Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001821.1 Hibiscus syriacus cultivar Beakdansim tig00003688_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: 188847
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4844 original size:33 final size:33
Alignment explanation
Indices: 4807--4970 Score: 143
Period size: 33 Copynumber: 5.0 Consensus size: 33
4797 TTGTTCCGGA
*
4807 CAAGTAGCAGGGATGATGCCCCCACATGCAGCC
1 CAAGTAGCAGGGATGATGCCCCCACAAGCAGCC
* * * * *
4840 CAAGTAGCAGGAATGATGCCCCTATAAGAAGGC
1 CAAGTAGCAGGGATGATGCCCCCACAAGCAGCC
* * * * *
4873 CAAGTAGGAGGGACGATGCCTCCGCATGCAGCC
1 CAAGTAGCAGGGATGATGCCCCCACAAGCAGCC
* * *
4906 CAAGTAGTC--GGATTGATGCCCCTATAAGCAGGC
1 CAAGTAG-CAGGGA-TGATGCCCCCACAAGCAGCC
* * *
4939 CAAGTAGCAGTGATGATGCCTCCATAAGCAGC
1 CAAGTAGCAGGGATGATGCCCCCACAAGCAGC
4971 AGGTTAATAT
Statistics
Matches: 99, Mismatches: 28, Indels: 8
0.73 0.21 0.06
Matches are distributed among these distances:
32 4 0.04
33 93 0.94
34 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.28, T:0.16
Consensus pattern (33 bp):
CAAGTAGCAGGGATGATGCCCCCACAAGCAGCC
Found at i:4970 original size:66 final size:66
Alignment explanation
Indices: 4807--4962 Score: 233
Period size: 66 Copynumber: 2.4 Consensus size: 66
4797 TTGTTCCGGA
*
4807 CAAGTAGCAGGGATGATGCCCCCACATGCAGCCCAAGTAGCAGGAATGATGCCCCTATAAGAAGG
1 CAAGTAGCAGGGATGATGCCTCCACATGCAGCCCAAGTAGCAGGAATGATGCCCCTATAAGAAGG
4872 C
66 C
* * * * *
4873 CAAGTAGGAGGGACGATGCCTCCGCATGCAGCCCAAGTAGTC-GGATTGATGCCCCTATAAGCAG
1 CAAGTAGCAGGGATGATGCCTCCACATGCAGCCCAAGTAG-CAGGAATGATGCCCCTATAAGAAG
4937 GC
65 GC
*
4939 CAAGTAGCAGTGATGATGCCTCCA
1 CAAGTAGCAGGGATGATGCCTCCA
4963 TAAGCAGCAG
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
66 78 0.99
67 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.28, T:0.16
Consensus pattern (66 bp):
CAAGTAGCAGGGATGATGCCTCCACATGCAGCCCAAGTAGCAGGAATGATGCCCCTATAAGAAGG
C
Found at i:10443 original size:36 final size:36
Alignment explanation
Indices: 10397--10510 Score: 142
Period size: 36 Copynumber: 3.2 Consensus size: 36
10387 TGAAACATTT
* * *
10397 ATATATTATATAATTTTTAAAACACTTTGAAAATAA
1 ATATAATATATAGTTTTTAAAACATTTTGAAAATAA
*
10433 ATATAATATATAGTTTTTAAAACGTTTTTGAAAAT--
1 ATATAATATATAGTTTTTAAAAC-ATTTTGAAAATAA
* * *
10468 ATATATTATATGGTTTTCAAAACATTTTGAAAATAA
1 ATATAATATATAGTTTTTAAAACATTTTGAAAATAA
10504 ATATAAT
1 ATATAAT
10511 TTTTTAAAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
34 10 0.15
35 20 0.30
36 27 0.41
37 9 0.14
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.43
Consensus pattern (36 bp):
ATATAATATATAGTTTTTAAAACATTTTGAAAATAA
Found at i:10699 original size:36 final size:35
Alignment explanation
Indices: 10396--10697 Score: 166
Period size: 35 Copynumber: 8.7 Consensus size: 35
10386 TTGAAACATT
*
10396 TATATATTATATAATTTTTAAAACAC-TTTGAAAA
1 TATATATTATATAATTTTGAAAACACTTTTGAAAA
* * * **
10430 TAAATATAATATATAGTTTTTAAAACGTTTTTGAAAA
1 T--ATATATTATATAATTTTGAAAACACTTTTGAAAA
** *
10467 TATATATTATATGGTTTTCAAAACA-TTTTGAAAA
1 TATATATTATATAATTTTGAAAACACTTTTGAAAA
* * * *
10501 TAAATA-TA-AT-TTTTTAAAAAGAAACATTTTGAAAACATA
1 TATATATTATATAATTTT-GAAA-ACAC-TTTTG--AA-A-A
*
10540 TATATATTATATAATTTTGAAATCA-TTTTGAAAA
1 TATATATTATATAATTTTGAAAACACTTTTGAAAA
* * *
10574 CT-TATAATATATAATTTTAAAAAAACATTTTCG---A
1 -TATATATTATATAATTTTGAAAACAC-TTTT-GAAAA
* ** *
10608 -A-A-ACTATATAA-TTTGAAAACGTTTTTAAAAA
1 TATATATTATATAATTTTGAAAACACTTTTGAAAA
*
10639 TATATATATATATAATTTT-AAAATACTTTTGAAAA
1 TATATAT-TATATAATTTTGAAAACACTTTTGAAAA
*
10674 TATATATTATATAGTTTTAGAAAA
1 TATATATTATATAATTTT-GAAAA
10698 TATTTTATAT
Statistics
Matches: 206, Mismatches: 33, Indels: 56
0.70 0.11 0.19
Matches are distributed among these distances:
29 4 0.02
30 7 0.03
31 13 0.06
32 7 0.03
33 5 0.02
34 47 0.23
35 53 0.26
36 34 0.17
37 12 0.06
38 6 0.03
39 6 0.03
40 3 0.01
41 5 0.02
42 4 0.02
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (35 bp):
TATATATTATATAATTTTGAAAACACTTTTGAAAA
Found at i:10705 original size:22 final size:23
Alignment explanation
Indices: 10665--10707 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
10655 TTTAAAATAC
10665 TTTTGAAAATATATATTATATAG
1 TTTTGAAAATATATATTATATAG
10688 TTTTAGAAAATAT-T-TTATAT
1 TTTT-GAAAATATATATTATAT
10708 TATTATTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 5 0.26
24 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (23 bp):
TTTTGAAAATATATATTATATAG
Found at i:10738 original size:11 final size:10
Alignment explanation
Indices: 10719--10757 Score: 53
Period size: 11 Copynumber: 3.9 Consensus size: 10
10709 ATTATTATCG
10719 TTTTTATTTA
1 TTTTTATTTA
10729 TTTATTATTTA
1 TTT-TTATTTA
10740 TTTTTA-TTA
1 TTTTTATTTA
*
10749 ATTTTATTT
1 TTTTTATTT
10758 TCATTTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 8 0.31
10 8 0.31
11 10 0.38
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:10743 original size:20 final size:20
Alignment explanation
Indices: 10698--10765 Score: 52
Period size: 20 Copynumber: 3.4 Consensus size: 20
10688 TTTTAGAAAA
*
10698 TATTTTATATTA-TTATTATCG
1 TATTTTAT-TTATTTATTAT-T
10719 T-TTTTATTTATTTATTATT
1 TATTTTATTTATTTATTATT
*
10738 TATTTTTATTAATTTTATT-TT
1 TA-TTTTATTTA-TTTATTATT
*
10759 CATTTTA
1 TATTTTA
10766 ATTGACTAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
19 4 0.10
20 18 0.45
21 12 0.30
22 6 0.15
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.71
Consensus pattern (20 bp):
TATTTTATTTATTTATTATT
Found at i:10763 original size:21 final size:20
Alignment explanation
Indices: 10719--10764 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
10709 ATTATTATCG
* *
10719 TTTTTATTTATTTATTATTTA
1 TTTTTATTAATTTATT-TTCA
10740 TTTTTATTAATTTTATTTTCA
1 TTTTTATTAA-TTTATTTTCA
10761 TTTT
1 TTTT
10765 AATTGACTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTATTAATTTATTTTCA
Found at i:13818 original size:19 final size:19
Alignment explanation
Indices: 13784--13828 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
13774 ATTTAGACAT
13784 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
13802 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
13821 TTTGCATT
1 TTTGCATT
13829 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:17351 original size:84 final size:83
Alignment explanation
Indices: 17159--17851 Score: 743
Period size: 84 Copynumber: 8.4 Consensus size: 83
17149 TAAACAAACT
* *
17159 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC--TGCCAAAGACCCCCGAGTTCGATTACACT
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGTGCCAAAGACCTCCGAGTTCGACTACACT
* *
17222 CAGCTTCGAGGGCACATC
66 CAGCTTCCAAGGCACATC
* * * * * * * * *
17240 ATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGTG-CC-AAAGACCTCCGAGTTCGACTACA
17305 CTCAGC-TCCAAGGCACATC
64 CTCAGCTTCCAAGGCACATC
