Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004394.1 Hibiscus syriacus cultivar Beakdansim tig00009638_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: 67331
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:14422 original size:21 final size:20
Alignment explanation
Indices: 14374--14422 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
14364 ACTTTTTAGG
*
14374 AAATTATCTTGGAAAATTTCG
1 AAATT-TCTTGGAAAATTTCA
*
14395 AAA-TTCTTGTAGAAATTTCA
1 AAATTTCTTGGA-AAATTTCA
14415 AAATTTCT
1 AAATTTCT
14423 AATCAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 6 0.25
20 11 0.46
21 7 0.29
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (20 bp):
AAATTTCTTGGAAAATTTCA
Found at i:21246 original size:3 final size:3
Alignment explanation
Indices: 21232--21301 Score: 83
Period size: 3 Copynumber: 24.0 Consensus size: 3
21222 TTTTTATCTG
** *
21232 TAA TAA -AA TAA TAA T-A TTT TAA TAA TAA TAA TAA TAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
21278 TAA TAA TAA TAA -ATA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA
21302 AAACCAAATG
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
2 5 0.09
3 52 0.90
4 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:22100 original size:111 final size:112
Alignment explanation
Indices: 21655--22144 Score: 653
Period size: 113 Copynumber: 4.4 Consensus size: 112
21645 AAAAGGTTGA
* *
21655 ATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAATGATGAATTTAAACAA
1 ATAAGTTCTTCTCATTATGAAC-TTCTCTGGAAATGCTGATCCATCGAATGATGAATTTAAACAA
* ** * *
21720 AAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAG
65 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
** * * **
21768 ACGAGTTCTTCTCATTATGAAC-TCTACCTGGCAATGTTGATCCATTAAATGATGAATTTAAACA
1 ATAAGTTCTTCTCATTATGAACTTCT--CTGGAAATGCTGATCCATCGAATGATGAATTTAAACA
21832 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
64 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* * * * *
21881 ACAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGAATTTGAGCAA
1 ATAAGTTCTTCTCATTATGAAC-TTCTCTGGAAATGCTGATCCATCGAATGATGAATTTAAACAA
21946 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
65 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* * * * ** *
21994 ATAAGTTTTTCTCATTATGAGCTT-TCTGGTAATGCTGATCCATCGAGTGATGAATTCGAGCAAA
1 ATAAGTTCTTCTCATTATGAACTTCTCTGGAAATGCTGATCCATCGAATGATGAATTTAAACAAA
* *
22058 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAG
66 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* *
22105 ATGAGTTCTTCTCATTATGAAC-TCTTCTGTAAATGCTGAT
1 ATAAGTTCTTCTCATTATGAACTTC-TCTGGAAATGCTGAT
22145 GACCCGAAGG
Statistics
Matches: 338, Mismatches: 33, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
110 1 0.00
111 104 0.31
112 15 0.04
113 215 0.64
115 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.38
Consensus pattern (112 bp):
ATAAGTTCTTCTCATTATGAACTTCTCTGGAAATGCTGATCCATCGAATGATGAATTTAAACAAA
AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
Found at i:22427 original size:75 final size:76
Alignment explanation
Indices: 22142--22448 Score: 535
Period size: 76 Copynumber: 4.1 Consensus size: 76
22132 TGTAAATGCT
* *
22142 GATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
22207 TAGGACTTACA
66 TAGGACTTACA
*
22218 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCACTG
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
22283 TAGGACTTACA
66 TAGGACTTACA
*
22294 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAATATCATGCACTG
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
* *
22359 CAGGACTTATA
66 TAGGACTTACA
* *
