Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005110.1 Hibiscus syriacus cultivar Beakdansim tig00011486_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: 64254
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:185 original size:1 final size:1
Alignment explanation
Indices: 181--227 Score: 76
Period size: 1 Copynumber: 47.0 Consensus size: 1
171 AAAATGAAAG
* *
181 AAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
228 GATGAACACC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.96, C:0.00, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:187 original size:13 final size:13
Alignment explanation
Indices: 177--227 Score: 93
Period size: 13 Copynumber: 3.9 Consensus size: 13
167 AGAAAAAATG
177 AAAGAAAAAAAAA
1 AAAGAAAAAAAAA
*
190 AAAAAAAAAAAAA
1 AAAGAAAAAAAAA
203 AAAGAAAAAAAAA
1 AAAGAAAAAAAAA
216 AAAGAAAAAAAA
1 AAAGAAAAAAAA
228 GATGAACACC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAAAA
Found at i:228 original size:22 final size:22
Alignment explanation
Indices: 169--229 Score: 90
Period size: 22 Copynumber: 2.8 Consensus size: 22
159 TATGCTGAAG
*
169 AAAAAATGAAAGAAAAA-AAAAA
1 AAAAAAAGAAA-AAAAAGAAAAA
191 AAAAAAA-AAAAAAAAGAAAAA
1 AAAAAAAGAAAAAAAAGAAAAA
212 AAAAAAAGAAAAAAAAGA
1 AAAAAAAGAAAAAAAAGA
230 TGAACACCCC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 5 0.14
21 15 0.42
22 16 0.44
ACGTcount: A:0.90, C:0.00, G:0.08, T:0.02
Consensus pattern (22 bp):
AAAAAAAGAAAAAAAAGAAAAA
Found at i:2429 original size:19 final size:19
Alignment explanation
Indices: 2407--2443 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2397 TTTTTCCTTT
*
2407 AGGGGGAATCGGTTCCCTA
1 AGGGGGAATCGATTCCCTA
*
2426 AGGGGGTATCGATTCCCT
1 AGGGGGAATCGATTCCCT
2444 CATGACATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.19, C:0.22, G:0.35, T:0.24
Consensus pattern (19 bp):
AGGGGGAATCGATTCCCTA
Found at i:5398 original size:113 final size:112
Alignment explanation
Indices: 4809--5462 Score: 746
Period size: 116 Copynumber: 5.9 Consensus size: 112
4799 AGTTCAAGTC
** * *
4809 CATCATTCAATGGATCAACATT-CCAGAGAAAGTTTATAATGAGAATAA--C-TCATCT---G-A
1 CATCATTTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
*
4866 -AAG-AATTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATT
66 GAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
*
4911 CATCATTTGATGGATCAACATTGCCA-AGTAGAGTTCATAAT--GAAGAACTCGTCATCTGAAGA
1 CATCATTTGATGGATCAACATTGCCAGAG-AAAGTTCATAATGAGAAGAACTCGTCATCTG-A-A
* * *
4973 TGGAAGAAGAAGTTCTTAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATT
63 --GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
*
5025 CATCATTTGATGGATCAACATTGCCTAGTAG--AGTTCATAATGAGAAGAACTCATCATCTGAAG
1 CATCATTTGATGGATCAACATTGCC-AG-AGAAAGTTCATAATGAGAAGAACTCGTCATCTGAAG
*
5088 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATT
64 AA-GAAG-A-AA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
*
5141 CATCATTTGATGGATCAACATTGCCA-AGTATAGTTCATAAT--G-AGAACTCGTCATCTGAAGA
1 CATCATTTGATGGATCAACATTGCCAGAG-AAAGTTCATAATGAGAAGAACTCGTCATCTGAAGA
**
5202 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACC-TTTGCTCAAATT
65 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
* * * *
5249 CATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 CATCATTTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
* ** *
5314 GAAGAAATTCACAATGAGAAGAATTTGTTTCAACCTTTTGCTCAAATC
66 GAAGAAATTCATAATGAGAAGAATTTG-TTCAACCTTTTGCTTGAATT
* * * *
5362 CATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAA
1 CATCATTTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
* * *
5424 TAAGAAGTTCA-CATGAGAAG-ATCTTGTTCAACCTTTTGC
66 GAAGAAATTCATAATGAGAAGAAT-TTGTTCAACCTTTTGC
5463 ATAATTCTAT
Statistics
Matches: 494, Mismatches: 24, Indels: 62
0.85 0.04 0.11
Matches are distributed among these distances:
101 5 0.01
102 22 0.04
103 14 0.03
104 6 0.01
108 57 0.12
109 40 0.08
110 24 0.05
111 49 0.10
112 15 0.03
113 88 0.18
114 78 0.16
115 4 0.01
116 90 0.18
117 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (112 bp):
CATCATTTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
GAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
Found at i:5536 original size:119 final size:120
Alignment explanation
Indices: 5382--5671 Score: 363
Period size: 124 Copynumber: 2.4 Consensus size: 120
