Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003432.1 Hibiscus syriacus cultivar Beakdansim tig00007231_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: 76171
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:5689 original size:24 final size:24
Alignment explanation
Indices: 5661--5719 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
5651 ATTATGGAAT
5661 CGAAGTGCCACGTAGAATATGCAC
1 CGAAGTGCCACGTAGAATATGCAC
* *
5685 TGAAGTGTCACGTAGAATATGCAC
1 CGAAGTGCCACGTAGAATATGCAC
*
5709 CGATGTGCCAC
1 CGAAGTGCCAC
5720 ATATAAATGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (24 bp):
CGAAGTGCCACGTAGAATATGCAC
Found at i:11725 original size:34 final size:31
Alignment explanation
Indices: 11676--11799 Score: 108
Period size: 31 Copynumber: 3.9 Consensus size: 31
11666 GAGTCGAGGG
* * *
11676 TTACCTATATATTTCGAGACATATAGATAGTTGT
1 TTACCTATGTCTTTCGAGACATATAGATA---GA
*
11710 TTACCTATGTCTTTCGAGACATATGGATAGA
1 TTACCTATGTCTTTCGAGACATATAGATAGA
* * * *
11741 TTACCTATGTCCTTCAAGACATATGGACAG-
1 TTACCTATGTCTTTCGAGACATATAGATAGA
* *
11771 TTACCTATGT-TCTTCGAAACATATGGATA
1 TTACCTATGTCT-TTCGAGACATATAGATA
11800 TGTTCTTCGG
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
30 24 0.31
31 28 0.36
34 26 0.33
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (31 bp):
TTACCTATGTCTTTCGAGACATATAGATAGA
Found at i:11777 original size:30 final size:31
Alignment explanation
Indices: 11710--11797 Score: 117
Period size: 31 Copynumber: 2.9 Consensus size: 31
11700 AGATAGTTGT
* * *
11710 TTACCTATGTCTTTCGAGACATATGGATAGA
1 TTACCTATGTCCTTCAAGACATATGGACAGA
11741 TTACCTATGTCCTTCAAGACATATGGACAG-
1 TTACCTATGTCCTTCAAGACATATGGACAGA
*
11771 TTACCTATGTTCTTCGAA-ACATATGGA
1 TTACCTATGTCCTTC-AAGACATATGGA
11798 TATGTTCTTC
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
30 23 0.44
31 29 0.56
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (31 bp):
TTACCTATGTCCTTCAAGACATATGGACAGA
Found at i:17338 original size:30 final size:30
Alignment explanation
Indices: 17253--17339 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 30
17243 ATGGATAGTT
17253 GTTTACCTATG-TCTTTCGAGACATATAGACA
1 GTTTACCTATGTTC-TTCGA-ACATATAGACA
* * * *
17284 GATTATCTATGTCCTTCGGGACATATAGACA
1 GTTTACCTATGTTCTTC-GAACATATAGACA
17315 -TTTACCTATGTTCTTCAGAACATAT
1 GTTTACCTATGTTCTTC-GAACATAT
17340 GGATAGGTCC
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
30 20 0.44
31 23 0.51
32 2 0.04
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (30 bp):
GTTTACCTATGTTCTTCGAACATATAGACA
Found at i:22491 original size:57 final size:57
Alignment explanation
Indices: 22026--22483 Score: 643
Period size: 57 Copynumber: 8.0 Consensus size: 57
22016 TGGGGGTGTT
* *
22026 ACAAAGTGCCTATACAGAATTTCATAAACTTATTATGAATTTCTTAAC-TTTTGCAC
1 ACAAAGTGCCCATACAGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCAC
* * * * * *
22082 ACAAAGTACCCATACGGAAATTCATATACTCATTACGAATTTCTTACCTTTTTTGCAC
1 ACAAAGTGCCCATACAGAAATTCATAAACTTATTATGAATTTCTTAAC-TTTTTGCAC
* *
22140 ACAAAGTGCACATACAGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCGC
1 ACAAAGTGCCCATACAGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCAC
*
22197 ACAAAGTGCCCATAC-GAAAATTCATAAACTTATTATGAATTTCTTAACTTTTTACAC
1 ACAAAGTGCCCATACAG-AAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCAC
* * * **
22254 ATAAAGTGCCCATA-AGGTAATTCAAAAACGCATTATGAATTTCTTAACTTTTTGCAC
1 ACAAAGTGCCCATACA-GAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCAC
* * *
22311 ACAAAGTGCTCATACGGAAGTTCATAAACTTATTATGAATTTCTTAACTTTTTGCAC
1 ACAAAGTGCCCATACAGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCAC
* * * *
22368 ACAAAGTACCCATACGGAAATTTATAAACTTATTATGAATTTCTTAATTTTTTGCAC
1 ACAAAGTGCCCATACAGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCAC
* *
22425 ACAAAGTGCCTATACATAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCAC
1 ACAAAGTGCCCATACAGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCAC
22482 AC
1 AC
22484 TCAGTGCCAT
Statistics
Matches: 352, Mismatches: 44, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
56 41 0.12
57 261 0.74
58 50 0.14
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (57 bp):
ACAAAGTGCCCATACAGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCAC
Found at i:27001 original size:41 final size:40
Alignment explanation
Indices: 26956--27087 Score: 165
Period size: 41 Copynumber: 3.2 Consensus size: 40
26946 GATTCTGACT
* * *
26956 ATCGCATTGCGATTTTCCTAATTCGCAATGCGAATACGTAA
1 ATCGCAATGCGA-TTTCGTAAATCGCAATGCGAATACGTAA
* * * *
26997 ATCGCAACGCGAATTTGGAAAATCGCAATGCGATTACGTAA
1 ATCGCAATGCG-ATTTCGTAAATCGCAATGCGAATACGTAA
* *
27038 ATCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAA
1 ATCGCAATGCGATTTCGTAAATCGCAATGCGAATACGTAA
27078 ATCGCAATGC
1 ATCGCAATGC
27088 AAATCTGACT
Statistics
Matches: 77, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
40 34 0.44
41 42 0.55
42 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (40 bp):
ATCGCAATGCGATTTCGTAAATCGCAATGCGAATACGTAA
Found at i:27002 original size:61 final size:60
Alignment explanation
Indices: 26937--27087 Score: 169
Period size: 61 Copynumber: 2.5 Consensus size: 60
26927 ATTTCCAGAT
** * * *
26937 TCGCAACGCGATTCT-GACTATCGCATTGCGATTTTCCTAATTCGCAATGCGAATACGTAAA
1 TCGCAACGCGATT-TGGAAAATCGCAATGCGA-TTACCTAAATCGCAATGCGAATACGTAAA
*
26998 TCGCAACGCGAATTTGGAAAATCGCAATGCGATTACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAACGCG-ATTTGGAAAATCGCAATGCGATTACCTAAATCGCAATGCGAATACGTAAA
* * ** *
27059 TCGCAATGCGAATACGTAAATCGCAATGC
1 TCGCAACGCGATTTGGAAAATCGCAATGC
27088 AAATCTGACT
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
60 15 0.19
61 46 0.60
62 16 0.21
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (60 bp):
TCGCAACGCGATTTGGAAAATCGCAATGCGATTACCTAAATCGCAATGCGAATACGTAAA
Found at i:27003 original size:20 final size:20
Alignment explanation
Indices: 26978--27087 Score: 166
Period size: 20 Copynumber: 5.5 Consensus size: 20
26968 TTTTCCTAAT
26978 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
26998 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
27019 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
27039 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
27059 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
27079 TCGCAATGC
1 TCGCAATGC
27088 AAATCTGACT
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
20 64 0.81
21 15 0.19
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:27107 original size:40 final size:39
Alignment explanation
Indices: 26978--27109 Score: 158
Period size: 40 Copynumber: 3.3 Consensus size: 39
26968 TTTTCCTAAT
* *
26978 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATCT-G-AAA
*
27019 TCGCAATGCGATTACGTAAATCGCAATGCGAATAC-GTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAAT-CTG-AAA
* *
27059 TCGCAATGCGAATACGTAAATCGCAATGCAAATCTGACTA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATCTGA-AA
*
27099 TCGTAATGCGA
1 TCGCAATGCGA
27110 TTTACATAGC
Statistics
Matches: 80, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
39 2 0.03
40 47 0.59
41 31 0.39
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (39 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGAATCTGAAA
Found at i:27309 original size:22 final size:22
Alignment explanation
Indices: 27284--27349 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
27274 GGCAACATCC
*
27284 GTCCCCATCTCCAACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
27306 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
27328 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
