Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004814.1 Hibiscus syriacus cultivar Beakdansim tig00010849_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: 61192
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:102 original size:24 final size:24
Alignment explanation
Indices: 67--113 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
57 TAAAAAATAT
*
67 ATTTAAATTTATTTATTAATTAAA
1 ATTTAAATTTATATATTAATTAAA
91 ATTT-AATATTATATATTAATTAA
1 ATTTAAAT-TTATATATTAATTAA
114 TTATAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTTAAATTTATATATTAATTAAA
Found at i:107 original size:28 final size:26
Alignment explanation
Indices: 75--137 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 26
65 ATATTTAAAT
* *
75 TTATTTATTAATTAAAATTTAATATTA
1 TTATTTATTAATTAAAATAT-ATATCA
* *
102 TATATTAATTAATTATAATATATATCA
1 T-TATTTATTAATTAAAATATATATCA
129 TTATTTATT
1 TTATTTATT
138 TTTCTATTAC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
26 7 0.23
27 7 0.23
28 16 0.53
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (26 bp):
TTATTTATTAATTAAAATATATATCA
Found at i:375 original size:23 final size:22
Alignment explanation
Indices: 332--385 Score: 99
Period size: 23 Copynumber: 2.4 Consensus size: 22
322 TCTTTAAGAA
332 TATAATTTAATATTATAATAAT
1 TATAATTTAATATTATAATAAT
354 TATAATTTAATATATATAATAAT
1 TATAATTTAATAT-TATAATAAT
377 TATAATTTA
1 TATAATTTA
386 GAGGAATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 13 0.42
23 18 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TATAATTTAATATTATAATAAT
Found at i:1523 original size:29 final size:31
Alignment explanation
Indices: 1490--1547 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
1480 AACTTAAAAG
*
1490 AGTTTTGCAATACT-AAATTT-AATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
1519 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
1548 CATACACTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 13 0.50
30 6 0.23
31 7 0.27
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:3306 original size:41 final size:42
Alignment explanation
Indices: 3224--3340 Score: 123
Period size: 41 Copynumber: 2.8 Consensus size: 42
3214 TAGATTGACA
* * * *
3224 TTTTATGGCGTTTGTTACAAAACAC-CGTTATATATATTGATC
1 TTTTACGGCGTTTGTT-CAAAAAACGCGCTATAGATATTGATC
*
3266 TTTTGCGGCGTTTGTTCAAAAAACGCGCTATAGATA-TGATC
1 TTTTACGGCGTTTGTTCAAAAAACGCGCTATAGATATTGATC
*
3307 TTTTACGACGTTTGTTTTCAAAAAA-GTCGCTATA
1 TTTTACGGCGTTTG--TTCAAAAAACG-CGCTATA
3341 TATCTTGACC
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
41 24 0.38
42 24 0.38
43 16 0.25
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.39
Consensus pattern (42 bp):
TTTTACGGCGTTTGTTCAAAAAACGCGCTATAGATATTGATC
Found at i:4462 original size:29 final size:29
Alignment explanation
Indices: 4420--4530 Score: 186
Period size: 29 Copynumber: 3.8 Consensus size: 29
4410 GTGCAGCCGT
4420 AGGTCGCCATGCCATCCGGGCGACCTTGG
1 AGGTCGCCATGCCATCCGGGCGACCTTGG
4449 AGGTCGCCATGCCATCCGGGCGACCTTGG
1 AGGTCGCCATGCCATCCGGGCGACCTTGG
**
4478 AGGTCGCCATGGAATCCGGGCGACCTTGG
1 AGGTCGCCATGCCATCCGGGCGACCTTGG
* *
4507 AGGTCGCCATGGCATCCGAGCGAC
1 AGGTCGCCATGCCATCCGGGCGAC
4531 ATGTGTGGTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 78 1.00
ACGTcount: A:0.16, C:0.32, G:0.35, T:0.16
Consensus pattern (29 bp):
AGGTCGCCATGCCATCCGGGCGACCTTGG
Found at i:4608 original size:20 final size:20
Alignment explanation
