Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003309.1 Hibiscus syriacus cultivar Beakdansim tig00006963_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: 134173
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2658 original size:80 final size:83
Alignment explanation
Indices: 2561--2724 Score: 235
Period size: 83 Copynumber: 2.0 Consensus size: 83
2551 CGTTGAATTT
* *
2561 TAGATGATACATTGTTTATATCATTCAAACTTCA-ATT-TTTT-TAATTGTAGCATTAAATTTTA
1 TAGATGATACATTGTTTATATCATTCAAACTTCATATTATTTTCTAATTATAACATTAAATTTTA
*
2623 ATTTTAACTTCAATTATG
66 ATTTTAACTTCAATCATG
* * * *
2641 TAGATGATACATTGTTTATATCATTCAAATTTTATTTTATTTTCTAATTATAACATTAAATTTTG
1 TAGATGATACATTGTTTATATCATTCAAACTTCATATTATTTTCTAATTATAACATTAAATTTTA
*
2706 ATTTTAATTTCAATCATG
66 ATTTTAACTTCAATCATG
2724 T
1 T
2725 CATTGTGCTA
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
80 32 0.44
81 2 0.03
82 4 0.05
83 35 0.48
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.51
Consensus pattern (83 bp):
TAGATGATACATTGTTTATATCATTCAAACTTCATATTATTTTCTAATTATAACATTAAATTTTA
ATTTTAACTTCAATCATG
Found at i:2692 original size:32 final size:32
Alignment explanation
Indices: 2656--2716 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
2646 GATACATTGT
* *
2656 TTATATCATTCAAATTTT-ATTTTATTTTCTAA
1 TTATAACATT-AAATTTTGATTTTAATTTCTAA
2688 TTATAACATTAAATTTTGATTTTAATTTC
1 TTATAACATTAAATTTTGATTTTAATTTC
2717 AATCATGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 7 0.27
32 19 0.73
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.57
Consensus pattern (32 bp):
TTATAACATTAAATTTTGATTTTAATTTCTAA
Found at i:15091 original size:3 final size:3
Alignment explanation
Indices: 15083--15134 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
15073 ATCCGCAACA
15083 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
15131 ATT A
1 ATT A
15135 AACTAGATTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:18397 original size:31 final size:32
Alignment explanation
Indices: 18362--18422 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
18352 TTTTTATAAA
18362 CTATC-AATTTTAG-TTAGTTTTAGTACCTATG
1 CTATCGAATTTTAGTTTA-TTTTAGTACCTATG
**
18393 CTATCGTTTTTTAGTTTATTTTAGTACCTA
1 CTATCGAATTTTAGTTTATTTTAGTACCTA
18423 AAGTTTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 5 0.19
32 18 0.69
33 3 0.12
ACGTcount: A:0.23, C:0.13, G:0.11, T:0.52
Consensus pattern (32 bp):
CTATCGAATTTTAGTTTATTTTAGTACCTATG
Found at i:20952 original size:21 final size:21
Alignment explanation
Indices: 20910--20953 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
20900 TATATTTTTA
*** *
20910 TTAAAATTTTATTTTTATATT
1 TTAAAATTTTATAAGTACATT
20931 TTAAAATTTTATAAGTACATT
1 TTAAAATTTTATAAGTACATT
20952 TT
1 TT
20954 TCATTGAAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTAAAATTTTATAAGTACATT
Found at i:22550 original size:22 final size:22
Alignment explanation
Indices: 22525--22574 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
22515 GCAGCACGGC
* *
22525 TCTCTGGATTCACCCACACGCT
1 TCTCTCGATGCACCCACACGCT
22547 TCTCTCGATGCACCCACACGCT
1 TCTCTCGATGCACCCACACGCT
22569 TCTCTC
1 TCTCTC
22575 AAGTCAGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.16, C:0.44, G:0.12, T:0.28
Consensus pattern (22 bp):
TCTCTCGATGCACCCACACGCT
Found at i:35272 original size:2 final size:2
Alignment explanation
Indices: 35265--35305 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
35255 TAAAATAGGG
35265 AT AT AT AT AT 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 AT AT AT AT AT A
35306 CATGATGCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41991 original size:21 final size:21
Alignment explanation
Indices: 41965--42044 Score: 96
Period size: 21 Copynumber: 4.0 Consensus size: 21
41955 ATGACCACTA
41965 TGTCCC-ATAGGACCACTGTAT
1 TGTCCCGA-AGGACCACTGTAT