27350 TTCACGGTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.26, C:0.39, G:0.14, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:27746 original size:20 final size:20
Alignment explanation
Indices: 27721--27768 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
27711 CGATTCTTGC
27721 GTTGCGATAGCCATTTTCGT
1 GTTGCGATAGCCATTTTCGT
***
27741 GTTGCGATTTTCATTTTCGT
1 GTTGCGATAGCCATTTTCGT
27761 GTTGCGAT
1 GTTGCGAT
27769 TTAAAGTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.12, C:0.17, G:0.25, T:0.46
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGT
Found at i:27769 original size:20 final size:20
Alignment explanation
Indices: 27732--27770 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
27722 TTGCGATAGC
27732 CATTTTCGTGTTGCGATTTT
1 CATTTTCGTGTTGCGATTTT
27752 CATTTTCGTGTTGCGATTT
1 CATTTTCGTGTTGCGATTT
27771 AAAGTTTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.15, G:0.21, T:0.54
Consensus pattern (20 bp):
CATTTTCGTGTTGCGATTTT
Found at i:29720 original size:33 final size:33
Alignment explanation
Indices: 29667--29821 Score: 125
Period size: 33 Copynumber: 4.4 Consensus size: 33
29657 TTTACTATCA
*
29667 CAATGCGAAAATGACTATCGCAACGAGAGAATCG
1 CAATGCG-AAATGACTATCGCAACGAAAGAATCG
** *
29701 CAATGCGAAATGAAAATCGCAAC-AACAAAATCG
1 CAATGCGAAATGACTATCGCAACGAA-AGAATCG
* *
29734 CAACGCGAAAATGACTATCGCAATGCGAAAAAGGACTATTG
1 CAATGCG-AAATGACTATCGCAA--CG--AAA-GA--ATCG
29775 CAATGC-AAATTTGACTATCGCAACGAAAGAATCG
1 CAATGCGAAA--TGACTATCGCAACGAAAGAATCG
*
29809 CAATGTGAAATGA
1 CAATGCGAAATGA
29822 AAATCGCATT
Statistics
Matches: 96, Mismatches: 12, Indels: 27
0.71 0.09 0.20
Matches are distributed among these distances:
32 1 0.01
33 29 0.30
34 28 0.29
35 3 0.03
36 3 0.03
37 3 0.03
38 1 0.01
39 8 0.08
41 20 0.21
ACGTcount: A:0.44, C:0.19, G:0.20, T:0.17
Consensus pattern (33 bp):
CAATGCGAAATGACTATCGCAACGAAAGAATCG
Found at i:29770 original size:21 final size:21
Alignment explanation
Indices: 29730--29797 Score: 77
Period size: 20 Copynumber: 3.3 Consensus size: 21
29720 CAACAACAAA
*
29730 ATCGCAACGCG-AAAATGACT
1 ATCGCAATGCGAAAAATGACT
*
29750 ATCGCAATGCGAAAAAGGACT
1 ATCGCAATGCGAAAAATGACT
* **
29771 ATTGCAATGC-AAATTTGACT
1 ATCGCAATGCGAAAAATGACT
29791 ATCGCAA
1 ATCGCAA
29798 CGAAAGAATC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 23 0.57
21 17 0.43
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGCAATGCGAAAAATGACT
Found at i:29868 original size:34 final size:37
Alignment explanation
Indices: 29825--29916 Score: 104
Period size: 40 Copynumber: 2.5 Consensus size: 37
29815 GAAATGAAAA
29825 TCGCATTGCGATTA-TC-TCG-TTGCGATAGTCAAAT
1 TCGCATTGCGATTAGTCATCGATTGCGATAGTCAAAT
29859 TCGCATTGCGA-TAGTCAAATTCGCATTGCGATAGTCAAAT
1 TCGCATTGCGATTAGTC--A-TCG-ATTGCGATAGTCAAAT
*
29899 TCGTATTGCGA-TAGTCAT
1 TCGCATTGCGATTAGTCAT
29917 TTTCGCGTTG
Statistics
Matches: 50, Mismatches: 1, Indels: 11
0.81 0.02 0.18
Matches are distributed among these distances:
33 2 0.04
34 13 0.26
37 1 0.02
38 4 0.08
40 30 0.60
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.34
Consensus pattern (37 bp):
TCGCATTGCGATTAGTCATCGATTGCGATAGTCAAAT
Found at i:29869 original size:20 final size:20
Alignment explanation
Indices: 29844--29950 Score: 151
Period size: 20 Copynumber: 5.3 Consensus size: 20
29834 GATTATCTCG
29844 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
29864 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
*
29884 TTGCGATAGTCAAATTCGTA
1 TTGCGATAGTCAAATTCGCA
** *
29904 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
** *
29924 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
29944 TTGCGAT
1 TTGCGAT
29951 TTTAAGTTTC
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 82 1.00
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:29960 original size:20 final size:20
Alignment explanation
Indices: 29842--29960 Score: 73
