACTTG
1 GACT--ATCGCAACGCGAACTTG
* * *
6820 GACTATCACAA--CTAATTTG
1 GACTATCGCAACGCGAACTTG
** *
6839 GAAAATCGCAACGCGAACTTC
1 GACTATCGCAACGCGAACTTG
* *
6860 GACTATTGTAACGCGAACTTG
1 GACTATCGCAACGCGAACTTG
6881 GACTATCGCAACGCGAACTTG
1 GACTATCGCAACGCGAACTTG
6902 TAAATCGCAT
Statistics
Matches: 114, Mismatches: 23, Indels: 18
0.74 0.15 0.12
Matches are distributed among these distances:
19 27 0.24
21 67 0.59
23 20 0.18
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (21 bp):
GACTATCGCAACGCGAACTTG
Found at i:6889 original size:82 final size:83
Alignment explanation
Indices: 6736--6901 Score: 239
Period size: 82 Copynumber: 2.0 Consensus size: 83
6726 GCGATAGTTC
*
6736 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAT
1 GACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAT
6801 AAATCGCAACGCGAACTTG
66 -AATCGCAACGCGAACTTG
* * *
6820 GACTATCACAACTAATTTGG-A-AAATCGCAACGCGAACTTCGACTATTGTAACGCGAACTTGGA
1 GACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA--CGAACTTGGA
*
6883 CT-ATCGCAACGCGAACTTG
64 ATAATCGCAACGCGAACTTG
6902 TAAATCGCAT
Statistics
Matches: 75, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
82 45 0.60
83 1 0.01
84 29 0.39
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (83 bp):
GACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAT
AATCGCAACGCGAACTTG
Found at i:6930 original size:21 final size:21
Alignment explanation
Indices: 6906--6958 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
6896 AACTTGTAAA
*
6906 TCGCATTGCGATAGTCCAAGT
1 TCGCGTTGCGATAGTCCAAGT
*
6927 TCGCGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCCAAGT
*
6948 TTGCGTTGCGA
1 TCGCGTTGCGA
6959 ATCTGGAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.19, C:0.21, G:0.30, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCCAAGT
Found at i:10639 original size:35 final size:35
Alignment explanation
Indices: 10591--10657 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
10581 AAAAGTGTAG
* * * *
10591 ATTTAGAACGTTATATTATAAATTTAGGGATAAGA
1 ATTTAAAAAGTTATATTAGAAATTTAGAGATAAGA
10626 ATTTAAAAAGTTATATTAGAAATTTAGAGATA
1 ATTTAAAAAGTTATATTAGAAATTTAGAGATA
10658 CAACCTTACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.46, C:0.01, G:0.15, T:0.37
Consensus pattern (35 bp):
ATTTAAAAAGTTATATTAGAAATTTAGAGATAAGA
Found at i:15857 original size:37 final size:37
Alignment explanation
Indices: 15786--15858 Score: 94
Period size: 38 Copynumber: 2.0 Consensus size: 37
15776 TGAAAAATAA
* *
15786 TTATATATTTTCTTTAAAAAATTTAAATTCATAAAAT
1 TTATATATTTTCTTTAAAAAATTAAAAATCATAAAAT
* *
15823 TTATATAATTTTTTTTACAAAATTAAAAAT-ATAAAA
1 TTATAT-ATTTTCTTTAAAAAATTAAAAATCATAAAA
15859 CGGTTTAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 12 0.39
38 19 0.61
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (37 bp):
TTATATATTTTCTTTAAAAAATTAAAAATCATAAAAT
Found at i:21461 original size:18 final size:18
Alignment explanation
Indices: 21438--21477 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
21428 GCCCAAAAGG
*
21438 ACCTACAAGTACTGAAGC
1 ACCTACAAGTAATGAAGC
*
21456 ACCTACTAGTAATGAAGC
1 ACCTACAAGTAATGAAGC
21474 ACCT
1 ACCT
21478 CTGAATGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.28, G:0.15, T:0.20
Consensus pattern (18 bp):
ACCTACAAGTAATGAAGC
Found at i:21475 original size:189 final size:188
Alignment explanation
Indices: 21163--21623 Score: 586
Period size: 189 Copynumber: 2.4 Consensus size: 188
21153 TAACGGAGGT
* *
21163 TTGAGCGTTAGCAGTGGTAAGCTGAGGAGAAGGACGTGCTACCAGTGCGGACAAAAGGGTCATAT
1 TTGAGCGTTAGCAGTGGTAAGTTGAGGAGAAGGACGTGCTACGAGTGCGGACAAAAGGGTCATAT
* * * * * * * * *
21228 TTCTTCTGCTTGCCCTAAAGGACCTGCGAGTGCCGAAGCGCCTATTGGTCACGAAGCACGTACTG
66 TTCTTCTGCTTGCCCAAAAGGACCTACAAGTACCGAAGCACCTACTAGTAACGAAGCACCT-CTG
* * ** * * *
21293 -GTAATGAAGCACCTCT-GAGCGTCGAAGCACCTACAGTTAATGAAGTTGATAATGTTGG-C
130 AATAATGAAGCACCACTAGAGAAT-GAACCACCTACAGTTAATGAAGTTGAGAACG--GGAC
* * *
21352 TTGAGCGTTAGCAGTGGTAAGTTGAGGAGAAGGACGTGCTATGTGTGCGGACAAAAGGGCCATAT
1 TTGAGCGTTAGCAGTGGTAAGTTGAGGAGAAGGACGTGCTACGAGTGCGGACAAAAGGGTCATAT
* *
21417 TTCTTCTGCTTGCCCAAAAGGACCTACAAGTACTGAAGCACCTACTAGTAATGAAGCACCTCTGA