*
17324 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC--TGCCAAAGACC-CCGAGTTCGATTACACT
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGTGCCAAAGACCTCCGAGTTCGACTACACT
* *
17386 CAGCTTCGAGGGCACATC
66 CAGCTTCCAAGGCACATC
* * * * * * * *
17404 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGTG-CC-AAAGACCTCCGAGTTCGACTACA
*
17469 CTTAGC-TCCAAGGCACATC
64 CTCAGCTTCCAAGGCACATC
* *
17488 ATTTGCAGCATAGCTTAAGTCGAGAGGGGCTATC--TGCCAAAGACC-CCGAGTTCGATTACACT
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGTGCCAAAGACCTCCGAGTTCGACTACACT
* *
17550 CAGCTTCGAGGGCACATC
66 CAGCTTCCAAGGCACATC
* * * * * * * * *
17568 ATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGTG-CC-AAAGACCTCCGAGTTCGACTACA
17633 CTCAGC-TCCAAGGCACATC
64 CTCAGCTTCCAAGGCACATC
* *
17652 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC--TGCCAAAGACCCCCGAGTTCGATTACACT
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGTGCCAAAGACCTCCGAGTTCGACTACACT
* *
17715 CAGCTTCGAGGGCACATC
66 CAGCTTCCAAGGCACATC
* * * * * * **
17733 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAG-CAAAGACCTTTGAGTTCGACTACA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-T-GCCAAAGACCTCCGAGTTCGACTACA
17797 CTCAGC-T-CAACGGCACATC
64 CTCAGCTTCCAA-GGCACATC
17816 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
17852 CTAAAGACCT
Statistics
Matches: 496, Mismatches: 94, Indels: 42
0.78 0.15 0.07
Matches are distributed among these distances:
79 35 0.07
80 115 0.23
81 72 0.15
82 11 0.02
83 45 0.09
84 157 0.32
85 61 0.12
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.23
Consensus pattern (83 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGTGCCAAAGACCTCCGAGTTCGACTACACT
CAGCTTCCAAGGCACATC
Found at i:17874 original size:164 final size:164
Alignment explanation
Indices: 17159--17860 Score: 1282
Period size: 164 Copynumber: 4.3 Consensus size: 164
17149 TAAACAAACT
17159 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA-CCCCGAGTTCGATTACACTCA
*
17224 GCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
65 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
17289 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
130 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
17324 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCGAGTTCGATTACACTCAG
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCGAGTTCGATTACACTCAG
17389 CTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCT
66 CTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCT
*
17454 TCGAGTTCGACTACGCTTAGCTCCAAGGCACATC
131 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
*
17488 ATTTGCAGCATAGCTTAAGTCGAGAGGGGCTATCTGCCAAAGACCCCGAGTTCGATTACACTCAG
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCGAGTTCGATTACACTCAG
*
17553 CTTCGAGGGCACATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCT
66 CTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCT
17618 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
131 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
17652 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA-CCCCGAGTTCGATTACACTCA
* *
17717 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGC-AAAGACC
65 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
* *
17781 TTTGAGTTCGACTACACTCAGCT-CAACGGCACATC
130 TTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATC
*
17816 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCTAAAGACC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
17861 TTCGGGGTCG
Statistics
Matches: 523, Mismatches: 12, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
163 5 0.01
164 400 0.76
165 118 0.23
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.23
Consensus pattern (164 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCGAGTTCGATTACACTCAG
CTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCT
TCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
Found at i:19093 original size:30 final size:30
Alignment explanation
Indices: 19008--19103 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
18998 AAAATATTTT
* * * *
19008 TTTTAATCCAAATAGATACCTAAAATTGTC
1 TTTTAATCAAAATAGGTATCTAAAATTATC
* * *
19038 ATTTTCATCAAAACAAGTA-CATAAAATATAT-
1 -TTTTAATCAAAATAGGTATC-TAAAAT-TATC
19069 TTTTAATCAAAATAGGTATCTAAAATTATC
1 TTTTAATCAAAATAGGTATCTAAAATTATC
19099 TTTTA
1 TTTTA
19104 CCTAAAATAT
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
29 3 0.06
30 27 0.52
31 20 0.38
32 2 0.04
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (30 bp):
TTTTAATCAAAATAGGTATCTAAAATTATC
Found at i:28394 original size:31 final size:32
Alignment explanation
Indices: 28350--28411 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 32
28340 ATTATTAAAA
*
28350 AAATTAAAAAAATATAACGGTAGACACCTAAT
1 AAATTAAAAAAATATAACGGTAAACACCTAAT
28382 AAATT-AAAAAATATAACGGTAAACACCTAA
1 AAATTAAAAAAATATAACGGTAAACACCTAA
28412 AAGTATAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 24 0.83
32 5 0.17
ACGTcount: A:0.58, C:0.13, G:0.08, T:0.21
Consensus pattern (32 bp):
AAATTAAAAAAATATAACGGTAAACACCTAAT
Found at i:29084 original size:37 final size:37
Alignment explanation
Indices: 29007--29086 Score: 101
Period size: 38 Copynumber: 2.1 Consensus size: 37
28997 AACAAGTTAG
* *
29007 AAAATATTTATATATTTTTTTAAAATATTTAAATTCAT
1 AAAA-ATTTATATATTTTTTTAAAATATTAAAAATCAT
29045 AAAAATTTATATAATTTTTTTATAAA-ATTAAAAAT-AT
1 AAAAATTTATAT-ATTTTTTTA-AAATATTAAAAATCAT
29082 AAAAA
1 AAAAA
29087 AGTTTAATGA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
37 15 0.39
38 20 0.53
39 3 0.08
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (37 bp):
AAAAATTTATATATTTTTTTAAAATATTAAAAATCAT
Found at i:34717 original size:33 final size:32
Alignment explanation
Indices: 34673--34773 Score: 118
Period size: 33 Copynumber: 3.2 Consensus size: 32
34663 CTTTCTTAAT
34673 TTACA-AT-ATTCGTAATCATATCTCATAGAA
1 TTACAGATGATTCGTAATCATATCTCATAGAA
*
34703 TTACTTAGA-GATTCGCAATCATATCTCATAGAA
1 TTAC--AGATGATTCGTAATCATATCTCATAGAA
* **
34736 TTACAGATGAGTTCATAATCATATCTTGTAGAA
1 TTACAGATGA-TTCGTAATCATATCTCATAGAA
34769 TTACA
1 TTACA
34774 AAGGGGTTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
30 4 0.07
31 3 0.05
32 3 0.05
33 50 0.83
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.36
Consensus pattern (32 bp):
TTACAGATGATTCGTAATCATATCTCATAGAA
Found at i:37080 original size:11 final size:11
Alignment explanation
Indices: 37064--37089 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
37054 TAACCAAATT
37064 TATAAATAATA
1 TATAAATAATA
37075 TATAAATAATA
1 TATAAATAATA
37086 TATA
1 TATA
37090 TTGTATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TATAAATAATA
Found at i:38000 original size:23 final size:23
Alignment explanation