Period size: 20 Copynumber: 6.0 Consensus size: 20
29832 GCGATTATCT
*
29842 CGTTGCGATAGTCAA-ATTCG
1 CGTTGCGATAGT-AAGTTTCG
* *
29862 CATTGCGATAGTCAA-ATTCG
1 CGTTGCGATAGT-AAGTTTCG
* *
29882 CATTGCGATAGTCAA-ATTCG
1 CGTTGCGATAGT-AAGTTTCG
** * *
29902 TATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTAAGTTTCG
* *
29922 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTAAGTTTCG
**
29942 CGTTGCGATTTTAAGTTTC
1 CGTTGCGATAGTAAGTTTC
29961 AGATTCTATT
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
19 1 0.01
20 87 0.99
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTAAGTTTCG
Found at i:30525 original size:21 final size:21
Alignment explanation
Indices: 30434--30538 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
30424 GACTCACCTG
*
30434 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
30456 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
30476 TCATCCATCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
30497 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
30518 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
30539 CCAACATTCT
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:30531 original size:42 final size:42
Alignment explanation
Indices: 30431--30541 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
30421 CCCGACTCAC
* * * *
30431 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
30473 CTATCATCCATCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
30515 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
30542 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.93
43 2 0.04
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:31943 original size:14 final size:14
Alignment explanation
Indices: 31924--31959 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
31914 ATTGTTTAAT
31924 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
31938 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
31952 TGATTTGT
1 TGATTTGT
31960 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:32084 original size:14 final size:14
Alignment explanation
Indices: 32065--32118 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
32055 AAAACAGACT
32065 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
32079 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
32098 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
32112 ATCGCAA
1 ATCGCAA
32119 TGCGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:32102 original size:33 final size:34
Alignment explanation
Indices: 32065--32140 Score: 145
Period size: 33 Copynumber: 2.3 Consensus size: 34
32055 AAAACAGACT
32065 ATCGCAACGAGAGAATCGCAATGCG-AAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
32098 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
32132 ATCGCAACG
1 ATCGCAACG
32141 CGAAACTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 25 0.60
34 17 0.40
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.12
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
Found at i:32136 original size:20 final size:19
Alignment explanation
Indices: 32078--32145 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 19
32068 GCAACGAGAG
32078 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
32097 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
32111 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
32131 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
32146 CTAAATTCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
19 12 0.30
20 13 0.32
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:32182 original size:20 final size:19
Alignment explanation
Indices: 32157--32251 Score: 84
Period size: 16 Copynumber: 5.4 Consensus size: 19
32147 TAAATTCACG
32157 TTGCGATTTTCATTTTCGCA
1 TTGCGATTTTCA-TTTCGCA
*
32177 TTGCGA--TTCA-CTCG--
1 TTGCGATTTTCATTTCGCA