66 TTCTTCTGCTTGCCCAAAAGGACCTACAAGTACCGAAGCACCTACTAGTAACGAAGCACCTCTGA
** * * *
21482 ATGTTGAAGCACCACTAGATAATGAACCACCTCCAGTTAATGAAGTTGAGAACGGGAT
131 ATAATGAAGCACCACTAGAGAATGAACCACCTACAGTTAATGAAGTTGAGAACGGGAC
*
21540 TTCGAGCGTTAGTAGTGGTAAGTTGAGGAGAAGGACGTGCTACGAGTGCGGACAAAAGGGTCATA
1 TT-GAGCGTTAGCAGTGGTAAGTTGAGGAGAAGGACGTGCTACGAGTGCGGACAAAAGGGTCATA
*
21605 TTTCTTCTGCCTGCCCAAA
65 TTTCTTCTGCTTGCCCAAA
21624 TAAGAAATCT
Statistics
Matches: 235, Mismatches: 33, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
187 2 0.01
188 5 0.02
189 225 0.96
190 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (188 bp):
TTGAGCGTTAGCAGTGGTAAGTTGAGGAGAAGGACGTGCTACGAGTGCGGACAAAAGGGTCATAT
TTCTTCTGCTTGCCCAAAAGGACCTACAAGTACCGAAGCACCTACTAGTAACGAAGCACCTCTGA
ATAATGAAGCACCACTAGAGAATGAACCACCTACAGTTAATGAAGTTGAGAACGGGAC
Found at i:21507 original size:18 final size:18
Alignment explanation
Indices: 21450--21526 Score: 59
Period size: 18 Copynumber: 4.3 Consensus size: 18
21440 CTACAAGTAC
21450 TGAAGCACCTACTAG-TAA
1 TGAAGCACC-ACTAGATAA
* **
21468 TGAAGCACCTCT-GAATGT
1 TGAAGCACCACTAG-ATAA
21486 TGAAGCACCACTAGATAA
1 TGAAGCACCACTAGATAA
* * * *
21504 TGAACCACCTCCAGTTAA
1 TGAAGCACCACTAGATAA
21522 TGAAG
1 TGAAG
21527 TTGAGAACGG
Statistics
Matches: 45, Mismatches: 11, Indels: 6
0.73 0.18 0.10
Matches are distributed among these distances:
16 1 0.02
17 2 0.04
18 41 0.91
19 1 0.02
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.22
Consensus pattern (18 bp):
TGAAGCACCACTAGATAA
Found at i:32317 original size:59 final size:60
Alignment explanation
Indices: 32254--32367 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
32244 ACTATGATAA
* * * *
32254 TCATTCTTAATTTGTCCTCAAAC-TTTTGAACATTT-ATTTTCATCCCCAAACTATCTCAT
1 TCATTCTAAATTAGTCCTCAAACTTTTTCAACATTTCAATTTCAT-CCCAAACTATCTCAT
*
32313 TCATTCTAAATTAGTCCTTAAACTTTTTCAACATTTCAATTTCATCCCAAACTAT
1 TCATTCTAAATTAGTCCTCAAACTTTTTCAACATTTCAATTTCATCCCAAACTAT
32368 ATGTATATAC
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 20 0.42
60 21 0.44
61 7 0.15
ACGTcount: A:0.30, C:0.25, G:0.03, T:0.43
Consensus pattern (60 bp):
TCATTCTAAATTAGTCCTCAAACTTTTTCAACATTTCAATTTCATCCCAAACTATCTCAT
Found at i:32563 original size:60 final size:60
Alignment explanation
Indices: 32494--32616 Score: 158
Period size: 60 Copynumber: 2.0 Consensus size: 60
32484 ATGAATTTAG
* * **
32494 GGATAAAATTGAAAGATTTAAAAGTTTG-GGAGCCAATTTAGAATGAGGGTCATAGTTTGA
1 GGATAAAATTAAAAGATTAAAAAGTTTGAGGA-CCAATTTAGAATGAGAATCATAGTTTGA
* * **
32554 GGATGAAATTAAAATATTAAAAAGTTTGAGGATTAATTTAGAATGAGAATCATAGTTTGA
1 GGATAAAATTAAAAGATTAAAAAGTTTGAGGACCAATTTAGAATGAGAATCATAGTTTGA
32614 GGA
1 GGA
32617 CATATGATGC
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
60 51 0.94
61 3 0.06
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (60 bp):
GGATAAAATTAAAAGATTAAAAAGTTTGAGGACCAATTTAGAATGAGAATCATAGTTTGA
Found at i:32614 original size:31 final size:31
Alignment explanation
Indices: 32528--32616 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 31
32518 TTTGGGAGCC
**
32528 AATTTAGAATGAGGGTCATAGTTTGAGGATG
1 AATTTAGAATGAGAATCATAGTTTGAGGATG
* * * * *
32559 AAATTAAAAT-ATTAA--AAAGTTTGAGGATT
1 AATTTAGAATGA-GAATCATAGTTTGAGGATG
32588 AATTTAGAATGAGAATCATAGTTTGAGGA
1 AATTTAGAATGAGAATCATAGTTTGAGGA
32617 CATATGATGC
Statistics
Matches: 43, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
29 22 0.51
30 2 0.05
31 19 0.44
ACGTcount: A:0.42, C:0.02, G:0.24, T:0.33
Consensus pattern (31 bp):
AATTTAGAATGAGAATCATAGTTTGAGGATG
Found at i:34186 original size:83 final size:84
Alignment explanation
Indices: 34085--34240 Score: 269
Period size: 83 Copynumber: 1.9 Consensus size: 84
34075 ATTTCTATGA
* *
34085 TATCAAAATTCAAAGAACCAGTCTGCAAGTCATCGCAAAGACAACATTA-GGAGGGTAATAATCA
1 TATCAAAATTCAAAGAACCAGTCTGCAAGTCATCGCAAAGACAACATTATGGAGGATAATAAGCA
34149 TATAAAAATGACGATACTT
66 TATAAAAATGACGATACTT
* *
34168 TATCAAAATTCAAAGAACCAGTCTGCAAGTGATCGCAATGACAACATTATGGAGGATAATAAGCA
1 TATCAAAATTCAAAGAACCAGTCTGCAAGTCATCGCAAAGACAACATTATGGAGGATAATAAGCA
34233 TATAAAAA
66 TATAAAAA
34241 GATTGGCATA
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
83 47 0.69
84 21 0.31
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (84 bp):