Indices: 37974--38033 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
37964 CACCACAGCT
37974 CATATAATTGCACCGGAGTGCCA
1 CATATAATTGCACCGGAGTGCCA
* *
37997 CATATAATAGCACCGGAGTGCCG
1 CATATAATTGCACCGGAGTGCCA
* *
38020 CGTAGAATTGCACC
1 CATATAATTGCACC
38034 ATAGTTCCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (23 bp):
CATATAATTGCACCGGAGTGCCA
Found at i:38229 original size:103 final size:103
Alignment explanation
Indices: 38058--38379 Score: 590
Period size: 103 Copynumber: 3.1 Consensus size: 103
38048 TAATGTCCAT
* * * *
38058 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGTTCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
38123 GACTTCACATATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
38161 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
38226 GACTTCATACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
38264 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
38329 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
38367 AAGGACCACATAT
1 AAGGACCACATAT
38380 ACCCTCGACT
Statistics
Matches: 212, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 212 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:38832 original size:16 final size:16
Alignment explanation
Indices: 38811--38852 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
38801 TCATATCAAT
38811 AACACATATACTCATG
1 AACACATATACTCATG
38827 AACACATATACTCATG
1 AACACATATACTCATG
38843 AACACATATA
1 AACACATATA
38853 AATCATAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.48, C:0.24, G:0.05, T:0.24
Consensus pattern (16 bp):
AACACATATACTCATG
Found at i:39266 original size:45 final size:45
Alignment explanation
Indices: 39217--39319 Score: 188
Period size: 45 Copynumber: 2.3 Consensus size: 45
39207 ATGCCTTATA
*
39217 CATCGATGCACTAATTGCATTCGATGCTTCGTTATTAATGGGATG
1 CATCGATGCACTAATTGCATTCAATGCTTCGTTATTAATGGGATG
*
39262 CATCGATGCACTAATTGCATTCAATGTTTCGTTATTAATGGGATG
1 CATCGATGCACTAATTGCATTCAATGCTTCGTTATTAATGGGATG
39307 CATCGATGCACTA
1 CATCGATGCACTA
39320 CTTATGCATT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (45 bp):
CATCGATGCACTAATTGCATTCAATGCTTCGTTATTAATGGGATG
Found at i:39327 original size:64 final size:64
Alignment explanation
Indices: 39259--39396 Score: 165
Period size: 64 Copynumber: 2.2 Consensus size: 64
39249 TATTAATGGG
* * * *
39259 ATGCATCGATGCACTAATTGCATTCAATGT-T-TCGTTATT-AATGGGATGCATCGATGCACTAC
1 ATGCATCGATGCACAAATTGCATTCAATGTATAT-ATT-TTAAAAGAG-TGCATCGATGCACTAC
*
39321 TT
63 TA
* *
39323 ATGCATTGATGCACAAATTGCATTCGATGTATATATTTTAAAAGAGTGCATCGATGCACTACTA
1 ATGCATCGATGCACAAATTGCATTCAATGTATATATTTTAAAAGAGTGCATCGATGCACTACTA
39387 ATGCATCGAT
1 ATGCATCGAT
39397 ACACCTTCAA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
64 55 0.87
65 7 0.11
66 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACAAATTGCATTCAATGTATATATTTTAAAAGAGTGCATCGATGCACTACTA
Found at i:39373 original size:109 final size:109
Alignment explanation
Indices: 39171--39383 Score: 256
Period size: 109 Copynumber: 2.0 Consensus size: 109
39161 CATAAAATGT
* * * *
39171 ATTCGATGTTTGTTTATTATTGGGATGCATCGATGCATGCCTTATACATCGATGCACTAATTGCA
1 ATTCAATGTTTGTTTATTAATGGGATGCATCGATGCATGACTTATACATCGATGCACAAATTGCA
* * *
39236 TTCGATGCTTCGTTATTAATGGGATGCATCGATGCACTAATTGC
66 TTCGATGCTTCATTATTAAAGAGATGCATCGATGCACTAATTGC
* *
39280 ATTCAATGTTTCG-TTATTAATGGGATGCATCGATGCACT-ACTTATGCATTGATGCACAAATTG
1 ATTCAATGTTT-GTTTATTAATGGGATGCATCGATGCA-TGACTTATACATCGATGCACAAATTG
*
39343 CATTCGATG-TAT-ATATTTTAAA-AGAGTGCATCGATGCACTA
64 CATTCGATGCT-TCAT-TATTAAAGAGA-TGCATCGATGCACTA
39384 CTAATGCATC
Statistics
Matches: 89, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
108 4 0.04
109 83 0.93
110 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (109 bp):
ATTCAATGTTTGTTTATTAATGGGATGCATCGATGCATGACTTATACATCGATGCACAAATTGCA
TTCGATGCTTCATTATTAAAGAGATGCATCGATGCACTAATTGC
Found at i:43819 original size:23 final size:23
Alignment explanation
Indices: 43774--43820 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
43764 TATCATTCAT
*
43774 ATCTCTTATCTCATATTCCTATA
1 ATCTCTTATCTCATATTCATATA
*
43797 ATCTCTTATGTCCATA-TCATATA
1 ATCTCTTATCT-CATATTCATATA
43820 A
1 A
43821 CATATACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.30, C:0.23, G:0.02, T:0.45
Consensus pattern (23 bp):
ATCTCTTATCTCATATTCATATA
Found at i:44131 original size:23 final size:23
Alignment explanation
Indices: 44105--44181 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
44095 ACCACAGCTC
44105 ATATAATTGCACCGAAGTGCCAT
1 ATATAATTGCACCGAAGTGCCAT
* * **
44128 ATATAATAGCACCGGAGTGCCGC
1 ATATAATTGCACCGAAGTGCCAT
* * *
44151 GTAGAATTGCACCGTAGTGCCAT
1 ATATAATTGCACCGAAGTGCCAT
44174 ATAATAAT
1 AT-ATAAT
44182 GTCCATAAGG
Statistics
Matches: 41, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
23 37 0.90
24 4 0.10
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (23 bp):
ATATAATTGCACCGAAGTGCCAT
Found at i:44359 original size:103 final size:103
Alignment explanation
Indices: 44191--44508 Score: 573
Period size: 103 Copynumber: 3.1 Consensus size: 103
44181 TGTCCATAAG
* * *
44191 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
44256 TTCATACATGTTCCAAAGAATACATATATGTCCCGAAT
66 TTCATACATGTTCCAAAGAATACATATATGTCCCGAAT
44294 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
*
44359 TTCATACATGTTCCAAAGAATACATATATGTCTCGAAT
66 TTCATACATGTTCCAAAGAATACATATATGTCCCGAAT
*
44397 AACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
* *
44462 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TTCATACATGTTCCAAAGAATACATATATGTCCCGAAT
44500 GACCACATA
1 GACCACATA
44509 GACCCTCGAC
Statistics
Matches: 206, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 206 1.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
TTCATACATGTTCCAAAGAATACATATATGTCCCGAAT
Found at i:45353 original size:64 final size:64
Alignment explanation
Indices: 45245--45465 Score: 223
Period size: 64 Copynumber: 3.5 Consensus size: 64
45235 TAATGAAGGT
* * * * * * * ** *
45245 ATGCATCAATGCACTACTGATACATCGGTGCATAAAATGTATTCGATGTTTGTTTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTTTCCTTATTAATGGG
* *
45309 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACAAATTGCATTCGATGTTTCCTTATTAATGGG
* ** **
45373 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCAATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGT-TTCCTTATTAATGGG
**
45436 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
45466 ACACCTTCAA
Statistics
Matches: 132, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
63 3 0.02
64 124 0.94
65 5 0.04
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTTTCCTTATTAATGGG
Found at i:51592 original size:31 final size:31
Alignment explanation
Indices: 51549--51609 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