5372 TGGATCAGCT
* * *
5382 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAATAAGAAGTTCA-CATGAGAAGAT
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCATAATGAGAAGAG
* * * * * *
5446 CTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATTAGCATCAACC
66 CTTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCAACATCAACC
5501 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT---GAAG-AAGAAGAAGTTCATAATGAGA
* * * *
5566 AGAGCTTATTCAACCTTTTGAATGACTCTATCACAGAATGAAATAGGTCAACATCATCC
62 AGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCAACATCAACC
* *
5625 ---CCAGCGGAAAGTTCATAATGAAAAGAACTCATCTGAAGAAAGAAGAA
1 TTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAG-AAGAAGAA
5672 TTTATTCAAC
Statistics
Matches: 150, Mismatches: 15, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
119 49 0.33
121 4 0.03
122 31 0.21
123 12 0.08
124 54 0.36
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.24
Consensus pattern (120 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCATAATGAGAAGAG
CTTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCAACATCAACC
Found at i:5874 original size:3 final size:3
Alignment explanation
Indices: 5810--5861 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
5800 TTCATTTAAA
* *
5810 TAT TAT T-T ATAT TAT CAT TAT TAT TAT AAT TAT TAT TAT TAT T-T
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5854 TAT TAT TA
1 TAT TAT TA
5862 ATAAATATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
2 3 0.07
3 38 0.90
4 1 0.02
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:7230 original size:3 final size:3
Alignment explanation
Indices: 7222--7256 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
7212 TTATTTACAA
*
7222 TAT TAT TAT TAT TAT TATT TAT TAT TTT TAT TAT T
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT T
7257 TATATAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:7245 original size:16 final size:16
Alignment explanation
Indices: 7224--7259 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
7214 ATTTACAATA
7224 TTATTATTATTATTAT
1 TTATTATTATTATTAT
*
7240 TTATTATTTTTATTAT
1 TTATTATTATTATTAT
7256 TTAT
1 TTAT
7260 ATAAATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTATTATTATTATTAT
Found at i:7285 original size:17 final size:16
Alignment explanation
Indices: 7257--7288 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
7247 TTTTATTATT
7257 TATATAAATAAATAAA
1 TATATAAATAAATAAA
7273 TATATATAATAAATAA
1 TATATA-AATAAATAA
7289 TTTGTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TATATAAATAAATAAA
Found at i:7566 original size:27 final size:27
Alignment explanation
Indices: 7528--7582 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
7518 ATATTTCTAA
7528 ATAAATAAATATTGTATTT-ATAAATAT
1 ATAAATAAATATT-TATTTCATAAATAT
* *
7555 ATAAATTAATATTTATTTCATAATTAT
1 ATAAATAAATATTTATTTCATAAATAT
7582 A
1 A
7583 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (27 bp):
ATAAATAAATATTTATTTCATAAATAT
Found at i:9964 original size:43 final size:43
Alignment explanation
Indices: 9911--10093 Score: 267
Period size: 43 Copynumber: 4.3 Consensus size: 43
9901 TGGTAACAAA
*** *
9911 AAACGCCGCAATAGGTAACGATATATAGCGGCGTTTGTCCAAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCCAAC
9954 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCCAAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCCAAC
* * *
9997 AAACACCGCAATAGGTGTTGATATTTAGCTGCGTTTTTCCAAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCCAAC
* * *
10040 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCCAAC
*
10083 AAACACCGCAA
1 AAACGCCGCAA
10094 AAGATCTGGT
Statistics
Matches: 128, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 128 1.00
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCCAAC
Found at i:10120 original size:43 final size:43
Alignment explanation
Indices: 9911--10119 Score: 258
Period size: 43 Copynumber: 4.9 Consensus size: 43
9901 TGGTAACAAA
* *** * *
9911 AAACGCCGCAATAGGTAACGATATATAGCGGCGTTTGTCCAAC
1 AAACACCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
* *
9954 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCCAAC
1 AAACACCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
*
9997 AAACACCGCAATAGGTGTTGATATTTAGCTGCGTTTTTCCAAC