22370 GATGACCCTAAGGC-TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGTATTG
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
22434 TAGGACTTACA
66 TAGGACTTACA
22445 GATG
1 GATG
22449 TGGGAAATAG
Statistics
Matches: 219, Mismatches: 12, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
75 60 0.27
76 159 0.73
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (76 bp):
GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
TAGGACTTACA
Found at i:23159 original size:21 final size:22
Alignment explanation
Indices: 23124--23177 Score: 101
Period size: 21 Copynumber: 2.5 Consensus size: 22
23114 GATAAAGCTT
23124 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
23146 TCATCTTT-AAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
23167 TCATCTTTGAA
1 TCATCTTTGAA
23178 GAATGTAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.68
22 10 0.32
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:28138 original size:8 final size:7
Alignment explanation
Indices: 28126--28175 Score: 64
Period size: 7 Copynumber: 6.9 Consensus size: 7
28116 GATTCAAATT
28126 TTTTTTC
1 TTTTTTC
28133 TTTTTTCC
1 TTTTTT-C
*
28141 TTTTTCC
1 TTTTTTC
28148 TTTTTTC
1 TTTTTTC
*
28155 CTTTTTC
1 TTTTTTC
28162 TTTTTTCC
1 TTTTTT-C
28170 TTTTTT
1 TTTTTT
28176 TATGAGTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
7 24 0.65
8 13 0.35
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTTC
Found at i:28150 original size:15 final size:14
Alignment explanation
Indices: 28127--28174 Score: 87
Period size: 14 Copynumber: 3.4 Consensus size: 14
28117 ATTCAAATTT
28127 TTTTTCTTTTTTCC
1 TTTTTCTTTTTTCC
28141 TTTTTCCTTTTTTCC
1 TTTTT-CTTTTTTCC
28156 TTTTTCTTTTTTCC
1 TTTTTCTTTTTTCC
28170 TTTTT
1 TTTTT
28175 TTATGAGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
14 19 0.58
15 14 0.42
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTCTTTTTTCC
Found at i:28175 original size:15 final size:15
Alignment explanation
Indices: 28126--28175 Score: 84
Period size: 15 Copynumber: 3.4 Consensus size: 15
28116 GATTCAAATT
28126 TTTTTTCTTTTTTCC
1 TTTTTTCTTTTTTCC
*
28141 TTTTTCCTTTTTTCC
1 TTTTTTCTTTTTTCC
28156 -TTTTTCTTTTTTCC
1 TTTTTTCTTTTTTCC
28170 TTTTTT
1 TTTTTT
28176 TATGAGTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 13 0.41
15 19 0.59
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTCTTTTTTCC
Found at i:30141 original size:12 final size:12
Alignment explanation
Indices: 30126--30153 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
30116 CAAACATAAA
30126 AAATGCAAATGT
1 AAATGCAAATGT
30138 AAATGCAAATGT
1 AAATGCAAATGT
30150 AAAT
1 AAAT
30154 ATGTGAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.07, G:0.14, T:0.25
Consensus pattern (12 bp):
AAATGCAAATGT
Found at i:30152 original size:27 final size:27
Alignment explanation
Indices: 30093--30152 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
30083 AAATGTAATT
30093 ATGT-AAAAATGAAAATGTAAATACAA
1 ATGTAAAAAATGAAAATGTAAATACAA
** * *
30119 ACATAAAAAATGCAAATGTAAATGCAA
1 ATGTAAAAAATGAAAATGTAAATACAA
30146 ATGTAAA
1 ATGTAAA
30153 TATGTGAATG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.60, C:0.07, G:0.12, T:0.22
Consensus pattern (27 bp):
ATGTAAAAAATGAAAATGTAAATACAA
Found at i:30246 original size:7 final size:7
Alignment explanation
Indices: 30212--30253 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
30202 ATAAAAGTAT
30212 AAATGCA
1 AAATGCA
* *
30219 CAATGAA
1 AAATGCA
30226 AAATGCA
1 AAATGCA
30233 AAGATGCA
1 AA-ATGCA
30241 AAATGC-
1 AAATGCA
30247 AAATGCA
1 AAATGCA
30254 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:31808 original size:26 final size:25