*
41986 TGTCCCGAAGGACCATTGTAT
1 TGTCCCGAAGGACCACTGTAT
*
42007 TGTCCCGAATGACCACTGTA-
1 TGTCCCGAAGGACCACTGTAT
*
42027 --TCCCGTAGGACCACTGTA
1 TGTCCCGAAGGACCACTGTA
42045 ACCCTCGACT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
18 16 0.30
21 36 0.68
22 1 0.02
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (21 bp):
TGTCCCGAAGGACCACTGTAT
Found at i:54773 original size:2 final size:2
Alignment explanation
Indices: 54766--54805 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
54756 ATCCTAACCC
54766 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
54806 TCTAACAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62452 original size:5 final size:5
Alignment explanation
Indices: 62442--62477 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
62432 GCAAGGTTTC
62442 TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT T
1 TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT T
62478 TTTAATGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (5 bp):
TCTCT
Found at i:63182 original size:22 final size:23
Alignment explanation
Indices: 63137--63196 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 23
63127 TTTACTTTAG
* *
63137 AATATAAATTTTGAGATTTTTTT
1 AATACAAATATTGAGATTTTTTT
63160 AAT-CGAAATATTGAGA-TTTTTT
1 AATAC-AAATATTGAGATTTTTTT
63182 AATACAAATATTGAG
1 AATACAAATATTGAG
63197 TACAAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 19 0.58
23 14 0.42
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (23 bp):
AATACAAATATTGAGATTTTTTT
Found at i:64424 original size:2 final size:2
Alignment explanation
Indices: 64417--64450 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
64407 AAATCCTTAA
*
64417 AT AT AT AT AT GT 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
64451 TGATAGTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69757 original size:11 final size:11
Alignment explanation
Indices: 69741--69765 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
69731 ATCCGATAAT
69741 ACCGTATATTA
1 ACCGTATATTA
69752 ACCGTATATTA
1 ACCGTATATTA
69763 ACC
1 ACC
69766 CGTCTTTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (11 bp):
ACCGTATATTA
Found at i:70288 original size:27 final size:26
Alignment explanation
Indices: 70250--70306 Score: 105
Period size: 27 Copynumber: 2.2 Consensus size: 26
70240 TCGGTGGTAA
70250 AAGAATTCTATTGTATCGTTAAAAGTT
1 AAGAATTCTATTGTATCGTT-AAAGTT
70277 AAGAATTCTATTGTATCGTTAAAGTT
1 AAGAATTCTATTGTATCGTTAAAGTT
70303 AAGA
1 AAGA
70307 GATGGGTGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 10 0.33
27 20 0.67
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.39
Consensus pattern (26 bp):
AAGAATTCTATTGTATCGTTAAAGTT
Found at i:76688 original size:23 final size:23
Alignment explanation
Indices: 76662--76787 Score: 146
Period size: 23 Copynumber: 5.5 Consensus size: 23
76652 GCTAAGCTCA
76662 GAATCGAGCTCAGAATCGAGCTT
1 GAATCGAGCTCAGAATCGAGCTT
*
76685 GAATCGAGCTCAAAATCGAGCTT
1 GAATCGAGCTCAGAATCGAGCTT
*
76708 GAATCGAGCTCAAAATCGAGCTT
1 GAATCGAGCTCAGAATCGAGCTT
* *
76731 TAATCGAGCT-TGAATCGAGCTT
1 GAATCGAGCTCAGAATCGAGCTT
* * **
76753 CAATCGAGTTCGAGTTTCGAGCTT
1 GAATCGAGCTC-AGAATCGAGCTT
* *
76777 TAGTCGAGCTC
1 GAATCGAGCTC
76788 TTGAATTTTT
Statistics
Matches: 89, Mismatches: 12, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
22 18 0.20
23 54 0.61
24 17 0.19
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (23 bp):
GAATCGAGCTCAGAATCGAGCTT
Found at i:76690 original size:11 final size:11
Alignment explanation
Indices: 76662--76760 Score: 108
Period size: 11 Copynumber: 8.7 Consensus size: 11
76652 GCTAAGCTCA
*
76662 GAATCGAGCTCA
1 GAATCGAGCT-T
76674 GAATCGAGCTT
1 GAATCGAGCTT
*
76685 GAATCGAGCTCA
1 GAATCGAGCT-T
*
76697 AAATCGAGCTT
1 GAATCGAGCTT
*
76708 GAATCGAGCTCA
1 GAATCGAGCT-T
*