Indices: 4583--4620 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4573 TGGGATGCAT
*
4583 GTGGGAGCTGTGCATGGGAC
1 GTGGGAACTGTGCATGGGAC
4603 GTGGGAACTGTGCATGGG
1 GTGGGAACTGTGCATGGG
4621 CCATGTCGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.13, G:0.50, T:0.21
Consensus pattern (20 bp):
GTGGGAACTGTGCATGGGAC
Found at i:4902 original size:30 final size:29
Alignment explanation
Indices: 4868--4944 Score: 110
Period size: 24 Copynumber: 2.8 Consensus size: 29
4858 CTCGAACGGT
4868 GTAGGTCGCCATGGAGTCACGGCGAGCTTG
1 GTAGGTCGCCATGGAGTCACGGC-AGCTTG
4898 GTAGGTCGCCATGGAGT-----CAGCTTG
1 GTAGGTCGCCATGGAGTCACGGCAGCTTG
4922 GTAGGTCGCCATGGAGTCACGGC
1 GTAGGTCGCCATGGAGTCACGGC
4945 TGGGAGATTC
Statistics
Matches: 42, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
24 23 0.55
25 1 0.02
29 1 0.02
30 17 0.40
ACGTcount: A:0.17, C:0.23, G:0.39, T:0.21
Consensus pattern (29 bp):
GTAGGTCGCCATGGAGTCACGGCAGCTTG
Found at i:5381 original size:22 final size:23
Alignment explanation
Indices: 5353--5397 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
5343 TAGTTAATTA
5353 GTTTGTTAGTATAA-ATTAGTTT
1 GTTTGTTAGTATAATATTAGTTT
*
5375 GTTTGTTAGTTTAATATTAGTTT
1 GTTTGTTAGTATAATATTAGTTT
5398 ATTAGTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (23 bp):
GTTTGTTAGTATAATATTAGTTT
Found at i:9009 original size:23 final size:23
Alignment explanation
Indices: 8978--9244 Score: 137
Period size: 23 Copynumber: 11.3 Consensus size: 23
8968 ATTTCTATGT
*
8978 ATTT-ATAATCATTATAAAAATG
1 ATTTAATAATCATTATAATAATG
*
9000 ATTTAATAATGATT-T-A-AAT-
1 ATTTAATAATCATTATAATAATG
* *
9019 ATTTAATGATTGATGATT-TAGTAATG
1 ATTTAAT-A---ATCATTATAATAATG
9045 ATTTGATAATAATCATTATAATAATG
1 A-TT--TAATAATCATTATAATAATG
9071 ATTGATAATAATCATTATAATAATG
1 ATT--TAATAATCATTATAATAATG
*
9096 ATTTATTAATAATCATTATAAAAATG
1 A--T-TTAATAATCATTATAATAATG
*
9122 ATTTAATAATGATT-T-A-AAT-
1 ATTTAATAATCATTATAATAATG
* *
9141 ATTTAATGATTGATGATT-TAGTAATG
1 ATTTAAT-A---ATCATTATAATAATG
*
9167 ATTTGATAATCATTATAATAATG
1 ATTTAATAATCATTATAATAATG
* * * *
9190 ATTT-ATAATAATTATTTAGTTATT
1 ATTTAATAATCATTA--TAATAATG
* *
9214 ATTTAGTAATTATT-TATATAATG
1 ATTTAATAATCATTATA-ATAATG
9237 ATTTAATA
1 ATTTAATA
9245 CTAATGATTT
Statistics
Matches: 198, Mismatches: 20, Indels: 53
0.73 0.07 0.20
Matches are distributed among these distances:
19 14 0.07
20 8 0.04
21 2 0.01
22 22 0.11
23 54 0.27
24 10 0.05
25 44 0.22
26 35 0.18
27 3 0.02
28 2 0.01
29 4 0.02
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (23 bp):
ATTTAATAATCATTATAATAATG
Found at i:9069 original size:26 final size:25
Alignment explanation
Indices: 9040--9273 Score: 156
Period size: 25 Copynumber: 9.7 Consensus size: 25
9030 GATGATTTAG
9040 TAATGATTTGATAATAATCATTATAA
1 TAATGATTT-ATAATAATCATTATAA
*
9066 TAATGATTGATAATAATCATTATAA
1 TAATGATTTATAATAATCATTATAA
9091 TAATGATTTATTAATAATCATTATAA
1 TAATGATTTA-TAATAATCATTATAA
* *
9117 AAATGA-TT-TAATAATGATT-T-A
1 TAATGATTTATAATAATCATTATAA
* * * *
9138 -AAT-ATTTAATGATTGATGATT-TAG
1 TAATGATTT-AT-AATAATCATTATAA
*
9162 TAATGA-TT-TGATAATCATTATAA
1 TAATGATTTATAATAATCATTATAA
* *
9185 TAATGATTTATAATAATTATT-TAG
1 TAATGATTTATAATAATCATTATAA
* * *
9209 TTATTATTTAGTAATTAT--TTAT-A
1 TAATGATTTA-TAATAATCATTATAA
* *
9232 TAATGATTTAATACTAATGATT-TAA
1 TAATGATTT-ATAATAATCATTATAA
*
9257 TAATTA-TTACTAATAAT
1 TAATGATTTA-TAATAAT
9274 ATAGAATACT
Statistics
Matches: 165, Mismatches: 25, Indels: 38