32191 TTGCGATTTTCATTTTCGCA
1 TTGCGATTTTCA-TTTCGCA
*
32211 TTGCGA--TTCA-CTCG--
1 TTGCGATTTTCATTTCGCA
32225 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
32244 TTGCGATT
1 TTGCGATT
32252 ATCTCGTTGC
Statistics
Matches: 60, Mismatches: 4, Indels: 23
0.69 0.05 0.26
Matches are distributed among these distances:
14 12 0.20
16 14 0.23
17 3 0.05
18 11 0.18
19 8 0.13
20 12 0.20
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:32273 original size:33 final size:34
Alignment explanation
Indices: 32155--32264 Score: 197
Period size: 34 Copynumber: 3.3 Consensus size: 34
32145 ACTAAATTCA
32155 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
32189 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
32223 CGTTGCGATTTTCA-TTTCGCATTGCGATT-ATCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCA-CT
32256 CGTTGCGAT
1 CGTTGCGAT
32265 AGTCATTTCC
Statistics
Matches: 75, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
32 1 0.01
33 26 0.35
34 48 0.64
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.44
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:32285 original size:20 final size:20
Alignment explanation
Indices: 32256--32364 Score: 131
Period size: 20 Copynumber: 5.7 Consensus size: 20
32246 GCGATTATCT
32256 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
32276 CGTTGTGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
32296 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
32316 TGTTGCGATAATCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
32336 CGTTGCG--A-T--TTTCCG
1 CGTTGCGATAGTCATTTCCG
32351 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
32365 AATGAATGTC
Statistics
Matches: 75, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
14 2 0.03
15 10 0.13
17 2 0.03
18 2 0.03
20 57 0.76
21 2 0.03
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:37739 original size:21 final size:21
Alignment explanation
Indices: 37713--37752 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
37703 TAGAACCCCA
*
37713 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
37734 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
37753 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:37781 original size:19 final size:20
Alignment explanation
Indices: 37735--37794 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 20
37725 TTCCCCTGTG
37735 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TC-AA
37758 GGGGGAATCGGTTCCCTC-A
1 GGGGGAATCGGTTCCCTCAA
* *
37777 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
37795 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.17, C:0.27, G:0.35, T:0.22
Consensus pattern (20 bp):
GGGGGAATCGGTTCCCTCAA
Found at i:41639 original size:22 final size:21
Alignment explanation
Indices: 41597--41636 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
41587 GAGTTTGTTT
*
41597 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
41618 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
41637 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:44444 original size:24 final size:24
Alignment explanation
Indices: 44410--44463 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
44400 CTGAAAAATC
44410 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
44434 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
44458 ATCAAA
1 ATCAAA
44464 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:45310 original size:20 final size:20
Alignment explanation
Indices: 45285--45331 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
45275 AAATTCATTA
*
45285 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
45305 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
45325 TTGCGAT
1 TTGCGAT
45332 TTACGTATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:45341 original size:20 final size:20