76720 AAATCGAGCTT
1 GAATCGAGCTT
*
76731 TAATCGAGCTT
1 GAATCGAGCTT
76742 GAATCGAGCTT
1 GAATCGAGCTT
*
76753 CAATCGAG
1 GAATCGAG
76761 TTCGAGTTTC
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
11 46 0.62
12 28 0.38
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.23
Consensus pattern (11 bp):
GAATCGAGCTT
Found at i:76882 original size:31 final size:31
Alignment explanation
Indices: 76815--76892 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 31
76805 CGAGCTTTTT
* * * *
76815 CGAGTTCGAGTCGAGTTTCAATATTATCTTT
1 CGAGTTCGAGTCGAGCTTCAAAATTAGCTTG
* * *
76846 AGAGTTCGAGTCGAGCTTGAAAATTGGCTTG
1 CGAGTTCGAGTCGAGCTTCAAAATTAGCTTG
76877 CGAGTTTTCGAGTCGA
1 CGAG--TTCGAGTCGA
76893 ACTGAGATTT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
31 27 0.73
33 10 0.27
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (31 bp):
CGAGTTCGAGTCGAGCTTCAAAATTAGCTTG
Found at i:80191 original size:26 final size:23
Alignment explanation
Indices: 80159--80206 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
80149 ACTGATAATT
*
80159 TTTAAAACAAAATAAAAGTAATAA
1 TTTAAAA-AAAATAAAAGAAATAA
80183 TTTAAAAAAAATAAAAGAAATAA
1 TTTAAAAAAAATAAAAGAAATAA
80206 T
1 T
80207 GTGTAATTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (23 bp):
TTTAAAAAAAATAAAAGAAATAA
Found at i:80810 original size:28 final size:28
Alignment explanation
Indices: 80779--80871 Score: 71
Period size: 28 Copynumber: 3.1 Consensus size: 28
80769 TAAACAATGA
80779 TTTTATTAAAAATATTATTTTTTAATAT
1 TTTTATTAAAAATATTATTTTTTAATAT
* * *
80807 TTTTGA-TAAAAAGATTATTTATAATATTATT
1 TTTT-ATTAAAAATATTATTT-T-TTAATA-T
*
80838 TTTTACTTAAAATATTAATATTTTTTGAATAT
1 TTTTA-TTAAAA-A-TATTATTTTTT-AATAT
80870 TT
1 TT
80872 CCGATAAAGT
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
28 17 0.35
29 2 0.04
30 5 0.10
31 5 0.10
32 9 0.18
33 5 0.10
34 6 0.12
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (28 bp):
TTTTATTAAAAATATTATTTTTTAATAT
Found at i:80997 original size:21 final size:21
Alignment explanation
Indices: 80973--81012 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
80963 TAAAACGCTC
*
80973 AATAATAATATTTTCAATAGA
1 AATAATAATATCTTCAATAGA
80994 AATAATAATATCTTCAATA
1 AATAATAATATCTTCAATA
81013 AATTTTACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.38
Consensus pattern (21 bp):
AATAATAATATCTTCAATAGA
Found at i:81346 original size:51 final size:50
Alignment explanation
Indices: 81286--81412 Score: 137
Period size: 51 Copynumber: 2.5 Consensus size: 50
81276 TTAGCAGTAA
* ** * * *
81286 AGCGCGCCCCCTGTACCGCGCTATACGATGATTTGGCGTCACGTGGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTGACGCCACGT-GGATAT
* * *
81337 AGCGCGCCCCTTGCACCACGCTATACGGTGAGCTGACGCCACGTGGATAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTGACGCCACGTGGATAT
* * *
81387 AGTGCGGCCCCTGCAGCGCGCTATAC
1 AGCGCGCCCCCTGCACCGCGCTATAC
81413 CTGTATATCT
Statistics
Matches: 62, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
50 26 0.42
51 36 0.58
ACGTcount: A:0.17, C:0.33, G:0.30, T:0.20
Consensus pattern (50 bp):
AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTGACGCCACGTGGATAT
Found at i:81568 original size:20 final size:20
Alignment explanation
Indices: 81523--81562 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
81513 TTATCACATC
*
81523 AAATTT-TCTCAAATTCTCT
1 AAATTTATCTCAAATACTCT
81542 AAATTTATCTCAAATACTCT
1 AAATTTATCTCAAATACTCT
81562 A
1 A
81563 TTTTTAAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATTTATCTCAAATACTCT
Found at i:81611 original size:13 final size:14
Alignment explanation
Indices: 81583--81611 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
81573 ATATATTATA
81583 ATGTTTTTACTATT
1 ATGTTTTTACTATT
81597 ATGTTTTTACT-TT
1 ATGTTTTTACTATT
81610 AT
1 AT
81612 TTAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (14 bp):