TATCAAAATTCAAAGAACCAGTCTGCAAGTCATCGCAAAGACAACATTATGGAGGATAATAAGCA
TATAAAAATGACGATACTT
Found at i:34663 original size:11 final size:12
Alignment explanation
Indices: 34641--34666 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
34631 CTATTAGCAA
34641 TTTCCTTTTTTT
1 TTTCCTTTTTTT
34653 TTTCCTTTTTTT
1 TTTCCTTTTTTT
34665 TT
1 TT
34667 GTTACACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTCCTTTTTTT
Found at i:41660 original size:2 final size:2
Alignment explanation
Indices: 41653--41725 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
41643 TTATACTTTC
41653 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41695 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41726 ATTACGTCTT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:44438 original size:3 final size:3
Alignment explanation
Indices: 44430--44476 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
44420 CAAATGCATC
44430 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
44477 AAGGTGTGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:46199 original size:15 final size:15
Alignment explanation
Indices: 46179--46209 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
46169 TTGGTTGGAG
*
46179 TGTGAATTTTCCTCA
1 TGTGAATTTTACTCA
46194 TGTGAATTTTACTCA
1 TGTGAATTTTACTCA
46209 T
1 T
46210 CTTCCTCACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.16, G:0.13, T:0.48
Consensus pattern (15 bp):
TGTGAATTTTACTCA
Found at i:52730 original size:21 final size:21
Alignment explanation
Indices: 52701--52747 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
52691 ATTCTGACTA
52701 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
52722 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
52743 TCGCA
1 TCGCA
52748 ATACGAATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:52768 original size:20 final size:20
Alignment explanation
Indices: 52743--52896 Score: 211
Period size: 20 Copynumber: 7.7 Consensus size: 20
52733 TTTTCCTAAT
*
52743 TCGCAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
52763 TCGCAACGCGAATTTA-GAAAA
1 TCGCAATGCGAA--TACGTAAA
*
52784 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
52804 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
52824 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
52844 TCGTAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
52864 TCGCAATTCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
52884 TCGCAATGCGAAT
1 TCGCAATGCGAAT
52897 CTGACTATCG
Statistics
Matches: 118, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
19 2 0.02
20 100 0.85
21 14 0.12
22 2 0.02
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:52880 original size:60 final size:59
Alignment explanation
Indices: 52743--52916 Score: 231
Period size: 60 Copynumber: 2.9 Consensus size: 59
52733 TTTTCCTAAT
*
52743 TCGCAATACGAATACGTAAATCGCAACGCGAATTTAGAAAATCGCAATGCGATTACGTAAA
1 TCGCAATACGAATACGTAAATCGCAATGCGAA--TAGAAAATCGCAATGCGATTACGTAAA
* * *
52804 TCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAATCGTAATGCGATTACGTAAA
1 TCGCAATACGAATACGTAAATCGCAATGCGAATA-GAAAATCGCAATGCGATTACGTAAA
* * * **
52864 TCGCAATTCGATTACGTAAATCGCAATGCGAATCTGACTATCGCAATGCGATT
1 TCGCAATACGAATACGTAAATCGCAATGCGAAT-AGAAAATCGCAATGCGATT
52917 TACATAACGC
Statistics
Matches: 100, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
59 2 0.02
60 68 0.68
61 30 0.30
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (59 bp):
TCGCAATACGAATACGTAAATCGCAATGCGAATAGAAAATCGCAATGCGATTACGTAAA
Found at i:52907 original size:40 final size:40
Alignment explanation
Indices: 52743--52916 Score: 185
Period size: 40 Copynumber: 4.3 Consensus size: 40
52733 TTTTCCTAAT
* * * * *
52743 TCGCAATACGAATACGTAAATCGCAACGCGAATTTAGAAAA
1 TCGCAATGCGATTACGTAAATCGCAATGCGAATCT-GACAA
52784 TCGCAATGCGATTACGTAAATCGCAATGCGAATAC-GTA-AA
1 TCGCAATGCGATTACGTAAATCGCAATGCGAAT-CTG-ACAA
* * *
52824 TCGCAATGCGAATACGTAAATCGTAATGCGATTAC-GTA-AA
1 TCGCAATGCGATTACGTAAATCGCAATGCGAAT-CTG-ACAA
* *
52864 TCGCAATTCGATTACGTAAATCGCAATGCGAATCTGACTA
1 TCGCAATGCGATTACGTAAATCGCAATGCGAATCTGACAA
52904 TCGCAATGCGATT
1 TCGCAATGCGATT