51539 TAATTATGTG
* **
51549 ATACATATCATGTATTTAAAGTGATGACATA
1 ATACATACCATGTATACAAAGTGATGACATA
*
51580 ATACATACCATGTGTACAAAGTGATGACAT
1 ATACATACCATGTATACAAAGTGATGACAT
51610 GATTTGTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (31 bp):
ATACATACCATGTATACAAAGTGATGACATA
Found at i:64698 original size:323 final size:324
Alignment explanation
Indices: 63640--64937 Score: 2330
Period size: 324 Copynumber: 4.0 Consensus size: 324
63630 TCATTGAAAT
* *
63640 CTCAATTGGCCTTTTGAGCTGATTTAAGATCAATTACACTATATTAAGTGCAATGGAATGTTAAA
1 CTCAATTGGCCTTTTGAGATGATTTAAGATCAATGACACTATATTAAGTGCAATGGAATGTTAAA
* *
63705 AAACATTGGACACACTAAGATATCCCTAAAGATAAAATTAAGAATACAACCATATGGTAATGTTT
66 AAACGTTGGACACACTAAGATATCCCTAAAAATAAAATTAAGAATACAACCATATGGTAATGTTT
*
63770 TACTGTAGTTCCACTCTTTTAATGACAACATCAAGAAGTTTGAGAAAAATAATCATAATAAAGTT
131 TACTGTAGTTCCACTCTTTTAATGACAACATCAACAAGTTTGAGAAAAATAATCATAATAAAGTT
* *
63835 TAGACAAATTTATTATTTGACATGATAAAACCACCAATAATTACATGCATAACTTTACCTTCGGA
196 TAGACAAATTTATTATTTGACATGATAAAACCACCAATAATCACATGCATAGCTTTACCTTCGGA
63900 AGGACAAAGAAACCAAATGATCATGAGAAGAAAGAAACAATCCGAAAACTTTTGGGATGTGGAA
261 AGGACAAAGAAACCAAATGATCATGAGAAGAAAGAAACAATCCGAAAACTTTTGGGATGTGGAA
*
63964 CTCAATTGGCCTTTTGAGCTGATTTAAGATCAATGACACTATATTAAGTGCAATGGAATGTTAAA
1 CTCAATTGGCCTTTTGAGATGATTTAAGATCAATGACACTATATTAAGTGCAATGGAATGTTAAA
* *
64029 AAACGTTGGACACCCTAAGATATCCCTAAAGATAAAATTAAGAATACAACCATATGGTAATGTTT
66 AAACGTTGGACACACTAAGATATCCCTAAAAATAAAATTAAGAATACAACCATATGGTAATGTTT
*
64094 TACTGTAGTTCCACTCTTTTAATGACAACATCAGCAAGTTTGAGAAAAATAATCATAATAAAGTT
131 TACTGTAGTTCCACTCTTTTAATGACAACATCAACAAGTTTGAGAAAAATAATCATAATAAAGTT
*
64159 TAGACAACTTTATTATTTGACATGATAAAACCACCAATAATCACATGCATAGCTTTACCTTCGGA
196 TAGACAAATTTATTATTTGACATGATAAAACCACCAATAATCACATGCATAGCTTTACCTTCGGA
64224 AGGACAAAGAAACCAAATGATCATGAGAAGAAAGAAACAATCCGAAAACTTTTGGGATGTGGAA
261 AGGACAAAGAAACCAAATGATCATGAGAAGAAAGAAACAATCCGAAAACTTTTGGGATGTGGAA
64288 CTCAATTGGCCTTTTGAGATGATTTAAGATCAATGACACTATATTAAGTGCAATGGAATGTTAAA
1 CTCAATTGGCCTTTTGAGATGATTTAAGATCAATGACACTATATTAAGTGCAATGGAATGTTAAA
*
64353 AAACGTTGGACACACAAAGATATCCCTAAAAATAAAATTAAGAATACAACCATATGGTAATGTTT
66 AAACGTTGGACACACTAAGATATCCCTAAAAATAAAATTAAGAATACAACCATATGGTAATGTTT
64418 TACTGTAGTTCCACTCTTTTAATGACAACATCAACAAGTTTGAGAAAAATAATCATAATAAAGTT
131 TACTGTAGTTCCACTCTTTTAATGACAACATCAACAAGTTTGAGAAAAATAATCATAATAAAGTT
64483 TAGACAAATTTATTATTTG-CATGATAAAACCACCAATAATCACATGCATAGCTTTACCTTCGGA
196 TAGACAAATTTATTATTTGACATGATAAAACCACCAATAATCACATGCATAGCTTTACCTTCGGA
*
64547 AGGACAAAGAAACCAAATGATCATGAGAAGAAAGAAACAATCTGAACAA-TTTTGGGATGTGGAA
261 AGGACAAAGAAACCAAATGATCATGAGAAGAAAGAAACAATCCGAA-AACTTTTGGGATGTGGAA
* *
64611 CTCAATTGGCCTTTTGAGATGATTTAAGATCAATGACGCTATATTAAGTGCAATGGAATGTTCAA
1 CTCAATTGGCCTTTTGAGATGATTTAAGATCAATGACACTATATTAAGTGCAATGGAATGTTAAA
* *
64676 AAACGTTGGACACCCTAAGATATCTCTAAAAATAAAATTAAGAATACAACCATATGGTAATGTTT
66 AAACGTTGGACACACTAAGATATCCCTAAAAATAAAATTAAGAATACAACCATATGGTAATGTTT
* * * *
64741 TACTGTAGTTCCACTCTTTTAGTAACAACATCAATAAGCTTGAGAAAAATAATCATAATAAAGTT
131 TACTGTAGTTCCACTCTTTTAATGACAACATCAACAAGTTTGAGAAAAATAATCATAATAAAGTT
* *
64806 TAGACAAATTTATTATTTGGCATGATAAAACCACCAATAATCACATGCATAGCTTTACCTTCAGA
196 TAGACAAATTTATTATTTGACATGATAAAACCACCAATAATCACATGCATAGCTTTACCTTCGGA
* * *
64871 AGGACAAAGAAACCAAATGATCATGAGAAAAAAGAGACAATCCGAAAACTTTTGGGACGTGGAA
261 AGGACAAAGAAACCAAATGATCATGAGAAGAAAGAAACAATCCGAAAACTTTTGGGATGTGGAA
64935 CTC
1 CTC
64938 TCATTAGGGA
Statistics
Matches: 942, Mismatches: 29, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
323 312 0.33
324 630 0.67
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (324 bp):
CTCAATTGGCCTTTTGAGATGATTTAAGATCAATGACACTATATTAAGTGCAATGGAATGTTAAA
AAACGTTGGACACACTAAGATATCCCTAAAAATAAAATTAAGAATACAACCATATGGTAATGTTT
TACTGTAGTTCCACTCTTTTAATGACAACATCAACAAGTTTGAGAAAAATAATCATAATAAAGTT
TAGACAAATTTATTATTTGACATGATAAAACCACCAATAATCACATGCATAGCTTTACCTTCGGA
AGGACAAAGAAACCAAATGATCATGAGAAGAAAGAAACAATCCGAAAACTTTTGGGATGTGGAA
Found at i:64875 original size:647 final size:648
Alignment explanation
Indices: 63640--64937 Score: 2348
Period size: 647 Copynumber: 2.0 Consensus size: 648
63630 TCATTGAAAT
* *
63640 CTCAATTGGCCTTTTGAGCTGATTTAAGATCAATTACACTATATTAAGTGCAATGGAATGTTAAA
1 CTCAATTGGCCTTTTGAGATGATTTAAGATCAATGACACTATATTAAGTGCAATGGAATGTTAAA
* *
63705 AAACATTGGACACACTAAGATATCCCTAAAGATAAAATTAAGAATACAACCATATGGTAATGTTT
66 AAACATTGGACACACAAAGATATCCCTAAAAATAAAATTAAGAATACAACCATATGGTAATGTTT
*
63770 TACTGTAGTTCCACTCTTTTAATGACAACATCAAGAAGTTTGAGAAAAATAATCATAATAAAGTT
131 TACTGTAGTTCCACTCTTTTAATGACAACATCAACAAGTTTGAGAAAAATAATCATAATAAAGTT
*
63835 TAGACAAATTTATTATTTGACATGATAAAACCACCAATAATTACATGCATAACTTTACCTTCGGA
196 TAGACAAATTTATTATTTGACATGATAAAACCACCAATAATCACATGCATAACTTTACCTTCGGA
63900 AGGACAAAGAAACCAAATGATCATGAGAAGAAAGAAACAATCCGAAAACTTTTGGGATGTGGAAC
261 AGGACAAAGAAACCAAATGATCATGAGAAGAAAGAAACAATCCGAAAACTTTTGGGATGTGGAAC
*
63965 TCAATTGGCCTTTTGAGCTGATTTAAGATCAATGACACTATATTAAGTGCAATGGAATGTTAAAA
326 TCAATTGGCCTTTTGAGATGATTTAAGATCAATGACACTATATTAAGTGCAATGGAATGTTAAAA
*
64030 AACGTTGGACACCCTAAGATATCCCTAAAGATAAAATTAAGAATACAACCATATGGTAATGTTTT
391 AACGTTGGACACCCTAAGATATCCCTAAAAATAAAATTAAGAATACAACCATATGGTAATGTTTT
* * *
64095 ACTGTAGTTCCACTCTTTTAATGACAACATCAGCAAGTTTGAGAAAAATAATCATAATAAAGTTT
456 ACTGTAGTTCCACTCTTTTAATAACAACATCAACAAGCTTGAGAAAAATAATCATAATAAAGTTT
* *
64160 AGACAACTTTATTATTTGACATGATAAAACCACCAATAATCACATGCATAGCTTTACCTTCGGAA
521 AGACAAATTTATTATTTGACATGATAAAACCACCAATAATCACATGCATAGCTTTACCTTCAGAA
* *
64225 GGACAAAGAAACCAAATGATCATGAGAAGAAAGAAACAATCCGAAAACTTTTGGGATGTGGAA
586 GGACAAAGAAACCAAATGATCATGAGAAAAAAGAAACAATCCGAAAACTTTTGGGACGTGGAA
64288 CTCAATTGGCCTTTTGAGATGATTTAAGATCAATGACACTATATTAAGTGCAATGGAATGTTAAA
1 CTCAATTGGCCTTTTGAGATGATTTAAGATCAATGACACTATATTAAGTGCAATGGAATGTTAAA
*
64353 AAACGTTGGACACACAAAGATATCCCTAAAAATAAAATTAAGAATACAACCATATGGTAATGTTT
66 AAACATTGGACACACAAAGATATCCCTAAAAATAAAATTAAGAATACAACCATATGGTAATGTTT
64418 TACTGTAGTTCCACTCTTTTAATGACAACATCAACAAGTTTGAGAAAAATAATCATAATAAAGTT
131 TACTGTAGTTCCACTCTTTTAATGACAACATCAACAAGTTTGAGAAAAATAATCATAATAAAGTT
*
64483 TAGACAAATTTATTATTTG-CATGATAAAACCACCAATAATCACATGCATAGCTTTACCTTCGGA
196 TAGACAAATTTATTATTTGACATGATAAAACCACCAATAATCACATGCATAACTTTACCTTCGGA
*
64547 AGGACAAAGAAACCAAATGATCATGAGAAGAAAGAAACAATCTGAACAA-TTTTGGGATGTGGAA
261 AGGACAAAGAAACCAAATGATCATGAGAAGAAAGAAACAATCCGAA-AACTTTTGGGATGTGGAA
* *
64611 CTCAATTGGCCTTTTGAGATGATTTAAGATCAATGACGCTATATTAAGTGCAATGGAATGTTCAA
325 CTCAATTGGCCTTTTGAGATGATTTAAGATCAATGACACTATATTAAGTGCAATGGAATGTTAAA
*
64676 AAACGTTGGACACCCTAAGATATCTCTAAAAATAAAATTAAGAATACAACCATATGGTAATGTTT
390 AAACGTTGGACACCCTAAGATATCCCTAAAAATAAAATTAAGAATACAACCATATGGTAATGTTT
* *
64741 TACTGTAGTTCCACTCTTTTAGTAACAACATCAATAAGCTTGAGAAAAATAATCATAATAAAGTT