0.72 0.11 0.17
Matches are distributed among these distances:
19 1 0.01
20 5 0.03
21 1 0.01
22 8 0.05
23 43 0.26
24 23 0.14
25 55 0.33
26 29 0.18
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.46
Consensus pattern (25 bp):
TAATGATTTATAATAATCATTATAA
Found at i:9191 original size:34 final size:32
Alignment explanation
Indices: 9104--9198 Score: 97
Period size: 34 Copynumber: 2.8 Consensus size: 32
9094 TGATTTATTA
*
9104 ATAATCATTATAAAAATGATTTAATAATGATTT
1 ATAATCATTATAATAATGATTT-ATAATGATTT
9137 A-AAT-ATT-TAATGATTGATGATTTAGTAATGATTT
1 ATAATCATTATAAT-A---ATGATTTA-TAATGATTT
9171 GATAATCATTATAATAATGATTTATAAT
1 -ATAATCATTATAATAATGATTTATAAT
9199 AATTATTTAG
Statistics
Matches: 52, Mismatches: 1, Indels: 18
0.73 0.01 0.25
Matches are distributed among these distances:
30 3 0.06
31 4 0.08
32 3 0.06
33 6 0.12
34 24 0.46
35 1 0.02
36 3 0.06
37 4 0.08
38 4 0.08
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (32 bp):
ATAATCATTATAATAATGATTTATAATGATTT
Found at i:9201 original size:122 final size:120
Alignment explanation
Indices: 8977--9201 Score: 398
Period size: 122 Copynumber: 1.9 Consensus size: 120
8967 TATTTCTATG
*
8977 TATTTATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTGATGATTTAGTA
1 TATTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTGATGATTTAGTA
*
9042 ATGATTTGATAATAATCATTATAATAATGATTGATAATAATCATTATAATAATGATT
66 ATGATTTG--AATAATCATTATAATAATGATTAATAATAATCATTATAATAATGATT
9099 TATTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTGATGATTTAGTA
1 TATTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTGATGATTTAGTA
*
9164 ATGATTTG-ATAATCATTATAATAATGATTTATAATAAT
66 ATGATTTGAATAATCATTATAATAATGATTAATAATAAT
9202 TATTTAGTTA
Statistics
Matches: 101, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
119 29 0.29
122 72 0.71
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (120 bp):
TATTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTGATGATTTAGTA
ATGATTTGAATAATCATTATAATAATGATTAATAATAATCATTATAATAATGATT
Found at i:9251 original size:14 final size:13
Alignment explanation
Indices: 9220--9258 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
9210 TATTATTTAG
*
9220 TAATTATTT-ATA
1 TAATGATTTAATA
9232 TAATGATTTAATA
1 TAATGATTTAATA
9245 CTAATGATTTAATA
1 -TAATGATTTAATA
9259 ATTATTACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 8 0.33
13 3 0.12
14 13 0.54
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (13 bp):
TAATGATTTAATA
Found at i:11861 original size:43 final size:41
Alignment explanation
Indices: 11813--11907 Score: 95
Period size: 44 Copynumber: 2.2 Consensus size: 41
11803 CAATATAACT
*
11813 TAACTAT-TTAACTAACACAAACTAATTAAATAATTTTTT-TATA
1 TAACTATATTAAC-AA-AAAAACTAATT-AAT-ATTTTTTATATA
11856 TAACTAACTATTAACAAAAAAACTAATTAATATTTTTTAACTATA
1 TAACT-A-TATTAACAAAAAAACTAATTAATATTTTTT-A-TATA
11901 TAACTAT
1 TAACTAT
11908 CAAACATATA
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
42 7 0.16
43 9 0.20
44 12 0.27
45 12 0.27
46 5 0.11
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (41 bp):
TAACTATATTAACAAAAAAACTAATTAATATTTTTTATATA
Found at i:11892 original size:40 final size:47
Alignment explanation
Indices: 11805--11894 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 47
11795 TCAACAAACA
*
11805 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTT
1 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAA-TTTTTT