52917 TACATAACGC
Statistics
Matches: 116, Mismatches: 13, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
39 2 0.02
40 83 0.72
41 31 0.27
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (40 bp):
TCGCAATGCGATTACGTAAATCGCAATGCGAATCTGACAA
Found at i:53561 original size:20 final size:20
Alignment explanation
Indices: 53489--53577 Score: 90
Period size: 20 Copynumber: 4.5 Consensus size: 20
53479 CGATTCTGTA
53489 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGC
** **
53508 GTTGCGATAGTCAAATTCGC
1 GTTGCGATTTTCATTTTCGC
** *
53528 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCGC
*
53548 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGC
*
53568 ATTGCGATTT
1 GTTGCGATTT
53578 AAAGTTTCAG
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
19 11 0.18
20 49 0.82
ACGTcount: A:0.16, C:0.17, G:0.22, T:0.45
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGC
Found at i:53585 original size:20 final size:20
Alignment explanation
Indices: 53542--53585 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
53532 CGATAGTCAT
* ** *
53542 TTTCGTGTTGCGATTTTCAT
1 TTTCGTATTGCGATTTAAAG
53562 TTTCGTATTGCGATTTAAAG
1 TTTCGTATTGCGATTTAAAG
53582 TTTC
1 TTTC
53586 AGAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.14, G:0.18, T:0.52
Consensus pattern (20 bp):
TTTCGTATTGCGATTTAAAG
Found at i:55532 original size:20 final size:20
Alignment explanation
Indices: 55467--55550 Score: 72
Period size: 20 Copynumber: 4.5 Consensus size: 20
55457 AGAATAGTTT
**
55467 ACTATCGCAACACGAAAATG
1 ACTATCGCAATGCGAAAATG
*
55487 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
55503 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* **
55521 ACTATCGTAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
55541 ACTATCGCAA
1 ACTATCGCAA
55551 CGAAAGAATC
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
14 7 0.13
16 4 0.08
17 4 0.08
18 4 0.08
20 33 0.63
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.20
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:55549 original size:54 final size:53
Alignment explanation
Indices: 55485--55588 Score: 154
Period size: 54 Copynumber: 1.9 Consensus size: 53
55475 AACACGAAAA
* **
55485 TGACTATCGCAACGAGAGAATCGCAATGCGAAAATGACTATCGTAATGCGAATT
1 TGACTATCGCAACGAAAGAATCGCAATGC-AAAATGAAAATCGTAATGCGAATT
* *
55539 TGACTATCGCAACGAAAGAATCGCAGTGCAAAATGAAAATCGTATTGCGA
1 TGACTATCGCAACGAAAGAATCGCAATGCAAAATGAAAATCGTAATGCGA
55589 TTCTCTCGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
53 18 0.40
54 27 0.60
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.21
Consensus pattern (53 bp):
TGACTATCGCAACGAAAGAATCGCAATGCAAAATGAAAATCGTAATGCGAATT
Found at i:55649 original size:20 final size:20
Alignment explanation
Indices: 55597--55655 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
55587 GATTCTCTCG
**
55597 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
55617 TTGCGATAATCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
55637 TTGCGATAGTCATTTTCGC
1 TTGCGATAGTCATTTTCGC
55656 GTTGTGATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:56255 original size:18 final size:19
Alignment explanation
Indices: 56216--56257 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
56206 CTCACCTGTC
56216 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
56237 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
56255 ATC
1 ATC
56258 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:56311 original size:42 final size:42
Alignment explanation
Indices: 56211--56321 Score: 109
Period size: 42 Copynumber: 2.6 Consensus size: 42
56201 CCCGACTCAC
* * * * *
56211 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTAAAGAGGCCA
* **
56253 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTAAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTAAAGAGGCCA
*
56295 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
56322 ACATTCTAGA
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
41 2 0.04
42 51 0.93
43 2 0.04
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTAAAGAGGCCA
Found at i:57700 original size:14 final size:14
Alignment explanation