455 TACTGTAGTTCCACTCTTTTAATAACAACATCAACAAGCTTGAGAAAAATAATCATAATAAAGTT
*
64806 TAGACAAATTTATTATTTGGCATGATAAAACCACCAATAATCACATGCATAGCTTTACCTTCAGA
520 TAGACAAATTTATTATTTGACATGATAAAACCACCAATAATCACATGCATAGCTTTACCTTCAGA
*
64871 AGGACAAAGAAACCAAATGATCATGAGAAAAAAGAGACAATCCGAAAACTTTTGGGACGTGGAA
585 AGGACAAAGAAACCAAATGATCATGAGAAAAAAGAAACAATCCGAAAACTTTTGGGACGTGGAA
64935 CTC
1 CTC
64938 TCATTAGGGA
Statistics
Matches: 624, Mismatches: 25, Indels: 3
0.96 0.04 0.00
Matches are distributed among these distances:
647 414 0.66
648 210 0.34
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (648 bp):
CTCAATTGGCCTTTTGAGATGATTTAAGATCAATGACACTATATTAAGTGCAATGGAATGTTAAA
AAACATTGGACACACAAAGATATCCCTAAAAATAAAATTAAGAATACAACCATATGGTAATGTTT
TACTGTAGTTCCACTCTTTTAATGACAACATCAACAAGTTTGAGAAAAATAATCATAATAAAGTT
TAGACAAATTTATTATTTGACATGATAAAACCACCAATAATCACATGCATAACTTTACCTTCGGA
AGGACAAAGAAACCAAATGATCATGAGAAGAAAGAAACAATCCGAAAACTTTTGGGATGTGGAAC
TCAATTGGCCTTTTGAGATGATTTAAGATCAATGACACTATATTAAGTGCAATGGAATGTTAAAA
AACGTTGGACACCCTAAGATATCCCTAAAAATAAAATTAAGAATACAACCATATGGTAATGTTTT
ACTGTAGTTCCACTCTTTTAATAACAACATCAACAAGCTTGAGAAAAATAATCATAATAAAGTTT
AGACAAATTTATTATTTGACATGATAAAACCACCAATAATCACATGCATAGCTTTACCTTCAGAA
GGACAAAGAAACCAAATGATCATGAGAAAAAAGAAACAATCCGAAAACTTTTGGGACGTGGAA
Found at i:66765 original size:21 final size:21
Alignment explanation
Indices: 66713--66765 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
66703 ATTTTTCACG
66713 AAAATATATAA-CAAATTATTT
1 AAAATATA-AATCAAATTATTT
* * * *
66734 AAAAAAAAAATCATATTTTTT
1 AAAATATAAATCAAATTATTT
66755 AAAATATAAAT
1 AAAATATAAAT
66766 TTTAACAATT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAATATAAATCAAATTATTT
Found at i:68970 original size:28 final size:28
Alignment explanation
Indices: 68927--68981 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
68917 ATCGTCGTTC
* *
68927 TTTCAAGCATTGATTTGACGACATAATG
1 TTTCAAGCACTAATTTGACGACATAATG
* *
68955 TTTCAAGCACTAATTTGATGGCATAAT
1 TTTCAAGCACTAATTTGACGACATAAT
68982 ATAAACAGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (28 bp):
TTTCAAGCACTAATTTGACGACATAATG
Found at i:69486 original size:16 final size:17
Alignment explanation
Indices: 69465--69497 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
69455 TTTTCATAAA
69465 TTAATA-AAATTAATTT
1 TTAATATAAATTAATTT
*
69481 TTAATATAAATTCATTT
1 TTAATATAAATTAATTT
69498 GGTTTTTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAATATAAATTAATTT
Found at i:74218 original size:38 final size:38
Alignment explanation
Indices: 74186--74268 Score: 130
Period size: 38 Copynumber: 2.2 Consensus size: 38
74176 TGAAGGGTTG
*
74186 AAAAGGCAGCAGCTATAATACTTAATTATGAAGGAATT
1 AAAAGGCAACAGCTATAATACTTAATTATGAAGGAATT
* *
74224 ATAAGGCAACATCTATAATACTTAATTATGAAGGAATT
1 AAAAGGCAACAGCTATAATACTTAATTATGAAGGAATT
*
74262 ATAAGGC
1 AAAAGGC
74269 GGCAAGTCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.45, C:0.11, G:0.17, T:0.28
Consensus pattern (38 bp):
AAAAGGCAACAGCTATAATACTTAATTATGAAGGAATT
Found at i:87180 original size:50 final size:50
Alignment explanation
Indices: 87101--87201 Score: 136
Period size: 50 Copynumber: 2.0 Consensus size: 50
87091 AAATTTAACG
* *
87101 ATTTATTTCTTTCTTTCAAAATAGAATCATACTTGATTTTCAAGAAAATA
1 ATTTATTTCTTTCTTTCAAAATAGAATCATACTTAATTTCCAAGAAAATA
87151 ATTTATTTTCTTT-TTT-AAAAGTATG-ATCATACTTAATTTCCAAGAAAATA
1 ATTTA-TTTCTTTCTTTCAAAA-TA-GAATCATACTTAATTTCCAAGAAAATA
87201 A
1 A
87202 ATGTAACACC
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
49 4 0.09
50 34 0.74
51 8 0.17
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.45
Consensus pattern (50 bp):
ATTTATTTCTTTCTTTCAAAATAGAATCATACTTAATTTCCAAGAAAATA
Found at i:87987 original size:13 final size:13
Alignment explanation
Indices: 87968--88043 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 13
87958 AACCCGACCC
87968 GACCCGACCCATT
1 GACCCGACCCATT
* *
87981 TACCCGACCCGTT
1 GACCCGACCCATT
87994 GACCCGACCCGACCTGTT
1 GACCCGACCC-A----TT
*
88012 GACCCGACCCGTT
1 GACCCGACCCATT
* *
88025 GACCCCACCCGTT
1 GACCCGACCCATT
88038 GACCCG
1 GACCCG
88044 TTCACCGTTG
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
13 39 0.76
18 12 0.24
ACGTcount: A:0.17, C:0.47, G:0.20, T:0.16
Consensus pattern (13 bp):
GACCCGACCCATT
Found at i:87998 original size:31 final size:31
Alignment explanation
Indices: 87963--88035 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
87953 GTCATAACCC
*
87963 GACCCGACCCGACCCATTTACCCGACCCGTT
1 GACCCGACCCGACCCATTGACCCGACCCGTT
**
87994 GACCCGACCCGACCTGTTGACCCGACCCGTT
1 GACCCGACCCGACCCATTGACCCGACCCGTT
*
88025 GACCCCACCCG
1 GACCCGACCCG
88036 TTGACCCGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.18, C:0.49, G:0.19, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGACCCATTGACCCGACCCGTT
Found at i:88003 original size:26 final size:26
Alignment explanation
Indices: 87968--88043 Score: 80
Period size: 31 Copynumber: 2.7 Consensus size: 26
87958 AACCCGACCC
87968 GACCCGACCCATTTACCCGACCCGTT
1 GACCCGACCCATTTACCCGACCCGTT
87994 GACCCGACCCGACCTGTTGACCCGACCCGTT
1 GACCCGACCC-A--T-TT-ACCCGACCCGTT
* * *
88025 GACCCCACCCGTTGACCCG
1 GACCCGACCCATTTACCCG
88044 TTCACCGTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
26 15 0.36
27 2 0.05
28 1 0.02
29 1 0.02
30 2 0.05
31 21 0.50
ACGTcount: A:0.17, C:0.47, G:0.20, T:0.16
Consensus pattern (26 bp):
GACCCGACCCATTTACCCGACCCGTT
Found at i:88035 original size:18 final size:18
Alignment explanation
Indices: 87982--88022 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
87972 CGACCCATTT
87982 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
*
88000 ACCCGACCTGTTGACCCG
1 ACCCGACCCGTTGACCCG
88018 ACCCG
1 ACCCG
88023 TTGACCCCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.49, G:0.22, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:89394 original size:18 final size:18
Alignment explanation
Indices: 89368--89405 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
89358 TCGAAAGGAC
*
89368 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
89386 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
89404 TG
1 TG
89406 GATGACAGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:90586 original size:48 final size:48
Alignment explanation
Indices: 90531--90641 Score: 120
Period size: 48 Copynumber: 2.3 Consensus size: 48
90521 AATTATTTTA
*
90531 TCTGATTTCTGACT-TGAATTCTGTTCCGATA-CATG-ACATGAATTCTGT
1 TCTGATTTCTGA-TATGAATTCTGTTCCAATATC-TGTAC-TGAATTCTGT
* * * *
90579 TCTGATTTTTGATATGGATTCTGTTCTAATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGTTCCAATATCTGTACTGAATTCTGT
*
90627 TTTGATTTCTGATAT
1 TCTGATTTCTGATAT
90642 CTCCGTTTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
47 1 0.02
48 50 0.94
49 2 0.04