Alignment explanation
Indices: 45318--45411 Score: 152
Period size: 20 Copynumber: 4.7 Consensus size: 20
45308 CGATAGTCAG
*
45318 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
45338 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
45358 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
45378 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
45398 AATCGCAATGCGAT
1 ATTCGCATTGCGAT
45412 AGTCAGAATC
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.37
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:45350 original size:60 final size:60
Alignment explanation
Indices: 45284--45430 Score: 142
Period size: 60 Copynumber: 2.5 Consensus size: 60
45274 GAAATTCATT
* * *
45284 ATTGCGATAGTCAGAATCTCGTTGCGATAGTCA-G-ATTCGCGTTGCGATTTACGTATTCGC
1 ATTGCGATAGTCAGAATCTCGTTGCGAT--TCACGTATTCACATTGCGATTTACGTAATCGC
* * *
45344 ATTGCGAT--TTACGTAT-TCGCATTGCGATTTACGTATTCACATTGCGATTTACGTAATCGC
1 ATTGCGATAGTCA-GAATCTCG--TTGCGATTCACGTATTCACATTGCGATTTACGTAATCGC
* *
45404 AATGCGATAGTCAGAATCGCGTTGCGA
1 ATTGCGATAGTCAGAATCTCGTTGCGA
45431 ATCTGGAAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 16
0.73 0.11 0.17
Matches are distributed among these distances:
58 7 0.10
59 4 0.06
60 51 0.74
61 3 0.04
62 4 0.06
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (60 bp):
ATTGCGATAGTCAGAATCTCGTTGCGATTCACGTATTCACATTGCGATTTACGTAATCGC
Found at i:52793 original size:60 final size:58
Alignment explanation
Indices: 52656--52803 Score: 154
Period size: 60 Copynumber: 2.5 Consensus size: 58
52646 GTTCATAAAT
* * *
52656 TTTTAAATATTTTAATTTCATCCCCAAATTATATCTCTCATTCTAAATTAGTCCTTAAAC
1 TTTTGAATA-TTTAATTTCAT-CCTAAATTATATCTCTCATTCTAAATTAGTCCTCAAAC
* * ** *
52716 ATTGGAGCATTATAATTTCATCCATAAATTATGA-CTCTCTTTCTAAATTAGTCCTCAAAC
1 TTTTGAATATT-TAATTTCATCC-TAAATTAT-ATCTCTCATTCTAAATTAGTCCTCAAAC
*
52776 TTTTGAATATTTCAATTTAATCCTAAAT
1 TTTTGAATATTT-AATTTCATCCTAAAT
52804 GCATTCAAAT
Statistics
Matches: 71, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
59 10 0.14
60 60 0.85
61 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.43
Consensus pattern (58 bp):
TTTTGAATATTTAATTTCATCCTAAATTATATCTCTCATTCTAAATTAGTCCTCAAAC
Found at i:55369 original size:28 final size:28
Alignment explanation
Indices: 55336--55392 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
55326 GTCAGAGGCA
55336 TACCGCTTTGGGTAATAAAAGAGGCGGT
1 TACCGCTTTGGGTAATAAAAGAGGCGGT
55364 TACCGCTTTGGGTAATAAAAGAGGCGGT
1 TACCGCTTTGGGTAATAAAAGAGGCGGT
55392 T
1 T
55393 CATCCTGGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.14, G:0.32, T:0.26
Consensus pattern (28 bp):
TACCGCTTTGGGTAATAAAAGAGGCGGT
Found at i:55833 original size:4 final size:4
Alignment explanation
Indices: 55824--55855 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
55814 CAATGCATGT
*
55824 ATAA ATAA ATAA ATAA ATAA ATAA ATAC ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
55856 TTATACTGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:57865 original size:16 final size:17
Alignment explanation
Indices: 57832--57867 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
57822 CGAATAACTA
*
57832 TTTTAGGTATCCGAAAT
1 TTTTAAGTATCCGAAAT
57849 TTTTAAGTATCCG-AAT
1 TTTTAAGTATCCGAAAT
57865 TTT
1 TTT
57868 CAAATCGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (17 bp):
TTTTAAGTATCCGAAAT
Found at i:64725 original size:17 final size:18
Alignment explanation
Indices: 64703--64749 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
64693 TGTGCATTTG
64703 ACTAATATTAATAAAAA-
1 ACTAATATTAATAAAAAT
64720 ACTAATA-TAATAAAAAT
1 ACTAATATTAATAAAAAT
* *
64737 AATAATATCAATA
1 ACTAATATTAATA
64750 TCAATCGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 9 0.35
17 13 0.50
18 4 0.15
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (18 bp):
ACTAATATTAATAAAAAT
Done.