Indices: 57681--57716 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
57671 ATTGTTTAAT
57681 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
57695 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
57709 TGATTTGT
1 TGATTTGT
57717 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:57906 original size:34 final size:33
Alignment explanation
Indices: 57818--57911 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 33
57808 AAAACAGACT
* **
57818 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
57852 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
57885 ATCGCAATGCGAAAATGAAAATCGCAA
1 ATCGCAATGCG-AAATGAAAATCGCAA
57912 TGCGAAACTA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 31 0.56
34 24 0.44
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:57909 original size:20 final size:19
Alignment explanation
Indices: 57851--57918 Score: 83
Period size: 20 Copynumber: 3.8 Consensus size: 19
57841 GCAACGAGAG
57851 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
57870 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
57884 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
57904 AATCGCAATGCGAAA
1 AATCGCAATGCGAAA
57919 CTAATTTCAC
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
14 8 0.20
16 5 0.12
17 2 0.05
18 3 0.07
19 11 0.27
20 12 0.29
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:57985 original size:33 final size:33
Alignment explanation
Indices: 57928--58012 Score: 134
Period size: 33 Copynumber: 2.5 Consensus size: 33
57918 ACTAATTTCA
57928 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
57962 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
**
57995 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
58013 CACGTTGCGA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 34 0.71
34 14 0.29
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:58020 original size:20 final size:20
Alignment explanation
Indices: 57995--58088 Score: 136
Period size: 20 Copynumber: 4.7 Consensus size: 20
57985 GCGATTCTCT
*
57995 CGTTGCGATAGTCATTTCCA
1 CGTTGCGATAGTCATTTCCG
* *
58015 CGTTGCGATAGTCAATTCTG
1 CGTTGCGATAGTCATTTCCG
58035 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
58055 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
58075 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
58089 AATGAATGTC
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 64 0.97
21 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:58044 original size:40 final size:40
Alignment explanation
Indices: 57995--58088 Score: 154
Period size: 40 Copynumber: 2.4 Consensus size: 40
57985 GCGATTCTCT
57995 CGTTGCGATAGTCATTTCCACGTTGCGATAGTCA-ATTCTG
1 CGTTGCGATAGTCATTTCCACGTTGCGATAGTCATATTC-G
**
58035 CGTTGCGATAGTCATTTCCGTGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCATTTCCACGTTGCGATAGTCATATTCG
58075 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
58089 AATGAATGTC
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
40 47 0.92
41 4 0.08
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.35
Consensus pattern (40 bp):
CGTTGCGATAGTCATTTCCACGTTGCGATAGTCATATTCG
Found at i:61526 original size:41 final size:40
Alignment explanation
Indices: 61416--61542 Score: 155
Period size: 40 Copynumber: 3.1 Consensus size: 40
61406 CAGAATCTCG
* *
61416 TTGCGATTTACAGATTCGCATTACGATTTACGTAATCGCA
1 TTGCGATTTACAAATTCGCATTACAATTTACGTAATCGCA
** * *
61456 TTGCGATTTACGTATTCGCATTACGATTTATGTAATCGCA
1 TTGCGATTTACAAATTCGCATTACAATTTACGTAATCGCA
* * * *
61496 TTGCGATTTTCCAAATTCGCGTTGCAATTTACGTATTCGCA
1 TTGCGA-TTTACAAATTCGCATTACAATTTACGTAATCGCA
61537 TTGCGA
1 TTGCGA
61543 ATTAGGAAAA
Statistics
Matches: 75, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
40 43 0.57
41 32 0.43
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (40 bp):
TTGCGATTTACAAATTCGCATTACAATTTACGTAATCGCA
Found at i:61540 original size:20 final size:20
Alignment explanation
Indices: 61416--61542 Score: 139
Period size: 20 Copynumber: 6.3 Consensus size: 20
61406 CAGAATCTCG
61416 TTGCGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
* *
61436 TTACGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