ATGTTTTTACTATT
Found at i:83925 original size:26 final size:24
Alignment explanation
Indices: 83853--83925 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 24
83843 TTATATTTGT
83853 ATTTACTTTATTTTGTTAAATTATA
1 ATTTACTTTATTTTGTTAAATT-TA
* *
83878 ATTT-TTTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
83901 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
83926 GTTGGAGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
23 4 0.11
24 10 0.27
25 12 0.32
26 11 0.30
ACGTcount: A:0.27, C:0.07, G:0.03, T:0.63
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:87519 original size:50 final size:51
Alignment explanation
Indices: 87444--87570 Score: 170
Period size: 50 Copynumber: 2.5 Consensus size: 51
87434 TTATACAAAG
*
87444 CGCGGTATCTGATCCGCGCTATATAAAATTATGTC-AGACTAAAGGTATGT
1 CGCGGTATCTGATCCGCGCTATATAAAATTATGTCGAGACTAAAAGTATGT
*
87494 CGCGGTATCT-ATCCCGCGCTATATAAAATTATGTCGAGAGTAAAAGTATAG-
1 CGCGGTATCTGAT-CCGCGCTATATAAAATTATGTCGAGACTAAAAGTAT-GT
* *
87545 CGCGATACCTGATCCGCGCTAGTATA
1 CGCGGTATCTGATCCGCGCTA-TATA
87571 GTGCGTTCCA
Statistics
Matches: 68, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
49 2 0.03
50 32 0.47
51 27 0.40
52 7 0.10
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (51 bp):
CGCGGTATCTGATCCGCGCTATATAAAATTATGTCGAGACTAAAAGTATGT
Found at i:99065 original size:2 final size:2
Alignment explanation
Indices: 99058--99092 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
99048 GGAGTGTGAA
99058 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
99093 TGATGGTGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:101110 original size:20 final size:20
Alignment explanation
Indices: 101076--101125 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
101066 AATTGGGAAA
* *
101076 ATCGCAATACGATACTGACT
1 ATCGCAATGCAATACTGACT
* *
101096 ATTGCAATGCAATACTTACT
1 ATCGCAATGCAATACTGACT
101116 ATCGCAATGC
1 ATCGCAATGC
101126 GATAATACAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (20 bp):
ATCGCAATGCAATACTGACT
Found at i:101182 original size:61 final size:61
Alignment explanation
Indices: 101073--101189 Score: 139
Period size: 61 Copynumber: 1.9 Consensus size: 61
101063 GCGAATTGGG
* * * *
101073 AAAATCGCAATACGATACTGACTATTGCAATGCAATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAAGACGATACTGACTATTGCAACGCAATACTGACTATCGCAACGCGATAATAC
* * *
101134 AAAATCGCAACGA-GATACTGACT-TTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAA-GACGATACTGACTATT-GCAACGCAATACTGACTATCGCAACGCGAT
101190 TTACATAGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
60 2 0.04
61 44 0.94
62 1 0.02
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (61 bp):
AAAATCGCAAGACGATACTGACTATTGCAACGCAATACTGACTATCGCAACGCGATAATAC
Found at i:101186 original size:20 final size:20
Alignment explanation
Indices: 101138--101190 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
101128 TAATACAAAA
* *
101138 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
101158 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
101178 TCGCAACGCGATT
1 TCGCAACGCGATT
101191 TACATAGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:101787 original size:19 final size:19
Alignment explanation
Indices: 101765--101969 Score: 178
Period size: 20 Copynumber: 11.1 Consensus size: 19
101755 GAAACCAAAA
*
101765 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
101784 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
101803 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
101822 TCGCGATTGCGATTTTCATT
1 TCGCG-TTGCGATTTTCATT
*
101842 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
** **
101858 T-G-GTCACGATAGTCATT
1 TCGCGTTGCGATTTTCATT
101875 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
101889 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