11853 ATATAAC-TAACTA-TTAAC-AA-AAAAACTAATT-AAT-ATTTTTT
1 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTT
11894 A
1 A
11895 ACTATATAAC
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
41 7 0.17
42 1 0.02
43 3 0.07
44 10 0.24
45 2 0.05
46 5 0.12
47 6 0.15
48 7 0.17
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (47 bp):
ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTT
Found at i:11934 original size:41 final size:43
Alignment explanation
Indices: 11804--11937 Score: 114
Period size: 41 Copynumber: 3.1 Consensus size: 43
11794 TTCAACAAAC
* *
11804 AATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
1 AATATAAC-TAACTA-TCAAC-AA-AAAAACTAATTAAATAA-TTTTT
* * *
11852 TATATAACTAACTATTAACAAAAAAACTAATT-AATATTTTTT
1 AATATAACTAACTATCAACAAAAAAACTAATTAAATAATTTTT
* * *
11894 AACTAT-A-TAACTATCAA-ACATATACTAATTAAATAATTTTT
1 AA-TATAACTAACTATCAACAAAAAAACTAATTAAATAATTTTT
11935 AAT
1 AAT
11938 TTATGTATAC
Statistics
Matches: 75, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
40 11 0.15
41 20 0.27
42 7 0.09
43 7 0.09
44 10 0.13
45 2 0.03
46 5 0.07
47 6 0.08
48 7 0.09
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (43 bp):
AATATAACTAACTATCAACAAAAAAACTAATTAAATAATTTTT
Found at i:11962 original size:41 final size:39
Alignment explanation
Indices: 11826--11962 Score: 89
Period size: 41 Copynumber: 3.3 Consensus size: 39
11816 CTATTTAACT
* *
11826 AACACAAACTAATTAAATAATTTTTTTA-TATAACTAACTATTA
1 AACATAAACTAATT-AATAA-TTTTTAACTAT-A-TAACTA-TA
* * *
11869 ACAAAAAAACTAATTAATATTTTTTAACTATATAACTATCA
1 A-ACATAAACTAATTAATAATTTTTAACTATATAACTAT-A
* * *
11910 AACATATACTAATTAAATAATTTTTAATTTATGTATACTAT-
1 AACATAAACTAATT-AATAATTTTTAA-CTATATA-ACTATA
*
11951 AACTTAAACTAA
1 AACATAAACTAA
11963 CATCATATAA
Statistics
Matches: 76, Mismatches: 12, Indels: 14
0.75 0.12 0.14
Matches are distributed among these distances:
40 11 0.14
41 29 0.38
42 12 0.16
43 13 0.17
44 11 0.14
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.39
Consensus pattern (39 bp):
AACATAAACTAATTAATAATTTTTAACTATATAACTATA
Found at i:12580 original size:28 final size:29
Alignment explanation
Indices: 12488--12592 Score: 149
Period size: 30 Copynumber: 3.6 Consensus size: 29
12478 TAGGACTATG
**
12488 GGGACTACATGGCGACCTACTTGGTCGCC
1 GGGACTACATGGCGACCTACAAGGTCGCC
12517 GGGGACTACATGGCGACCTACAAGGTCGCC
1 -GGGACTACATGGCGACCTACAAGGTCGCC
12547 GGGACTACATGGCGACCTAC-AGGTCGCC
1 GGGACTACATGGCGACCTACAAGGTCGCC
** *
12575 CAGACTGCATGGCGACCT
1 GGGACTACATGGCGACCT
12593 CTCCATTGGC
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
28 23 0.33
29 20 0.29
30 27 0.39
ACGTcount: A:0.21, C:0.31, G:0.31, T:0.16
Consensus pattern (29 bp):
GGGACTACATGGCGACCTACAAGGTCGCC
Found at i:12643 original size:28 final size:28
Alignment explanation
Indices: 12611--12664 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
12601 GCTCGTATGG
12611 CTCGTATAAGACTGCATGGCGACCTCTC
1 CTCGTATAAGACTGCATGGCGACCTCTC
12639 CTCGTATAAGACTGCATGGCGACCTC
1 CTCGTATAAGACTGCATGGCGACCTC
12665 CATTGGCTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.24
Consensus pattern (28 bp):
CTCGTATAAGACTGCATGGCGACCTCTC
Found at i:12682 original size:9 final size:9
Alignment explanation
Indices: 12668--12707 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
12658 CGACCTCCAT
12668 TGGCTCGTA
1 TGGCTCGTA
12677 TGGCTCGTATA
1 TGGCTCG--TA
*
12688 TGGCTTGTA
1 TGGCTCGTA
12697 TGGCTCGTA