61456 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
* * *
61476 TTACGATTTATGTAATCGCA
1 TTGCGATTTACGTATTCGCA
* ** *
61496 TTGCGATTTTCCAAATTCGCG
1 TTGCGA-TTTACGTATTCGCA
*
61517 TTGCAATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
61537 TTGCGA
1 TTGCGA
61543 ATTAGGAAAA
Statistics
Matches: 85, Mismatches: 20, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
19 1 0.01
20 71 0.84
21 13 0.15
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:61556 original size:21 final size:21
Alignment explanation
Indices: 61539--61579 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
61529 TATTCGCATT
61539 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
61560 GCGAATTTGGGAAATCGCAA
1 GCGAATTAGGAAAATCGCAA
61580 TACGATAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:61860 original size:21 final size:21
Alignment explanation
Indices: 61836--61886 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
61826 GTAACGAAAT
*
61836 TAATATTTTTGACAGAAAAAA
1 TAATATTTTTGACAAAAAAAA
61857 TAATATTTTTGACAAAAAAAA
1 TAATATTTTTGACAAAAAAAA
61878 TAATATTTT
1 TAATATTTT
61887 AAATAGTACT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (21 bp):
TAATATTTTTGACAAAAAAAA
Found at i:62958 original size:9 final size:8
Alignment explanation
Indices: 62936--63027 Score: 55
Period size: 9 Copynumber: 11.0 Consensus size: 8
62926 TGAATCCGAA
*
62936 AATATTAT
1 AATATAAT
62944 ATATATAATT
1 A-ATATAA-T
*
62954 AATATAAA
1 AATATAAT
62962 AATATAA-
1 AATATAAT
*
62969 AATATTAT
1 AATATAAT
62977 ATATATAATT
1 A-ATATAA-T
*
62987 AATATAAAA
1 AATAT-AAT
62996 AATATAA-
1 AATATAAT
*
63003 AATATTAT
1 AATATAAT
63011 -ATATATAT
1 AATATA-AT
63019 ATATATAAT
1 A-ATATAAT
63028 CGGGGCGGGG
Statistics
Matches: 67, Mismatches: 7, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
7 16 0.24
8 13 0.19
9 27 0.40
10 11 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
AATATAAT
Found at i:62976 original size:33 final size:34
Alignment explanation
Indices: 62934--63017 Score: 161
Period size: 33 Copynumber: 2.5 Consensus size: 34
62924 TTTGAATCCG
62934 AAAATATTATATATATAATTAATAT-AAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
62967 AAAATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
63001 AAAATATTATATATATA
1 AAAATATTATATATATA
63018 TATATATAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 25 0.50
34 25 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:63025 original size:33 final size:32
Alignment explanation
Indices: 62934--63026 Score: 134
Period size: 34 Copynumber: 2.8 Consensus size: 32
62924 TTTGAATCCG
62934 AAAATATTATATATATAAT-TAATATAAAAATAT
1 AAAATATTATATATATAATAT-ATA-AAAAATAT
62967 AAAATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAA-T-ATATAAAAAATAT
63001 AAAATATTATATATATATATATATAA
1 AAAATATTATATATATA-ATATATAA
63027 TCGGGGCGGG
Statistics
Matches: 56, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
33 24 0.43
34 27 0.48
35 4 0.07
36 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (32 bp):
AAAATATTATATATATAATATATAAAAAATAT
Found at i:76047 original size:29 final size:30
Alignment explanation
Indices: 76005--76066 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 30
75995 ATCCATAGTG
* *
76005 TGATGGGGAGCGGTGGA-ACCTTGTTGACT
1 TGATGGGAAGCGGTGGAGACATTGTTGACT
76034 TGATGGGAAGCGGTGGAGACATTGTTGACT
1 TGATGGGAAGCGGTGGAGACATTGTTGACT
76064 TGA
1 TGA
76067 ATGGAGCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 16 0.53
30 14 0.47
ACGTcount: A:0.21, C:0.11, G:0.40, T:0.27
Consensus pattern (30 bp):
TGATGGGAAGCGGTGGAGACATTGTTGACT
Found at i:77765 original size:21 final size:19
Alignment explanation
Indices: 77726--77765 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
77716 ATTTTAATCT
*
77726 ATAATATATATTCATAGAA
1 ATAATATATATTCAAAGAA
77745 ATAATATATAATTACAAAGAA
1 ATAATATAT-ATT-CAAAGAA
77766 GATTTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 3 0.17
21 6 0.33
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (19 bp):
ATAATATATATTCAAAGAA
Found at i:80422 original size:17 final size:19
Alignment explanation
Indices: 80400--80437 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