1 AAACACCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
* * *
10040 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
1 AAACACCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
* * * * *
10083 AAACACCGCAAAAGAT-CTGGTATATAGCGGCGTTTTT
1 AAACACCGCAATAGGTGTTGATATTTAGCGGCGTTTTT
10120 TTAGAACAAA
Statistics
Matches: 148, Mismatches: 18, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
42 17 0.11
43 131 0.89
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (43 bp):
AAACACCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
Found at i:10120 original size:86 final size:86
Alignment explanation
Indices: 9930--10142 Score: 284
Period size: 86 Copynumber: 2.5 Consensus size: 86
9920 AATAGGTAAC
* *
9930 GATATATAGCGGCGTTTGTCCAACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCCA
1 GATATATAGCGGCGTTTTTCCAACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTGTCCA
* * *
9995 ACAAACACCGCAATAGGTGTT
66 ACAAACACCGCAAAAGATGCT
* * * *
10016 GATATTTAGCTGCGTTTTTCCAACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCC
1 GATATATAGCGGCGTTTTTCCAACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTGTCCA
10081 ACAAACACCGCAAAAGAT-CT
66 ACAAACACCGCAAAAGATGCT
* ** *
10101 GGTATATAGCGGCGTTTTTTTAGAACAAACGCCGCAAAAGGT
1 GATATATAGCGGCG--TTTTTCCAACAAACGCCGCAATAGGT
10143 CATATCTATA
Statistics
Matches: 110, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
85 12 0.11
86 75 0.68
87 23 0.21
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (86 bp):
GATATATAGCGGCGTTTTTCCAACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTGTCCA
ACAAACACCGCAAAAGATGCT
Found at i:13795 original size:52 final size:52
Alignment explanation
Indices: 13727--13937 Score: 395
Period size: 52 Copynumber: 4.1 Consensus size: 52
13717 TAACAACAAA
*
13727 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCAAC
13779 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCAAC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCAAC
*
13831 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAGCAGTCTTCAAC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCAAC
*
13883 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCAAC
13935 ATA
1 ATA
13938 TTGTTCAGTA
Statistics
Matches: 155, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 155 1.00
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (52 bp):
ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCAAC
Found at i:15150 original size:42 final size:42
Alignment explanation
Indices: 15091--15171 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
15081 CGTTTACGCC
15091 GCTACATGTCTACTATATTACGGCATTTTTACTATAAACACA
1 GCTACATGTCTACTATATTACGGCATTTTTACTATAAACACA
* *
15133 GCTACATGTCTACTATATTGCGGCGTTTTTACTATAAAC
1 GCTACATGTCTACTATATTACGGCATTTTTACTATAAAC
15172 GCCGCTATTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (42 bp):
GCTACATGTCTACTATATTACGGCATTTTTACTATAAACACA
Found at i:17619 original size:2 final size:2
Alignment explanation
Indices: 17608--17641 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
17598 CACACACACA
*
17608 AT AT AC 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
17642 TCTCCCATTA
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:18241 original size:18 final size:19
Alignment explanation
Indices: 18207--18247 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
18197 GTTTATCTCC
18207 TTAACATTTTTACCTTTTT
1 TTAACATTTTTACCTTTTT
18226 TTAACATTTTTA-CTTTTT
1 TTAACATTTTTACCTTTTT
18244 TTAA
1 TTAA
18248 TAGAATTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.63
Consensus pattern (19 bp):
TTAACATTTTTACCTTTTT
Found at i:18724 original size:22 final size:22
Alignment explanation
Indices: 18699--18740 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
18689 GAAATGATAC
* *
18699 AAAAACGTGTCACAAAGACAAA
1 AAAAACATGCCACAAAGACAAA
*
18721 AAAAATATGCCACAAAGACA
1 AAAAACATGCCACAAAGACA
18741 GAATTATTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.60, C:0.19, G:0.12, T:0.10
Consensus pattern (22 bp):
AAAAACATGCCACAAAGACAAA
Found at i:22412 original size:24 final size:24
Alignment explanation
Indices: 22383--22436 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
22373 TATTCTTTAA
22383 AAATTTCAAATTTTCATATAATTT
1 AAATTTCAAATTTTCATATAATTT
22407 AAATTTCAAATTTTCATATAATTT
1 AAATTTCAAATTTTCATATAATTT