101908 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
*
101928 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
101948 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
101968 TC
1 TC
101970 AACCAAAAGA
Statistics
Matches: 156, Mismatches: 17, Indels: 26
0.78 0.09 0.13
Matches are distributed among these distances:
14 19 0.12
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 59 0.38
20 69 0.44
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:101843 original size:39 final size:38
Alignment explanation
Indices: 101765--101969 Score: 178
Period size: 33 Copynumber: 5.6 Consensus size: 38
101755 GAAACCAAAA
*
101765 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
101803 TCGCGTTGCGATTTTTATTTCGCGATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCG-TTGCGATTTTCATT
* ** **
101842 TCGCGTTGCGATTGTC---T-G-GTCACGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* **
101875 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
** *
101908 TCCGCGTTGCGATAGTCATTTCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATTT-CGCGTTGCGATTTTCATT
*
101948 ATCTCGTTGCGATTTTCATTTC
1 -TCGCGTTGCGATTTTCATTTC
101970 AACCAAAAGA
Statistics
Matches: 137, Mismatches: 19, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
31 3 0.02
33 35 0.26
34 11 0.08
35 1 0.01
36 3 0.02
38 22 0.16
39 30 0.22
40 31 0.23
41 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.43
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:102390 original size:20 final size:20
Alignment explanation
Indices: 102365--102422 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
102355 ATTCATTTGA
102365 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
102385 CTATCGCAATGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
102405 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
102423 CGCAATGCGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:102465 original size:14 final size:14
Alignment explanation
Indices: 102446--102499 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
102436 GAAAATCGCA
102446 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
102460 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
102477 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
102493 TTGCGAT
1 TTGCGAT
102500 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:102465 original size:33 final size:33
Alignment explanation
Indices: 102428--102498 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
102418 AAAATCGCAA
102428 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
102461 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
102494 TGCGA
1 TGCGA
102499 TAGCCATTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:102499 original size:33 final size:33
Alignment explanation
Indices: 102441--102518 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
102431 GAAATGAAAA
***
102441 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
102474 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
102507 TCGCGTTGCGAT
1 TCGCATTGCGAT
102519 AGTCTGTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:102625 original size:14 final size:14
Alignment explanation
Indices: 102606--102642 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
102596 CATCAATTAA
102606 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
102620 ACAAATCATCTTTT
1 ACAAATCAACATTT
102634 ACAAATCAA
1 ACAAATCAA
102643 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:104603 original size:19 final size:19
Alignment explanation
Indices: 104491--104612 Score: 92
Period size: 19 Copynumber: 6.6 Consensus size: 19
104481 TAGTTTACTT
* *
104491 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* **
104511 TCGCAACGCAAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