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.49
Consensus pattern (48 bp):
TCTGATTTCTGATATGAATTCTGTTCCAATATCTGTACTGAATTCTGT
Found at i:90599 original size:24 final size:24
Alignment explanation
Indices: 90531--90641 Score: 100
Period size: 24 Copynumber: 4.6 Consensus size: 24
90521 AATTATTTTA
90531 TCTGATTTCTGACT-TGAATTCTGT
1 TCTGATTTCTGA-TATGAATTCTGT
* * *
90555 TCCGA-TACATGACATGAATTCTGT
1 TCTGATTTC-TGATATGAATTCTGT
* *
90579 TCTGATTTTTGATATGGATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
* * * *
90603 TCTAATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
*
90627 TTTGATTTCTGATAT
1 TCTGATTTCTGATAT
90642 CTCCGTTTAA
Statistics
Matches: 65, Mismatches: 19, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
23 2 0.03
24 62 0.95
25 1 0.02
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.49
Consensus pattern (24 bp):
TCTGATTTCTGATATGAATTCTGT
Found at i:90615 original size:12 final size:12
Alignment explanation
Indices: 90569--90637 Score: 59
Period size: 12 Copynumber: 5.8 Consensus size: 12
90559 ATACATGACA
90569 TGAATTCTGTTC
1 TGAATTCTGTTC
* * * *
90581 TGATTTTTGATA
1 TGAATTCTGTTC
*
90593 TGGATTCTGTTC
1 TGAATTCTGTTC
90605 T-AATATCTGTTC
1 TGAAT-TCTGTTC
*
90617 TGAATTCTGTTT
1 TGAATTCTGTTC
*
90629 TGATTTCTG
1 TGAATTCTG
90638 ATATCTCCGT
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 2 0.05
12 38 0.88
13 3 0.07
ACGTcount: A:0.17, C:0.12, G:0.17, T:0.54
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:91614 original size:39 final size:39
Alignment explanation
Indices: 91560--91655 Score: 165
Period size: 39 Copynumber: 2.5 Consensus size: 39
91550 AATCTAGCTG
* *
91560 TTTATTTCATTTTACAAGATAGGAAAATAAACCCAATGA
1 TTTATTTCCTTTTACAAAATAGGAAAATAAACCCAATGA
*
91599 TTTATTTCCTTTTACAAAATAGGAAAATAAATCCAATGA
1 TTTATTTCCTTTTACAAAATAGGAAAATAAACCCAATGA
91638 TTTATTTCCTTTTACAAA
1 TTTATTTCCTTTTACAAA
91656 CCAATATCAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.39
Consensus pattern (39 bp):
TTTATTTCCTTTTACAAAATAGGAAAATAAACCCAATGA
Found at i:91750 original size:48 final size:49
Alignment explanation
Indices: 91684--91781 Score: 146
Period size: 48 Copynumber: 2.0 Consensus size: 49
91674 CTCAGGAAAA
*
91684 CAATTTATTTTCTATTACAAAATATGAAAATAAAT-CAACGATTTGTTT
1 CAATTTATTTTCTATTACAAAATATGAAAATAAATCCAACGATTTATTT
* *
91732 CAATTTA-TTTCATTTTACAAAATATGAAACTAAATCCAACGATTTATTT
1 CAATTTATTTTC-TATTACAAAATATGAAAATAAATCCAACGATTTATTT
91781 C
1 C
91782 CTTTTATAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
47 4 0.09
48 28 0.62
49 13 0.29
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.41
Consensus pattern (49 bp):
CAATTTATTTTCTATTACAAAATATGAAAATAAATCCAACGATTTATTT
Found at i:91794 original size:40 final size:39
Alignment explanation
Indices: 91734--91868 Score: 152
Period size: 40 Copynumber: 3.5 Consensus size: 39
91724 ATTTGTTTCA
* * *
91734 ATTTATTTCATTTTA-CAAAATATGAAACTAAATCCAACG
1 ATTTATTTCCTTTTATAAAAATA-GAAAATAAATCCAACG
*
91773 ATTTATTTCCTTTTATAAAAATAGGAAAATAAATTC-ACTG
1 ATTTATTTCCTTTTATAAAAATA-GAAAATAAATCCAAC-G
* *
91813 ATTTATTTCC--TTATACAAATAGTAAAATAAATCAAACG
1 ATTTATTTCCTTTTATAAAAATAG-AAAATAAATCCAACG
91851 ATTTATTTCCTTTTATAA
1 ATTTATTTCCTTTTATAA
91869 TTAGAATCAT
Statistics
Matches: 81, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
37 1 0.01
38 30 0.37
39 18 0.22
40 32 0.40
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.40
Consensus pattern (39 bp):
ATTTATTTCCTTTTATAAAAATAGAAAATAAATCCAACG
Found at i:91840 original size:38 final size:37
Alignment explanation
Indices: 91734--91862 Score: 134
Period size: 38 Copynumber: 3.3 Consensus size: 37
91724 ATTTGTTTCA
* * * *
91734 ATTTATTTCATTTTACAAAATATGAAACTAAATCCAACG
1 ATTTATTTCCTTATA-AAAATAGGAAAATAAAT-CAACG
91773 ATTTATTTCCTTTTATAAAAATAGGAAAATAAATTC-ACTG
1 ATTTATTTCC--TTATAAAAATAGGAAAATAAA-TCAAC-G
* *
91813 ATTTATTTCCTTATACAAATAGTAAAATAAATCAAACG
1 ATTTATTTCCTTATAAAAATAGGAAAATAAATC-AACG
91851 ATTTATTTCCTT
1 ATTTATTTCCTT
91863 TTATAATTAG
Statistics
Matches: 78, Mismatches: 6, Indels: 13
0.80 0.06 0.13
Matches are distributed among these distances:
37 2 0.03
38 32 0.41
39 13 0.17
40 26 0.33
41 5 0.06
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.40
Consensus pattern (37 bp):
ATTTATTTCCTTATAAAAATAGGAAAATAAATCAACG
Found at i:92080 original size:58 final size:58
Alignment explanation
Indices: 91996--92208 Score: 246
Period size: 58 Copynumber: 3.8 Consensus size: 58
91986 TAGAATCATT
*
91996 TCAAGGAAATAAATTCAACAATTTATTTTCCTTACAAAATTAGAATCATTCAAGAATC
1 TCAAGGAAATAAATTCAACAATTTATTTTCCTTACAAAATTAGAATCATTCAAGATTC
* * * *
92054 TCAAGGAAATAAATTCAGCTATTTATTTTCTTTAC--AA--AG-----TTAAAGATTC
1 TCAAGGAAATAAATTCAACAATTTATTTTCCTTACAAAATTAGAATCATTCAAGATTC
* ** * *
92103 TCAAGGAAATAAATTCAACTATTTATTTTCCTTACAATGTTAGAATTATTCAACATTC
1 TCAAGGAAATAAATTCAACAATTTATTTTCCTTACAAAATTAGAATCATTCAAGATTC
* * *
92161 TCAAGGAAATAAATTCAACAATTTATTTTTCTTACGAAGTTAGAATCA
1 TCAAGGAAATAAATTCAACAATTTATTTTCCTTACAAAATTAGAATCA
92209 ACGCAAGATT
Statistics
Matches: 130, Mismatches: 16, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
49 41 0.32
53 2 0.02
54 2 0.02
56 2 0.02
58 83 0.64
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (58 bp):
TCAAGGAAATAAATTCAACAATTTATTTTCCTTACAAAATTAGAATCATTCAAGATTC
Found at i:92109 original size:49 final size:49
Alignment explanation
Indices: 92047--92144 Score: 160
Period size: 49 Copynumber: 2.0 Consensus size: 49
92037 AGAATCATTC
* *
92047 AAGAATCTCAAGGAAATAAATTCAGCTATTTATTTTCTTTACAAAGTTA
1 AAGAATCTCAAGGAAATAAATTCAACTATTTATTTTCCTTACAAAGTTA
* *
92096 AAGATTCTCAAGGAAATAAATTCAACTATTTATTTTCCTTACAATGTTA
1 AAGAATCTCAAGGAAATAAATTCAACTATTTATTTTCCTTACAAAGTTA
92145 GAATTATTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (49 bp):
AAGAATCTCAAGGAAATAAATTCAACTATTTATTTTCCTTACAAAGTTA
Found at i:92127 original size:107 final size:107
Alignment explanation
Indices: 91996--92202 Score: 317
Period size: 107 Copynumber: 1.9 Consensus size: 107
91986 TAGAATCATT
*
91996 TCAAGGAAATAAATTCAACAATTTATTTTCCTTACAAAATTAGAATCATTCAAGAATCTCAAGGA
1 TCAAGGAAATAAATTCAACAATTTATTTTCCTTACAAAATTAGAATCATTCAACAATCTCAAGGA
* *
92061 AATAAATTCAGCTATTTA-TTTTCTTTACAAAGTTAAAGATTC
66 AATAAATTCAACAATTTATTTTTC-TTACAAAGTTAAAGATTC
* ** * *
92103 TCAAGGAAATAAATTCAACTATTTATTTTCCTTACAATGTTAGAATTATTCAACATTCTCAAGGA
1 TCAAGGAAATAAATTCAACAATTTATTTTCCTTACAAAATTAGAATCATTCAACAATCTCAAGGA
*
92168 AATAAATTCAACAATTTATTTTTCTTACGAAGTTA
66 AATAAATTCAACAATTTATTTTTCTTACAAAGTTA
92203 GAATCAACGC
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
107 85 0.94
108 5 0.06
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (107 bp):
TCAAGGAAATAAATTCAACAATTTATTTTCCTTACAAAATTAGAATCATTCAACAATCTCAAGGA
AATAAATTCAACAATTTATTTTTCTTACAAAGTTAAAGATTC