22431 AAATTT
1 AAATTT
22437 TATAATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (24 bp):
AAATTTCAAATTTTCATATAATTT
Found at i:22683 original size:59 final size:59
Alignment explanation
Indices: 22555--22733 Score: 202
Period size: 59 Copynumber: 3.1 Consensus size: 59
22545 ATCATATATC
* * *
22555 CCCAAACTATGACTCTCATTTC-AAATTAGTCCT-AAATTTTTAAACATTTCACTTTCAT
1 CCCAAACTATGACTCTC-TTTCTAAATTAGTCCTCAAACTTTTAAATATTTCAATTTCAT
** * * *
22613 CTTAAACTATGACTATCTTTCTAAATTAGTCCTCAAACTTTTGAATATTTCATTTTCAT
1 CCCAAACTATGACTCTCTTTCTAAATTAGTCCTCAAACTTTTAAATATTTCAATTTCAT
* * * * *
22672 CCCAAACTATGAATCTCATTCTAAATT-GGCCTCTAAACTTTTAAATCTTCCAATTTCAT
1 CCCAAACTATGACTCTCTTTCTAAATTAGTCCTC-AAACTTTTAAATATTTCAATTTCAT
22731 CCC
1 CCC
22734 CAAATTCATT
Statistics
Matches: 101, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
57 4 0.04
58 30 0.30
59 67 0.66
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.40
Consensus pattern (59 bp):
CCCAAACTATGACTCTCTTTCTAAATTAGTCCTCAAACTTTTAAATATTTCAATTTCAT
Found at i:24224 original size:15 final size:13
Alignment explanation
Indices: 24190--24228 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
24180 CGGAAAAGAA
24190 ACCCCCC-CCCCC
1 ACCCCCCACCCCC
24202 ACCCCCCACCCCC
1 ACCCCCCACCCCC
24215 ACCTCACCCACCCC
1 ACC-C-CCCACCCC
24229 GCAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 1 0.04
15 8 0.33
ACGTcount: A:0.15, C:0.82, G:0.00, T:0.03
Consensus pattern (13 bp):
ACCCCCCACCCCC
Found at i:30857 original size:17 final size:17
Alignment explanation
Indices: 30823--30858 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
30813 TTTCTTTTTG
* *
30823 ATTTATTATTATTTAAA
1 ATTTATTATTAATAAAA
30840 ATTTATTATTAATAAAA
1 ATTTATTATTAATAAAA
30857 AT
1 AT
30859 ATAAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTATTATTAATAAAA
Found at i:35756 original size:3 final size:3
Alignment explanation
Indices: 35743--35774 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
35733 TAATTTCTTA
35743 TCT TCT T-T TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
35775 GACGACGACG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:47490 original size:3 final size:3
Alignment explanation
Indices: 47482--47549 Score: 77
Period size: 3 Copynumber: 23.0 Consensus size: 3
47472 TCATTTAAAT
** * *
47482 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA GTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
47530 TTA TTA -TA TT- TTA TTTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA
47550 AATATTACAA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
2 4 0.07
3 47 0.87
4 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:56833 original size:114 final size:114
Alignment explanation
Indices: 56633--56855 Score: 356
Period size: 114 Copynumber: 2.0 Consensus size: 114
56623 TGCTATGTGA
* * *
56633 TCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGG
* * * *
56698 TTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGC
66 TTCGGTAGGAACCCCAAAACCAATCATTGAAATTGAAAGATGAATTTGC
*
56747 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGG
* *
56812 TTCGGTAGGAATCCCATAACCAATCATTGAAATTGAAAGATGAA
66 TTCGGTAGGAACCCCAAAACCAATCATTGAAATTGAAAGATGAA
56856 CTGCATGATC
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 99 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (114 bp):
TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGG
TTCGGTAGGAACCCCAAAACCAATCATTGAAATTGAAAGATGAATTTGC
Found at i:58879 original size:54 final size:54
Alignment explanation
Indices: 58794--58948 Score: 256
Period size: 54 Copynumber: 2.9 Consensus size: 54
58784 GAAATCTTGG
*
58794 CAGAAGCCACAGGAAAGGATGAATGTATTGTCAAATGTTTTACGAACATTTGAA
1 CAGAAGCCACAGGAAAGGATGAATGTATTGTCAAATGTTTTACGAACATCTGAA
* * *
58848 CAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAG
1 CAGAAGCCACAGGAAAGGATGAATGTATTGTCAAATGTTTTACGAACATCTGAA
* *
58902 CAGAAGCCACAGGAAAGGATGAATGCACTGTCAAATGTTTTACGAAC
1 CAGAAGCCACAGGAAAGGATGAATGTATTGTCAAATGTTTTACGAAC
58949 CTGTTATTCT
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 93 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (54 bp):
CAGAAGCCACAGGAAAGGATGAATGTATTGTCAAATGTTTTACGAACATCTGAA
Found at i:59340 original size:22 final size:22
Alignment explanation
Indices: 59314--59412 Score: 171