104530 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
104550 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
104569 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
104583 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
104602 TCGCAATGCGA
1 TCGCAACGCGA
104613 TTTTCATTTC
Statistics
Matches: 82, Mismatches: 14, Indels: 13
0.75 0.13 0.12
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 39 0.48
20 27 0.33
ACGTcount: A:0.43, C:0.24, G:0.20, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:104643 original size:14 final size:14
Alignment explanation
Indices: 104624--104745 Score: 109
Period size: 14 Copynumber: 7.9 Consensus size: 14
104614 TTTCATTTCG
104624 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
104638 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
104654 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
104670 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
104686 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
104702 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
104718 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
104734 CGTTGCGATTTT
1 CGTTGCGATTTT
104746 CATTTCGCAT
Statistics
Matches: 90, Mismatches: 6, Indels: 24
0.75 0.05 0.20
Matches are distributed among these distances:
14 43 0.48
16 16 0.18
18 31 0.34
ACGTcount: A:0.10, C:0.18, G:0.25, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:104653 original size:32 final size:32
Alignment explanation
Indices: 104608--104761 Score: 272
Period size: 32 Copynumber: 4.8 Consensus size: 32
104598 AAAATCGCAA
104608 TGCGATTTTCATTTCGCGTTGCGATTTTGTCGT
1 TGCGA-TTTCATTTCGCGTTGCGATTTTGTCGT
104641 TGCGATTTCATTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTCATTTCGCGTTGCGATTTTGTCGT
104673 TGCGATTTCATTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTCATTTCGCGTTGCGATTTTGTCGT
*
104705 TGCGATTTCATTTCGCATTGCGATTTTGTCGT
1 TGCGATTTCATTTCGCGTTGCGATTTTGTCGT
*
104737 TGCGATTTTCATTTCGCATTGCGAT
1 TGCGA-TTTCATTTCGCGTTGCGAT
104762 AGCCATTTCC
Statistics
Matches: 119, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
32 95 0.80
33 24 0.20
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (32 bp):
TGCGATTTCATTTCGCGTTGCGATTTTGTCGT
Found at i:104768 original size:19 final size:20
Alignment explanation
Indices: 104746--104789 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
104736 TTGCGATTTT
104746 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
* *
104765 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCATTGCGATAGC
104785 CATTT
1 CATTT
104790 TCGTGTTACG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:105308 original size:18 final size:18
Alignment explanation
Indices: 105282--105326 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
105272 GTCGATCAGA
*
105282 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
105300 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
105318 TGATGGCTC
1 TGATGGCTC
105327 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:106670 original size:20 final size:20
Alignment explanation
Indices: 106645--106682 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
106635 AATAGTTTCT
106645 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
106665 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
106683 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:106973 original size:22 final size:22
Alignment explanation
Indices: 106946--106989 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
106936 GATGGAGATA
106946 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
106968 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
106990 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:107202 original size:20 final size:20
Alignment explanation
Indices: 107177--107229 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