Found at i:92408 original size:45 final size:46
Alignment explanation
Indices: 92357--92604 Score: 260
Period size: 45 Copynumber: 5.5 Consensus size: 46
92347 GAATTAATCC
* *
92357 TTTAATTTTACG-AATC-CATTAATCGAAAGGAACTAATCCTTTGAT
1 TTTAATTTT-CGCAATCTCAATAATCGAAAGAAACTAATCCTTTGAT
*
92402 TTTAATTTTCGCAATC-CAATAATTGAAAGAAACTAATCCTTTGAT
1 TTTAATTTTCGCAATCTCAATAATCGAAAGAAACTAATCCTTTGAT
* *
92447 TTTAATTTTTGC-ATCTCAATAATCGAAAGGAAA-TAATCCATTGAT
1 TTTAATTTTCGCAATCTCAATAATCGAAA-GAAACTAATCCTTTGAT
* *
92492 TTTAATTTTGGCAA-CTCAATAATCAAAAGAAACTAATCCTTTGAT
1 TTTAATTTTCGCAATCTCAATAATCGAAAGAAACTAATCCTTTGAT
** * * * * **
92537 TTTGTTTTTGGCAA-CACAATAATCAAAAGGAACTAATAATTTGAT
1 TTTAATTTTCGCAATCTCAATAATCGAAAGAAACTAATCCTTTGAT
* * *
92582 TTTACTTTTGGTAATCT-AATAAT
1 TTTAATTTTCGCAATCTCAATAAT
92605 TAAAAGCCTT
Statistics
Matches: 178, Mismatches: 19, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
44 9 0.05
45 163 0.92
46 6 0.03
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (46 bp):
TTTAATTTTCGCAATCTCAATAATCGAAAGAAACTAATCCTTTGAT
Found at i:92471 original size:90 final size:90
Alignment explanation
Indices: 92376--92610 Score: 312
Period size: 90 Copynumber: 2.6 Consensus size: 90
92366 ACGAATCCAT
* *
92376 TAATCGAAAGGAACTAATCCTTTGATTTTAATTTTCGCAATCCAATAATTGAAAGAAACTAATCC
1 TAATCGAAAGGAACTAATCCTTTGATTTTAATTTTGGCAATCCAATAATTAAAAGAAACTAATCC
* *
92441 TTTGATTTTAATTTTT-GCATCTCAA
66 TTTGATTTT-ATTTTTGGCAACACAA
* * *
92466 TAATCGAAAGGAAATAATCCATTGATTTTAATTTTGGCAA-CTCAATAATCAAAAGAAACTAATC
1 TAATCGAAAGGAACTAATCCTTTGATTTTAATTTTGGCAATC-CAATAATTAAAAGAAACTAATC
*
92530 CTTTGATTTTGTTTTTGGCAACACAA
65 CTTTGATTTTATTTTTGGCAACACAA
* ** * * *
92556 TAATCAAAAGGAACTAATAATTTGATTTTACTTTTGGTAATCTAATAATTAAAAG
1 TAATCGAAAGGAACTAATCCTTTGATTTTAATTTTGGCAATCCAATAATTAAAAG
92611 CCTTGTATTA
Statistics
Matches: 125, Mismatches: 17, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
89 6 0.05
90 118 0.94
91 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (90 bp):
TAATCGAAAGGAACTAATCCTTTGATTTTAATTTTGGCAATCCAATAATTAAAAGAAACTAATCC
TTTGATTTTATTTTTGGCAACACAA
Found at i:95750 original size:41 final size:41
Alignment explanation
Indices: 95688--95767 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
95678 TTTGATGTCA
*
95688 AAATAAAGTCTTTCTTCTCAATTAATAAATAAGAGAAATAC
1 AAATAAAGTCATTCTTCTCAATTAATAAATAAGAGAAATAC
* * *
95729 AAATAAATTCATTCTTTTCAATTAATAAATAAGGGAAAT
1 AAATAAAGTCATTCTTCTCAATTAATAAATAAGAGAAAT
95768 GCGTAGTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (41 bp):
AAATAAAGTCATTCTTCTCAATTAATAAATAAGAGAAATAC
Found at i:98808 original size:24 final size:25
Alignment explanation
Indices: 98781--98827 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
98771 TAACATGTTT
98781 AAAAAT-AAAACTT-AAAAGAAAAG
1 AAAAATGAAAACTTGAAAAGAAAAG
98804 AAAAATGAAAACTTGAAAAGAAAA
1 AAAAATGAAAACTTGAAAAGAAAA
98828 TAAAGGAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 6 0.27
24 7 0.32
25 9 0.41
ACGTcount: A:0.72, C:0.04, G:0.11, T:0.13
Consensus pattern (25 bp):
AAAAATGAAAACTTGAAAAGAAAAG
Found at i:104707 original size:32 final size:31
Alignment explanation
Indices: 104641--104716 Score: 73
Period size: 32 Copynumber: 2.4 Consensus size: 31
104631 TAACAATAAT
* *
104641 ATGTCTAAGTTTACTTTAAAAGATGAACACC
1 ATGTCCAAATTTACTTTAAAAGATGAACACC
* * *
104672 ATGTTCAAATTTACTTATAAAAAGATGGA-AGC
1 ATGTCCAAATTTACTT-T-AAAAGATGAACACC
*
104704 ATGTCCAATTTTA
1 ATGTCCAAATTTA
104717 TAAAAGATAG
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
31 13 0.36
32 14 0.39
33 9 0.25
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (31 bp):
ATGTCCAAATTTACTTTAAAAGATGAACACC
Found at i:105887 original size:36 final size:38
Alignment explanation
Indices: 105814--105913 Score: 98
Period size: 36 Copynumber: 2.7 Consensus size: 38
105804 AGATGAAGTT
* * * * * *
105814 GAAAAGATATAATAAATTAAATAATTATAATTTAAAAA-
1 GAAAACAT-TAATAAAATAAATAATAAAAAATAAAAAAG
105852 GAAAA-ATTAATAAAATAAATAATAAAAAATAAAAAAG
1 GAAAACATTAATAAAATAAATAATAAAAAATAAAAAAG
*
105889 GAAAACAATAA-AATAATAAATAATA
1 GAAAACATTAATAA-AATAAATAATA
105914 GTAGTAAAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
36 24 0.45
37 9 0.17
38 20 0.38
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.24
Consensus pattern (38 bp):
GAAAACATTAATAAAATAAATAATAAAAAATAAAAAAG
Found at i:105901 original size:8 final size:7
Alignment explanation
Indices: 105847--105913 Score: 53
Period size: 7 Copynumber: 9.0 Consensus size: 7
105837 ATTATAATTT
*
105847 AAAAAGA
1 AAAAATA
*
105854 AAAATTA
1 AAAAATA
105861 ATAAAATA
1 A-AAAATA
*
105869 AATAATA
1 AAAAATA
105876 AAAAATA
1 AAAAATA
*
105883 AAAAAGGA
1 AAAAA-TA
105891 AAACAATA
1 AAA-AATA
105899 AAATAATA
1 AAA-AATA
*
105907 AATAATA
1 AAAAATA
105914 GTAGTAAAGA
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
7 26 0.54
8 20 0.42
9 2 0.04
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.18
Consensus pattern (7 bp):
AAAAATA
Found at i:124802 original size:26 final size:26
Alignment explanation
Indices: 124773--124836 Score: 101
Period size: 26 Copynumber: 2.4 Consensus size: 26
124763 GAGGGAATGA
* *
124773 CGAGCTAGGCGTTCGAGAGGAGCTAG
1 CGAGCTAGGCATTCGAGAGAAGCTAG
124799 CGAGCTAGGCATTCGAGAGAAGCTAG
1 CGAGCTAGGCATTCGAGAGAAGCTAG
124825 CGAGCTGAGGCA
1 CGAGCT-AGGCA
124837 ATTTGTGGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 30 0.86
27 5 0.14
ACGTcount: A:0.27, C:0.20, G:0.39, T:0.14
Consensus pattern (26 bp):
CGAGCTAGGCATTCGAGAGAAGCTAG
Found at i:125885 original size:297 final size:297
Alignment explanation
Indices: 125351--125946 Score: 1174
Period size: 297 Copynumber: 2.0 Consensus size: 297
125341 TCATGTTATC
125351 TGGACATATAGGATCCCTGCACTTGCTAACGCCTATATGTTTGTCATGGCATCTTGAACCTGTTG
1 TGGACATATAGGATCCCTGCACTTGCTAACGCCTATATGTTTGTCATGGCATCTTGAACCTGTTG
125416 AATCTCTTGACTAGAGATAGCATAGGGCACCCTTAGTAAACTCTGTCAGGCAGATAAGGCAGAGA
66 AATCTCTTGACTAGAGATAGCATAGGGCACCCTTAGTAAACTCTGTCAGGCAGATAAGGCAGAGA
125481 AGTAAGACCATCTTGAGAAGTAACTTAAATTTCCTAAGTGACTCATATCATTCATTCATGTAGTA
131 AGTAAGACCATCTTGAGAAGTAACTTAAATTTCCTAAGTGACTCATATCATTCATTCATGTAGTA
125546 GCTTGTTATGTGATGAGTCTAAAGTCCTAATAATCAAATCCAGTATTTACATTTTGTTTTTCCTT
196 GCTTGTTATGTGATGAGTCTAAAGTCCTAATAATCAAATCCAGTATTTACATTTTGTTTTTCCTT
*
125611 TACATTTTTAATTGATTGCGCTAAACACAATATAATT
261 TACATTTTTAATTGATTGCACTAAACACAATATAATT
125648 TGGACATATAGGATCCCTGCACTTGCTAACGCCTATATGTTTGTCATGGCATCTTGAACCTGTTG
1 TGGACATATAGGATCCCTGCACTTGCTAACGCCTATATGTTTGTCATGGCATCTTGAACCTGTTG
125713 AATCTCTTGACTAGAGATAGCATAGGGCACCCTTAGTAAACTCTGTCAGGCAGATAAGGCAGAGA
66 AATCTCTTGACTAGAGATAGCATAGGGCACCCTTAGTAAACTCTGTCAGGCAGATAAGGCAGAGA
125778 AGTAAGACCATCTTGAGAAGTAACTTAAATTTCCTAAGTGACTCATATCATTCATTCATGTAGTA
131 AGTAAGACCATCTTGAGAAGTAACTTAAATTTCCTAAGTGACTCATATCATTCATTCATGTAGTA