Alignment explanation
Indices: 31743--31809 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 25
31733 ATTTAATACT
31743 TGAAAATAA-AATA-A-AAATATTA
1 TGAAAATAATAATATATAAATATTA
** *
31765 AAAAAATAATATACATATAAATATTA
1 TGAAAATAATA-ATATATAAATATTA
31791 TGAAAATAATAAGTATATA
1 TGAAAATAATAA-TATATA
31810 TAAACATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
22 7 0.21
23 1 0.03
24 2 0.06
25 2 0.06
26 22 0.65
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.30
Consensus pattern (25 bp):
TGAAAATAATAATATATAAATATTA
Found at i:31810 original size:28 final size:26
Alignment explanation
Indices: 31757--31824 Score: 73
Period size: 28 Copynumber: 2.5 Consensus size: 26
31747 AATAAAATAA
**
31757 AAATATTAAAAAAATAATATACATAT
1 AAATATTATGAAAATAATATACATAT
*
31783 AAATATTATGAAAATAATAAGTATATAT
1 AAATATTATGAAAATAAT-A-TACATAT
* *
31811 AAACATTTTGAAAA
1 AAATATTATGAAAA
31825 GAAAGAATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 16 0.46
27 1 0.03
28 18 0.51
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.32
Consensus pattern (26 bp):
AAATATTATGAAAATAATATACATAT
Found at i:32449 original size:20 final size:19
Alignment explanation
Indices: 32410--32451 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
32400 TTTCTTTGAT
32410 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
32429 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
32449 ATT
1 ATT
32452 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:32562 original size:120 final size:120
Alignment explanation
Indices: 32323--32555 Score: 303
Period size: 120 Copynumber: 2.0 Consensus size: 120
32313 TATATTAATT
* * *
32323 TATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGTGCCT
1 TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTGCCT
* *
32388 TAAGACAGCTCTTTTCTTTGATATTAAAAAATAAATAAATAATTAAAACAATTAA
66 TAAGACAGCTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAACAATTAA
** * *
32443 TATATA-ATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGTTGT
1 TATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACATCCAGGTGC
* ** *
32507 TTTAAGATTGC-CCTTTC-TTAATATTGAAAAATAAATAAAT-ATTAAAACA
64 CTTAAGACAGCTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAACA
32556 GGATTAAAAT
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
118 9 0.09
119 27 0.28
120 44 0.45
121 18 0.18
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (120 bp):
TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTGCCT
TAAGACAGCTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAACAATTAA
Found at i:34060 original size:3 final size:3
Alignment explanation
Indices: 34046--34118 Score: 89
Period size: 3 Copynumber: 25.0 Consensus size: 3
34036 TTTGTATCTG
** *
34046 TAA TAA -AA TAA TAA T-A TTT TAA TAA TAA TAA TAA TAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
34092 TAA TAA TAA TAA TAA -ATA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA
34119 AAACCAAATG
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
2 5 0.08
3 55 0.90
4 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:36369 original size:11 final size:11
Alignment explanation
Indices: 36353--36378 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
36343 TTCATAAATA
36353 TAATTTATTTT
1 TAATTTATTTT
36364 TAATTTATTTT
1 TAATTTATTTT
36375 TAAT
1 TAAT
36379 AATTAAATCT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TAATTTATTTT
Found at i:38269 original size:29 final size:30
Alignment explanation
Indices: 38212--38269 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
38202 ATTTTCGTCT