107167 GATTATGTAT
*
107177 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
107197 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
107217 TATCTCGTTGCGA
1 TATCGCGTTGCGA
107230 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:107284 original size:20 final size:20
Alignment explanation
Indices: 107240--107332 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
107230 TTTTTTATTA
* **
107240 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
107261 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
107281 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
107302 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
107322 TCGCATTGCGA
1 TCGCATTGCGA
107333 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:107285 original size:41 final size:41
Alignment explanation
Indices: 107222--107332 Score: 188
Period size: 41 Copynumber: 2.7 Consensus size: 41
107212 GTAAGTATCT
*
107222 CGTTGCGATTT-TTTATTATCGCATTGCGATTTTCCCAATTCG
1 CGTTGCGATTTACTTA-T-TCGCATTGCGATTTTCCCAATTCG
107264 CGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCG
1 CGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCG
107305 CGTTGCGATTTACTTATTCGCATTGCGA
1 CGTTGCGATTTACTTATTCGCATTGCGA
107333 ATTGGGAAAA
Statistics
Matches: 67, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
41 52 0.78
42 12 0.18
43 3 0.04
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (41 bp):
CGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCG
Found at i:107403 original size:21 final size:21
Alignment explanation
Indices: 107363--107403 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
107353 ATTGTAGACC
**
107363 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
107384 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
107404 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:115902 original size:2 final size:2
Alignment explanation
Indices: 115895--115935 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
115885 TTTTAAATTA
115895 AT AT AT AT AT 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 AT AT AT AT AT A
115936 AAAGTTTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:122880 original size:29 final size:29
Alignment explanation
Indices: 122814--122881 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 29
122804 GAAAATATAT
122814 TTTCGCCCCTAAAATTTTATAAGTTCAAG
1 TTTCGCCCCTAAAATTTTATAAGTTCAAG
*
122843 TTTAC-CCCCTGAAATTTTTATAAGTTCAA-
1 TTT-CGCCCCT-AAAATTTTATAAGTTCAAG
122872 TTTCGCCCCT
1 TTTCGCCCCT
122882 CCTAACTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
28 1 0.03
29 16 0.46
30 18 0.51
ACGTcount: A:0.26, C:0.25, G:0.09, T:0.40
Consensus pattern (29 bp):
TTTCGCCCCTAAAATTTTATAAGTTCAAG
Found at i:131716 original size:120 final size:119
Alignment explanation
Indices: 131551--131777 Score: 314
Period size: 120 Copynumber: 1.9 Consensus size: 119
131541 CTAGACATTA
* * * * *
131551 TATGATTTTTAAAAAATTAAAAGTTTAGGTCTTAAAACAGACCAAACTT-ATAGTTTAGATACTA
1 TATGATTTTGAAAAAATAAAAAATTTAAGTATTAAAACAGACCAAA-TTAATAGTTTAGATACTA
* *
131615 AATGCGTAACTTACCCATGTATTTATTTCATTCTTTTAATCAAAACTAAACATCAAG
65 AATGCATAACTTACCCATGTATTTA--TCATTCTTTGAATCAAAACTAAACATCAAG
* *
131672 TATGATTTTGAAAAAA-AAAAAATTTAAGTATTAAAACAGACCAAATTAATAGTTTAGGTATTAA
1 TATGATTTTGAAAAAATAAAAAATTTAAGTATTAAAACAGACCAAATTAATAGTTTAGATACTAA
* *
131736 ATGTATAATTTACCCATGTATTTATCATTCTTTGAATCAAAA
66 ATGCATAACTTACCCATGTATTTATCATTCTTTGAATCAAAA
131778 TTGATATGTT
Statistics
Matches: 94, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
118 17 0.18
119 2 0.02
120 60 0.64
121 15 0.16
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (119 bp):
TATGATTTTGAAAAAATAAAAAATTTAAGTATTAAAACAGACCAAATTAATAGTTTAGATACTAA
ATGCATAACTTACCCATGTATTTATCATTCTTTGAATCAAAACTAAACATCAAG
Done.