1 TGGCTCGTA
12706 TG
1 TG
12708 TCACCCCGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 19 0.70
11 8 0.30
ACGTcount: A:0.12, C:0.17, G:0.33, T:0.38
Consensus pattern (9 bp):
TGGCTCGTA
Found at i:12697 original size:20 final size:20
Alignment explanation
Indices: 12668--12706 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12658 CGACCTCCAT
12668 TGGCTCGTATGGCTCGTATA
1 TGGCTCGTATGGCTCGTATA
*
12688 TGGCTTGTATGGCTCGTAT
1 TGGCTCGTATGGCTCGTAT
12707 GTCACCCCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.18, G:0.31, T:0.38
Consensus pattern (20 bp):
TGGCTCGTATGGCTCGTATA
Found at i:12737 original size:20 final size:21
Alignment explanation
Indices: 12694--12739 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
12684 TATATGGCTT
12694 GTATGGCTCGTATGTCACCCC
1 GTATGGCTCGTATGTCACCCC
*
12715 GTATGGGTCGTATGTCA-CCC
1 GTATGGCTCGTATGTCACCCC
12735 GTATG
1 GTATG
12740 TCGCCTGGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
GTATGGCTCGTATGTCACCCC
Found at i:14544 original size:13 final size:13
Alignment explanation
Indices: 14526--14550 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14516 TTTCTACCAT
14526 ATATATATATATA
1 ATATATATATATA
14539 ATATATATATAT
1 ATATATATATAT
14551 TATGTAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATATATATATA
Found at i:34816 original size:14 final size:14
Alignment explanation
Indices: 34797--34826 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
34787 TGATTTCCAC
34797 GCTTTTGGACTGAA
1 GCTTTTGGACTGAA
34811 GCTTTTGGACTGAA
1 GCTTTTGGACTGAA
34825 GC
1 GC
34827 CAGCCATCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.33
Consensus pattern (14 bp):
GCTTTTGGACTGAA
Found at i:43391 original size:16 final size:16
Alignment explanation
Indices: 43370--43403 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
43360 AAAAGAGGAA
43370 GGTCAT-TTGGTATGCC
1 GGTCATGTT-GTATGCC
43386 GGTCATGTTGTATGCC
1 GGTCATGTTGTATGCC
43402 GG
1 GG
43404 AGGAGTTGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.12, C:0.18, G:0.35, T:0.35
Consensus pattern (16 bp):
GGTCATGTTGTATGCC
Found at i:45877 original size:27 final size:27
Alignment explanation
Indices: 45839--45892 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
45829 GTAATTTAAG
*
45839 GACTTAGAGCCTCGTCTTACTAAAAAT
1 GACTTAGAGCCTCATCTTACTAAAAAT
* *
45866 GACTTAGAGCCTTATCTTACTATAAAT
1 GACTTAGAGCCTCATCTTACTAAAAAT
45893 AACAAAGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (27 bp):
GACTTAGAGCCTCATCTTACTAAAAAT
Found at i:50183 original size:16 final size:17
Alignment explanation
Indices: 50164--50204 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
50154 AACCGAAAGC
50164 AACCTGAATC-GAATTT
1 AACCTGAATCTGAATTT
*
50180 AACCCGAA-CTGAATTT
1 AACCTGAATCTGAATTT
50196 AACCT-AATC
1 AACCTGAATC
50205 CAAAAATAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
15 3 0.14
16 18 0.86
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (17 bp):
AACCTGAATCTGAATTT
Found at i:50985 original size:5 final size:5
Alignment explanation
Indices: 50975--51000 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
50965 TGACTTAGAA
50975 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
51001 AATAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:53105 original size:41 final size:41
Alignment explanation
Indices: 53060--53154 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
53050 ATATTTGTAT