125843 GCTTGTTATGTGATGAGTCTAAAGTCCTAATAATCAAATCCAGTATTTACATTTTGTTTTTCCTT
196 GCTTGTTATGTGATGAGTCTAAAGTCCTAATAATCAAATCCAGTATTTACATTTTGTTTTTCCTT
*
125908 TACATTTTTATTTGATTGCACTAAACACAATATAATT
261 TACATTTTTAATTGATTGCACTAAACACAATATAATT
125945 TG
1 TG
125947 CCATGACATC
Statistics
Matches: 297, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
297 297 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (297 bp):
TGGACATATAGGATCCCTGCACTTGCTAACGCCTATATGTTTGTCATGGCATCTTGAACCTGTTG
AATCTCTTGACTAGAGATAGCATAGGGCACCCTTAGTAAACTCTGTCAGGCAGATAAGGCAGAGA
AGTAAGACCATCTTGAGAAGTAACTTAAATTTCCTAAGTGACTCATATCATTCATTCATGTAGTA
GCTTGTTATGTGATGAGTCTAAAGTCCTAATAATCAAATCCAGTATTTACATTTTGTTTTTCCTT
TACATTTTTAATTGATTGCACTAAACACAATATAATT
Found at i:137612 original size:29 final size:29
Alignment explanation
Indices: 137570--137628 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
137560 ATTTTCACCT
137570 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
137599 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
137628 A
1 A
137629 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:142305 original size:29 final size:29
Alignment explanation
Indices: 142263--142348 Score: 172
Period size: 29 Copynumber: 3.0 Consensus size: 29
142253 TTTTCACCTA
142263 ACTAAATTGATGTAAGCAATGACATCAAG
1 ACTAAATTGATGTAAGCAATGACATCAAG
142292 ACTAAATTGATGTAAGCAATGACATCAAG
1 ACTAAATTGATGTAAGCAATGACATCAAG
142321 ACTAAATTGATGTAAGCAATGACATCAA
1 ACTAAATTGATGTAAGCAATGACATCAA
142349 ATTAATTTAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 57 1.00
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.24
Consensus pattern (29 bp):
ACTAAATTGATGTAAGCAATGACATCAAG
Found at i:142542 original size:19 final size:19
Alignment explanation
Indices: 142518--142555 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
142508 ATATTTTTTA
142518 TTGAAAACTATAATTATTT
1 TTGAAAACTATAATTATTT
* *
142537 TTGAAATCTATAGTTATTT
1 TTGAAAACTATAATTATTT
142556 AATATTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (19 bp):
TTGAAAACTATAATTATTT
Found at i:147535 original size:19 final size:19
Alignment explanation
Indices: 147511--147548 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
147501 TCCAAAAACG
147511 TGTTCTTTATTTGCAAATT
1 TGTTCTTTATTTGCAAATT
147530 TGTTCTTTATTTGCAAATT
1 TGTTCTTTATTTGCAAATT
147549 GACAAATGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.11, G:0.11, T:0.58
Consensus pattern (19 bp):
TGTTCTTTATTTGCAAATT
Found at i:160828 original size:17 final size:18
Alignment explanation
Indices: 160806--160847 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
160796 TTACACCTTT
*
160806 AAATAAATTTTTACAT-A
1 AAATAAATTTTTAAATGA
*
160823 AAATAATTTTTTAAATGA
1 AAATAAATTTTTAAATGA
160841 AAATAAA
1 AAATAAA
160848 ATTAAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (18 bp):
AAATAAATTTTTAAATGA
Found at i:160880 original size:27 final size:27
Alignment explanation
Indices: 160850--160938 Score: 80
Period size: 25 Copynumber: 3.3 Consensus size: 27
160840 AAAATAAAAT
160850 TAAAATATTTTTAAATTAAGTTAATAA
1 TAAAATATTTTTAAATTAAGTTAATAA
* *
160877 TAAAATATTGTT-GA-TAAGTTAAT-A
1 TAAAATATTTTTAAATTAAGTTAATAA
*
160901 TAAAAATATTTTTTAAGTTAA--TATATATA
1 T-AAAATA-TTTTTAAATTAAGTTA-ATA-A
160930 TAAAATATT
1 TAAAATATT
160939 ATGAATTTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
24 2 0.04
25 15 0.30
26 7 0.14
27 15 0.30
28 9 0.18
29 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (27 bp):
TAAAATATTTTTAAATTAAGTTAATAA
Found at i:160921 original size:23 final size:26
Alignment explanation
Indices: 160865--160927 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 26
160855 TATTTTTAAA
160865 TTAAGTTAATA-ATAAAATATTGTTG
1 TTAAGTTAATATATAAAATATTGTTG
*
160890 ATAAGTTAATATA-AAAATATT-TT-
1 TTAAGTTAATATATAAAATATTGTTG
160913 TTAAGTTAATATATA
1 TTAAGTTAATATATA
160928 TATAAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 12 0.35
24 3 0.09
25 18 0.53
26 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (26 bp):
TTAAGTTAATATATAAAATATTGTTG
Found at i:161965 original size:15 final size:15
Alignment explanation
Indices: 161945--161984 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
161935 ATAAAAAACA
*
161945 ATATATAATATATAT
1 ATATATAATATAAAT
161960 ATATATAATATAAAT
1 ATATATAATATAAAT
*
161975 ACATA-AATAT
1 ATATATAATAT
161985 CTTTAGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
ATATATAATATAAAT
Found at i:175548 original size:15 final size:15
Alignment explanation
Indices: 175525--175576 Score: 86
Period size: 15 Copynumber: 3.5 Consensus size: 15
175515 ATATTTGGCT
*
175525 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
*
175540 GGGCAGGCGGATGCG
1 GGGCGGGCGGATGCG
175555 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
175570 GGGCGGG
1 GGGCGGG
175577 TAATGTCTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.08, C:0.17, G:0.67, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:178089 original size:19 final size:19
Alignment explanation
Indices: 178067--178115 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
178057 GTAATCTGAG
178067 CAGAGATCAGA-ATAGAAAT
1 CAGAGATCAGAGA-AGAAAT
*
178086 CAGAGTTCAGAGAAGAAAT
1 CAGAGATCAGAGAAGAAAT
*
178105 CAGAGGTCAGA
1 CAGAGATCAGA
178116 TTGTATTCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 26 0.96
20 1 0.04
ACGTcount: A:0.47, C:0.12, G:0.27, T:0.14
Consensus pattern (19 bp):
CAGAGATCAGAGAAGAAAT
Found at i:178906 original size:25 final size:25
Alignment explanation
Indices: 178872--178928 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
178862 TTGTTCATTT
178872 CAGAGCTGAGGGTAATTAATTATTC
1 CAGAGCTGAGGGTAATTAATTATTC
178897 CAGAGCTGAGGGTAATTAATTATTC
1 CAGAGCTGAGGGTAATTAATTATTC
178922 CAGAGCT
1 CAGAGCT
178929 TGGACGTGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (25 bp):
CAGAGCTGAGGGTAATTAATTATTC
Found at i:179449 original size:18 final size:18
Alignment explanation
Indices: 179426--179463 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
179416 GTCTAAGTCC
179426 TATACAATGCTCCATCTT
1 TATACAATGCTCCATCTT
179444 TATACAATGCTCCATCTT
1 TATACAATGCTCCATCTT
179462 TA
1 TA
179464 ATCCAATTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.26, G:0.05, T:0.39
Consensus pattern (18 bp):
TATACAATGCTCCATCTT
Found at i:185773 original size:12 final size:12
Alignment explanation
Indices: 185730--185770 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
185720 ATTACTTTTA
185730 TATTTTAATTAT
1 TATTTTAATTAT
**
185742 TGCTTTAATTAT
1 TATTTTAATTAT
185754 TATTTT-ATTAT
1 TATTTTAATTAT
185765 TATTTT
1 TATTTT
185771 TATCTTATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 11 0.44
12 14 0.56
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (12 bp):
TATTTTAATTAT
Done.