*
38212 AATATTTAATGATCAATGACTTATTTATAAA
1 AATATTTAAT-ATAAATGACTTATTTATAAA
* *
38243 AATATTTAAT-TAAATTACTTGTTTATA
1 AATATTTAATATAAATGACTTATTTATA
38270 TTTTTTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 14 0.58
31 10 0.42
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (30 bp):
AATATTTAATATAAATGACTTATTTATAAA
Found at i:48650 original size:51 final size:52
Alignment explanation
Indices: 48590--48708 Score: 136
Period size: 51 Copynumber: 2.3 Consensus size: 52
48580 GAGTTTGTAC
** *
48590 AAATAATATTTTTTATTTAAA-TTCGTCACGTCGAT-ATGATGATTTTTAATAA
1 AAAT-ATATTTTTTATTTAAATTTCGTCACGTC-ATGATGACAATTTCTAATAA
* *
48642 AAATATATTTTTTA-TTAAATTTTGTCATGTCATGATGACAATTTCTAATAA
1 AAATATATTTTTTATTTAAATTTCGTCACGTCATGATGACAATTTCTAATAA
* *
48693 AAAAATATATTTTATT
1 AAATATATTTTTTATT
48709 AGAACTTATC
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
50 7 0.12
51 45 0.79
52 5 0.09
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.47
Consensus pattern (52 bp):
AAATATATTTTTTATTTAAATTTCGTCACGTCATGATGACAATTTCTAATAA
Found at i:49143 original size:23 final size:23
Alignment explanation
Indices: 49117--49160 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
49107 TCATTGTGAC
49117 ACGCTTTTCTATGCTCTTGTGCT
1 ACGCTTTTCTATGCTCTTGTGCT
*
49140 ACGCTTTTTTATGCTCTTGTG
1 ACGCTTTTCTATGCTCTTGTG
49161 ACACATTCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.09, C:0.23, G:0.18, T:0.50
Consensus pattern (23 bp):
ACGCTTTTCTATGCTCTTGTGCT
Found at i:52612 original size:21 final size:22
Alignment explanation
Indices: 52588--52630 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
52578 AGTTTATTTT
52588 TAAAC-TTTGTTTCAATTATCG
1 TAAACTTTTGTTTCAATTATCG
*
52609 TAAACTTTTTTTTCAATTATCG
1 TAAACTTTTGTTTCAATTATCG
52631 AACTTGGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.51
Consensus pattern (22 bp):
TAAACTTTTGTTTCAATTATCG
Found at i:52667 original size:33 final size:33
Alignment explanation
Indices: 52619--52691 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
52609 TAAACTTTTT
*
52619 TTTCAA-TTATCGAACTTGGAAGTTTTTAAGTA
1 TTTCAATTTATCGAACTTGGAAGTATTTAAGTA
*
52651 TTTGAATTTATCGAACTTGGAAGTATTTAAGTA
1 TTTCAATTTATCGAACTTGGAAGTATTTAAGTA
52684 TTTCAATT
1 TTTCAATT
52692 ACCGTAAACT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
32 5 0.14
33 32 0.86
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (33 bp):
TTTCAATTTATCGAACTTGGAAGTATTTAAGTA
Found at i:53290 original size:27 final size:22
Alignment explanation
Indices: 53224--53306 Score: 132
Period size: 22 Copynumber: 3.8 Consensus size: 22
53214 TATGAAAAAA
53224 CCGGATCGA-TTTTTATCCGAT
1 CCGGATCGATTTTTTATCCGAT
*
53245 CTGGATCGATTTTTTATCCGAT
1 CCGGATCGATTTTTTATCCGAT
*
53267 CCGGATCGATTTTTTATTCGAT
1 CCGGATCGATTTTTTATCCGAT
*
53289 CCGAATCGATTTTTTATC
1 CCGGATCGATTTTTTATC
53307 TGACTTTGTG
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
21 8 0.14
22 48 0.86
ACGTcount: A:0.19, C:0.20, G:0.17, T:0.43
Consensus pattern (22 bp):
CCGGATCGATTTTTTATCCGAT
Found at i:55091 original size:16 final size:15
Alignment explanation
Indices: 55066--55106 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
55056 AATAAAATAA
55066 TAAA-AAAAATT-AT
1 TAAACAAAAATTAAT
55079 TGAATACAAAAATTAAT
1 T-AA-ACAAAAATTAAT
55096 TAAACAAAAAT
1 TAAACAAAAAT
55107 AATAAAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 1 0.04
14 2 0.08
15 9 0.38
16 9 0.38
17 3 0.12
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (15 bp):
TAAACAAAAATTAAT
Found at i:55145 original size:40 final size:43
Alignment explanation
Indices: 55059--55139 Score: 112