*
53060 TTTAGTGGCGTTTGTATGAAAACGCCGCTATAGACTTATAC
1 TTTAGTGGCGTTTGTATGAAAACGCCGCTATAGACTCATAC
* *
53101 TTTAGTGGCGTTCGTATGAAAACGCCGCTATAGACTCGTAC
1 TTTAGTGGCGTTTGTATGAAAACGCCGCTATAGACTCATAC
53142 TTTAGTGGCGTTT
1 TTTAGTGGCGTTT
53155 TTGTTAAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (41 bp):
TTTAGTGGCGTTTGTATGAAAACGCCGCTATAGACTCATAC
Found at i:53954 original size:21 final size:21
Alignment explanation
Indices: 53912--53954 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
53902 TTTCTGGGTT
* * *
53912 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
53933 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
53954 A
1 A
53955 CGAATATGGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:54061 original size:66 final size:67
Alignment explanation
Indices: 53934--54083 Score: 250
Period size: 66 Copynumber: 2.3 Consensus size: 67
53924 ACCCATTCAA
*
53934 GGGGAACCGATACCCCCTCAACGAATATGGATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGGAATTCCAGAATGCTAGAGGGGAATCGATA-CCCCA
53999 -GG
65 GGG
*
54001 GGGGAACCGATACCCCCTCAACGAATAT-GAATTCCAGAATGCTAGTGGGGAATCGATACCCCAG
1 GGGGAACCGATACCCCCTCAACGAATATGGAATTCCAGAATGCTAGAGGGGAATCGATACCCCAG
54065 GG
66 GG
*
54067 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
54084 ATGAAAAAAA
Statistics
Matches: 79, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
65 5 0.06
66 46 0.58
67 28 0.35
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAATATGGAATTCCAGAATGCTAGAGGGGAATCGATACCCCAG
GG
Found at i:54730 original size:22 final size:23
Alignment explanation
Indices: 54698--54754 Score: 98
Period size: 22 Copynumber: 2.5 Consensus size: 23
54688 ATCATTATAT
*
54698 GGCACTACGGTGCAATTCTAC-G
1 GGCACTTCGGTGCAATTCTACGG
54720 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
54743 GGCACTTCGGTG
1 GGCACTTCGGTG
54755 TATTTATACG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 20 0.61
23 13 0.39
ACGTcount: A:0.18, C:0.26, G:0.32, T:0.25
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:54764 original size:23 final size:23
Alignment explanation
Indices: 54698--54764 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 23
54688 ATCATTATAT
* *
54698 GGCACTACGGTGCAATTCTAC-G
1 GGCACTTCGGTGCAATTATACGG
*
54720 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTATACGG
* *
54743 GGCACTTCGGTGTATTTATACG
1 GGCACTTCGGTGCAATTATACG
54765 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 20 0.50
23 20 0.50
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.28
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTATACGG
Found at i:60889 original size:67 final size:65
Alignment explanation
Indices: 60817--60964 Score: 235
Period size: 66 Copynumber: 2.2 Consensus size: 65
60807 ACCCATTCAA
*
60817 GGGAACCGATACCCCCTCAACGAATATGGATTTCCAGAATGCTAGAGGGGAATCGATAACCCTCA
1 GGGAACCGATACCCCCTCAACGAATAT-GAATTCCAGAATGCTAGAGGGGAATCGAT-ACCC-CA
60882 -GG
63 GGG
*
60884 GGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGTGGGGAATCGATACCCCAGGG
1 GGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCAGGG
*
60949 GGGAACCGATTCCCCC
1 GGGAACCGATACCCCC
60965 ATGAAAAAAA
Statistics
Matches: 77, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
64 2 0.03
65 21 0.27
66 27 0.35
67 27 0.35
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.17
Consensus pattern (65 bp):
GGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCAGGG
Done.