80390 TAATCTTGCA
80400 CTCTTTGA-C-CCATACTT
1 CTCTTTGATCTCCATACTT
*
80417 CTCTTTTATCTCCATACTT
1 CTCTTTGATCTCCATACTT
80436 CT
1 CT
80438 TTTTAACTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 1 0.06
19 10 0.56
ACGTcount: A:0.16, C:0.34, G:0.03, T:0.47
Consensus pattern (19 bp):
CTCTTTGATCTCCATACTT
Found at i:80447 original size:18 final size:19
Alignment explanation
Indices: 80409--80447 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
80399 ACTCTTTGAC
*
80409 CCATACTTCTCTTTTATCT
1 CCATACTTCTCTTTTAACT
80428 CCATACTTCT-TTTTAACT
1 CCATACTTCTCTTTTAACT
80446 CC
1 CC
80448 TCAGAACTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.18, C:0.33, G:0.00, T:0.49
Consensus pattern (19 bp):
CCATACTTCTCTTTTAACT
Found at i:82251 original size:2 final size:2
Alignment explanation
Indices: 82244--82277 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
82234 GAACAGTTGC
82244 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
82278 GTATGTGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82558 original size:60 final size:60
Alignment explanation
Indices: 82476--82620 Score: 148
Period size: 60 Copynumber: 2.4 Consensus size: 60
82466 GATACATCGT
* * * * * * * * *
82476 TAAATTATGACCCTTATTCTAAATTAATTCTTAAACTTTTAAATTTTTTAATTTCATCTC
1 TAAACTATGACTCTCATTCTAAATTAATCCCTAAACTTTTAAATATTCTAAATTCATCCC
* *
82536 TAAACTATGACTCTCATTCTAAATTCATCCCTAAATTTTTAAATATTCTAAATTCATCCC
1 TAAACTATGACTCTCATTCTAAATTAATCCCTAAACTTTTAAATATTCTAAATTCATCCC
* * *
82596 CATACTAT-AATCCTCATTCTAAATT
1 TAAACTATGACT-CTCATTCTAAATT
82621 GGTGCTCAGA
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
59 2 0.03
60 68 0.97
ACGTcount: A:0.34, C:0.20, G:0.01, T:0.44
Consensus pattern (60 bp):
TAAACTATGACTCTCATTCTAAATTAATCCCTAAACTTTTAAATATTCTAAATTCATCCC
Found at i:85034 original size:18 final size:19
Alignment explanation
Indices: 85011--85047 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
85001 GGGGAAAGAA
85011 AAATGA-AAA-AAAATAAAG
1 AAATGATAAAGAAAA-AAAG
85029 AAATGATAAAGAAAAAAAG
1 AAATGATAAAGAAAAAAAG
85048 GATTTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
19 7 0.41
20 4 0.24
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.11
Consensus pattern (19 bp):
AAATGATAAAGAAAAAAAG
Found at i:88323 original size:17 final size:18
Alignment explanation
Indices: 88303--88346 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
88293 AGATTAATTT
*
88303 TTTTATATATAAT-TATA
1 TTTTATATAAAATATATA
*
88320 TTTTATA-AAAATATGTA
1 TTTTATATAAAATATATA
88337 TTTTATATAA
1 TTTTATATAA
88347 TATTAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 4 0.17
17 17 0.74
18 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
TTTTATATAAAATATATA
Found at i:89300 original size:34 final size:33
Alignment explanation
Indices: 89262--89365 Score: 121
Period size: 34 Copynumber: 3.2 Consensus size: 33
89252 CAGTTGAGAT
89262 TAAACAAACCCAAATTGAAATTTCACAGAAACTA
1 TAAACAAACCC-AATTGAAATTTCACAGAAACTA
**
89296 TAAACAAAATC-A--GAAA--TCGA-AGAAACTA
1 TAAACAAACCCAATTGAAATTTC-ACAGAAACTA
89324 TAAACAAACCCAGATTGAAATTTCACAGAAACTA
1 TAAACAAACCCA-ATTGAAATTTCACAGAAACTA
89358 TAAACAAA
1 TAAACAAA
89366 ATCATAAATC
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
28 19 0.33
29 1 0.02
30 5 0.09
32 5 0.09
33 1 0.02
34 27 0.47
ACGTcount: A:0.56, C:0.18, G:0.08, T:0.18
Consensus pattern (33 bp):
TAAACAAACCCAATTGAAATTTCACAGAAACTA
Found at i:89319 original size:28 final size:28
Alignment explanation
Indices: 89288--89381 Score: 91
Period size: 28 Copynumber: 3.1 Consensus size: 28
89278 GAAATTTCAC
89288 AGAAACTATAAACAAAATCAGAAATCGA
1 AGAAACTATAAACAAAATCAGAAATCGA
**
89316 AGAAACTATAAACAAACCCAGATTGAAATTTC-A
1 AGAAACTATAAACAAAATC--A--GAAA--TCGA
*
89349 CAGAAACTATAAACAAAATCATAAATCGA
1 -AGAAACTATAAACAAAATCAGAAATCGA
89378 AGAA
1 AGAA
89382 GTGAAATAAG
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
28 23 0.43
29 1 0.02
30 4 0.08
32 5 0.09
33 1 0.02
34 19 0.36
ACGTcount: A:0.57, C:0.16, G:0.10, T:0.17
Consensus pattern (28 bp):
AGAAACTATAAACAAAATCAGAAATCGA
Found at i:89328 original size:62 final size:62
Alignment explanation
Indices: 89262--89381 Score: 222