Period size: 42 Copynumber: 1.9 Consensus size: 43
55049 AATTTACAAT
*
55059 AAAATAATAAAAAAAATTATTGAATACAAAAATTAATTAAACA
1 AAAATAATAAAAAAAATTATTGAATACAAAAATAAATTAAACA
** *
55102 AAAATAAT-AAAAATCTTATTGAATA-AAATATAAATTAA
1 AAAATAATAAAAAAAATTATTGAATACAAAAATAAATTAA
55140 TAAAAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 11 0.32
42 15 0.44
43 8 0.24
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.28
Consensus pattern (43 bp):
AAAATAATAAAAAAAATTATTGAATACAAAAATAAATTAAACA
Found at i:55147 original size:42 final size:41
Alignment explanation
Indices: 55056--55147 Score: 107
Period size: 41 Copynumber: 2.2 Consensus size: 41
55046 ATAAATTTAC
* *
55056 AATAAAATAATAAAAAAAATTATTGAATACAAAAATTAATT
1 AATAAAAAAATAAAAAAAATTATTGAATACAAAAATAAATT
* * *
55097 AA-ACAAAAATAATAAAAATCTTATTGAATA-AAATATAAATT
1 AATAAAAAAATAA-AAAAA-ATTATTGAATACAAAAATAAATT
55138 AATAAAAAAA
1 AATAAAAAAA
55148 AATGGTAAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
40 8 0.19
41 18 0.43
42 16 0.38
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.27
Consensus pattern (41 bp):
AATAAAAAAATAAAAAAAATTATTGAATACAAAAATAAATT
Found at i:58678 original size:21 final size:20
Alignment explanation
Indices: 58648--58699 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
58638 CTTATTTTAT
58648 AATTCGGAGTTG-GTTTAAAAA
1 AATTC-GAGTTGAGTTT-AAAA
* *
58669 AATTTCGAGTCGAGTTTATAA
1 AA-TTCGAGTTGAGTTTAAAA
58690 AATTCGAGTT
1 AATTCGAGTT
58700 TATTTTTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 7 0.27
21 12 0.46
22 7 0.27
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.37
Consensus pattern (20 bp):
AATTCGAGTTGAGTTTAAAA
Found at i:60187 original size:31 final size:30
Alignment explanation
Indices: 60133--60199 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
60123 ATCGTTTTAT
*
60133 TCATTAA-ATTTTTAAAAATTATAAAATAA
1 TCATTAATTTTTTTAAAAATTATAAAATAA
* * *
60162 TTATTAATTTTTTTGAATAATTATAAAATGA
1 TCATTAATTTTTTT-AAAAATTATAAAATAA
60193 TCATTAA
1 TCATTAA
60200 ATTTATCAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 6 0.19
30 5 0.16
31 20 0.65
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (30 bp):
TCATTAATTTTTTTAAAAATTATAAAATAA
Found at i:60620 original size:86 final size:87
Alignment explanation
Indices: 60474--60721 Score: 430
Period size: 87 Copynumber: 2.9 Consensus size: 87
60464 TATGTTATAT
*
60474 TATTTAACCGGAAATATTATCAAGTACAAT-ACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
60538 AGCGCTTATATAATAAAAT-GG
66 AGCGCTTATATAATAAAATAGG
*
60559 -ATTTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACACTTATATAATGTAATAGA
1 TA-TTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGA
60623 TAGCGCTTATATAATAAAATAGG
65 TAGCGCTTATATAATAAAATAGG
* *
60646 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
60711 AGCGCTTATAT
66 AGCGCTTATAT
60722 TGACCTATTT
Statistics
Matches: 154, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
84 1 0.01
85 27 0.18
86 52 0.34
87 73 0.47
88 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (87 bp):
TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
AGCGCTTATATAATAAAATAGG
Found at i:63080 original size:17 final size:18
Alignment explanation
Indices: 63060--63096 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
63050 ATGAATCTTC
63060 ACTAGCTATTGC-CTGAA
1 ACTAGCTATTGCACTGAA
63077 ACTAGCTATTGCACTGAA
1 ACTAGCTATTGCACTGAA
63095 AC
1 AC
63097 ACAAGAAGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (18 bp):
ACTAGCTATTGCACTGAA
Found at i:64735 original size:118 final size:119
Alignment explanation
Indices: 64527--64770 Score: 402