Period size: 62 Copynumber: 1.9 Consensus size: 62
89252 CAGTTGAGAT
89262 TAAACAAACCCAAATTGAAATTTCACAGAAACTATAAACAAAATCAGAAATCGAAGAAACTA
1 TAAACAAACCCAAATTGAAATTTCACAGAAACTATAAACAAAATCAGAAATCGAAGAAACTA
* *
89324 TAAACAAACCCAGATTGAAATTTCACAGAAACTATAAACAAAATCATAAATCGAAGAA
1 TAAACAAACCCAAATTGAAATTTCACAGAAACTATAAACAAAATCAGAAATCGAAGAA
89382 GTGAAATAAG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.56, C:0.17, G:0.08, T:0.18
Consensus pattern (62 bp):
TAAACAAACCCAAATTGAAATTTCACAGAAACTATAAACAAAATCAGAAATCGAAGAAACTA
Found at i:90323 original size:14 final size:13
Alignment explanation
Indices: 90291--90324 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
90281 ATTTTTTTAT
90291 TAAAAAAATAAAA
1 TAAAAAAATAAAA
90304 TGAAAAAAATAAAAA
1 T-AAAAAAAT-AAAA
90319 TAAAAA
1 TAAAAA
90325 TAGAAGAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.05
14 13 0.68
15 5 0.26
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (13 bp):
TAAAAAAATAAAA
Found at i:92406 original size:23 final size:23
Alignment explanation
Indices: 92380--92448 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
92370 CACCACAGCT
* *
92380 CGTATAATTACACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
92403 CGTAGAATTGCACCGGAGTGTCG
1 CGTAGAATTGCACCGAAGTGCCA
*
92426 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
92449 TATAATAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:92896 original size:17 final size:17
Alignment explanation
Indices: 92874--92907 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
92864 CACATATCTC
*
92874 ATAGTCATGTATTTCAT
1 ATAGTCATATATTTCAT
*
92891 ATAGTCTTATATTTCAT
1 ATAGTCATATATTTCAT
92908 TATCTTATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (17 bp):
ATAGTCATATATTTCAT
Found at i:92915 original size:15 final size:17
Alignment explanation
Indices: 92883--92915 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
92873 CATAGTCATG
92883 TATTTCATATAGTCTTA
1 TATTTCATATAGTCTTA
92900 TATTTCAT-TA-TCTTA
1 TATTTCATATAGTCTTA
92915 T
1 T
92916 TACTTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 2 0.12
17 8 0.50
ACGTcount: A:0.27, C:0.12, G:0.03, T:0.58
Consensus pattern (17 bp):
TATTTCATATAGTCTTA
Found at i:93315 original size:18 final size:18
Alignment explanation
Indices: 93288--93329 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
93278 CAATGATTCT
93288 TGAA-CTCGTTCAGGCTC
1 TGAATCTCGTTCAGGCTC
*
93305 TGAATCTCGTTTAGGCTC
1 TGAATCTCGTTCAGGCTC
93323 TGAATCT
1 TGAATCT
93330 TTTCTCTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (18 bp):
TGAATCTCGTTCAGGCTC
Found at i:94358 original size:7 final size:8
Alignment explanation
Indices: 94341--94367 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
94331 GCAAAACGTT
94341 AAAAATAA
1 AAAAATAA
94349 AAAAATAA
1 AAAAATAA
94357 AAAAATAA
1 AAAAATAA
94365 AAA
1 AAA
94368 TATTTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAATAA
Found at i:104971 original size:29 final size:29
Alignment explanation
Indices: 104930--104988 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
104920 TCTTTGTGGT
*
104930 GTAGTAAGTGGTTTTTCATGTTTTAACCA
1 GTAGTAAGTGGTTTCTCATGTTTTAACCA
104959 GTAGTAAGTGGTTTCTCATGTTTTAACCA
1 GTAGTAAGTGGTTTCTCATGTTTTAACCA
104988 G
1 G
104989 GAGTGACTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.42
Consensus pattern (29 bp):
GTAGTAAGTGGTTTCTCATGTTTTAACCA
Found at i:108097 original size:21 final size:21
Alignment explanation
Indices: 108073--108119 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
108063 AGTTAGATCT
108073 CATG-AATTTTTCATAAATAGA
1 CATGCAATTTTTC-TAAATAGA
*
108094 CATGCCATTTTTCTAAATA-A
1 CATGCAATTTTTCTAAATAGA
108114 -ATGCAA
1 CATGCAA
108120 ACAAGTCGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 5 0.22
20 1 0.04
21 10 0.43
22 7 0.30
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (21 bp):
CATGCAATTTTTCTAAATAGA
Found at i:117914 original size:2 final size:2
Alignment explanation
Indices: 117907--117932 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
117897 TCTTTTGAAC
117907 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
117933 GTATGTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.