Period size: 118 Copynumber: 2.1 Consensus size: 119
64517 TTTTTCTTCC
*
64527 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGAAATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGAAATAGGTTGTAGACCTATTCGCT
*
64592 AATAAACCGGTATACTTATACCGGTTATATTACAAAA-TATCTAGTACATTATA
66 AATAAACCGGTATACTTATACCGGTTATAATACAAAATTATCTAGTACATTATA
*
64645 ATTCTGGACATAAAGTACCGACACAAAATT-AAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGAAATAGGTTGTAGACCTATTCGCT
* * * *
64709 CATAAAACCGGTATATTTATACCGGTTATAATATAAAATTATCTATTACATTATA
66 AAT-AAACCGGTATACTTATACCGGTTATAATACAAAATTATCTAGTACATTATA
64764 ATTCTGG
1 ATTCTGG
64771 GTTCCGGTGT
Statistics
Matches: 117, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
117 35 0.30
118 60 0.51
119 22 0.19
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (119 bp):
ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGAAATAGGTTGTAGACCTATTCGCT
AATAAACCGGTATACTTATACCGGTTATAATACAAAATTATCTAGTACATTATA
Found at i:65172 original size:179 final size:178
Alignment explanation
Indices: 64645--65214 Score: 821
Period size: 179 Copynumber: 3.2 Consensus size: 178
64635 GTACATTATA
*
64645 ATTCTGGACATAAAGTACCGACACAAAATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTC
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTC
64710 ATAAAACCGGTATATTTATACCGGTTATAATATA-AAATTATCTATTACATTATAATTCTGGGTT
66 ATAAAACCGGTATATTTATACCGGTTAT-AT-TACAAATTA-CTATTACATTATAATTCTGGGTT
* *
64774 CCGGTG-TA-AATGTCGACACTTTTTGACAAGGCATCGACACATTTTTCTTCC
128 CCGATGTTATAA--TCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
*
64825 ATTCTGGACATAAAGTACCG--ACAATATTAAAAAGGGTCGATATAGGTTGTAGACCTA-----T
1 ATTCTGGACATAAAGTACCGACACAATATT-AAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
64883 C--AAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
65 CATAAAACCGGTATATTTATACCGGTTATATTAC-AAATTA-CTATTACATTATAATTCTGGGTT
64946 CCGATGTGTA-AATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
128 CCGATGT-TATAA--TCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
*
64999 ATTATGGACATAAAGTACCGACACAATATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTC
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTC
* *
65064 ATAAAACCGGTATATTTATACCGATTATATTACAAATTA-TATTACA-TATAATTATGGGTTCCG
66 ATAAAACCGGTATATTTATACCGGTTATATTACAAATTACTATTACATTATAATTCTGGGTTCCG
* *
65127 ATGTTTTTTCAATCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCC
131 ATG--TTAT-AATCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
65178 ATTCTGGACATAAAGTACCGACACAATA-TAAAAGTGT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAGTGT
65215 GAAAACTTTG
Statistics
Matches: 361, Mismatches: 11, Indels: 38
0.88 0.03 0.09
Matches are distributed among these distances:
170 2 0.01
171 2 0.01
172 61 0.17
174 65 0.18
175 27 0.07
176 8 0.02
178 35 0.10
179 100 0.28
180 23 0.06
181 8 0.02
182 30 0.08
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (178 bp):
ATTCTGGACATAAAGTACCGACACAATATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTC
ATAAAACCGGTATATTTATACCGGTTATATTACAAATTACTATTACATTATAATTCTGGGTTCCG
ATGTTATAATCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
Found at i:65599 original size:21 final size:21
Alignment explanation
Indices: 65574--65624 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
65564 CCCCTTATGC
65574 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
65595 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
*
65616 CTATCAAGT
1 CTCTCAAGT
65625 TTTTTTCTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.20, C:0.29, G:0.12, T:0.39
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Done.