Period size: 22 Copynumber: 4.5 Consensus size: 22
59304 ATCTACACTC
59314 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
59336 TTCAAATATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
59358 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
59380 TTTAAAGATGATATATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
59402 TTCAAAGATGA
1 TTCAAAGATGA
59413 AAGCTTTATG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 72 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:60229 original size:76 final size:76
Alignment explanation
Indices: 60083--60794 Score: 1228
Period size: 76 Copynumber: 9.5 Consensus size: 76
60073 CTATTTCTCA
*
60083 CATCTGTAAGTCCTGCAGTGCATGA-GTTTCCAAAAAGCCTT-GGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
60145 AGCCTTAGGGT
66 AGCCTTAGGGT
60156 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
60221 AGCCTTAGGGT
66 AGCCTTAGGGT
60232 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
60297 AAGCCTTAGGGT
65 AAGCCTTAGGGT
60309 CATCTGTAAGTCCTACAGTGCATGATG-TTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
60372 AGCCTTAGGGT
66 AGCCTTAGGGT
60383 CATCTGTAAGT-CTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
60447 AG-CTTAGGGT
66 AGCCTTAGGGT
60457 CATCTGTAAGTCCTACAGTGCATGATGTTTCCGAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
60522 AAGCCTTAGGGT
65 AAGCCTTAGGGT
60534 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
60599 AGCCTTAGGGT
66 AGCCTTAGGGT
*
60610 CATCTGTAAGTCCTACAGTGCATGGTGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
60674 A-CCTTCGTGT
66 AGCCTTAGGGT
* *
60684 CATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTAGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
* *
60749 AAACCTTCGGGT
65 AAGCCTTAGGGT
* * *
60761 CATCTGTAA-CCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAA
60795 CATTTCCATC
Statistics
Matches: 615, Mismatches: 12, Indels: 21
0.95 0.02 0.03
Matches are distributed among these distances:
73 39 0.06
74 146 0.24
75 89 0.14
76 214 0.35
77 127 0.21
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:60596 original size:227 final size:227
Alignment explanation
Indices: 60083--60794 Score: 1224
Period size: 227 Copynumber: 3.2 Consensus size: 227
60073 CTATTTCTCA
*
60083 CATCTGTAAGTCCTGCAGTGCATGA-GTTTCCAAAAAGCCTT-GGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
60145 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
60210 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTT
131 GATGTTTTCAAAG-CTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTT
60275 CGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
194 CGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
60309 CATCTGTAAGTCCTACAGTGCATGATG-TTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
60372 AGCCTTAGGGTCATCTGTAAGT-CTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
60436 GATGTTTTCAAAGCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCGAAAAAGCCTTC
131 GATGTTTTCAAAGCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTTC
60501 GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
195 GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
60534 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
60599 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGGTGTTTCCAAAAAGCCTTCGGGAGC-TTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
* * * * *
60663 GATGTTTTCAAACCTTCGTGTCATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTAG
131 GATGTTTTCAAAGCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCG
* *
60728 GGAGCTTTTTGATGTTTTCAAAAACCTTCGGGT
196 GGAGCTTTTTGATGTTTTC-AAAGCCTTAGGGT
* * *
60761 CATCTGTAA-CCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAA
60795 CATTTCCATC
Statistics
Matches: 466, Mismatches: 13, Indels: 14
0.95 0.03 0.03
Matches are distributed among these distances:
225 120 0.26
226 145 0.31
227 165 0.35
228 36 0.08
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (227 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAGCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCG
GGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
Found at i:60669 original size:302 final size:300
Alignment explanation
Indices: 60083--60794 Score: 1211
Period size: 302 Copynumber: 2.4 Consensus size: 300
60073 CTATTTCTCA
*
60083 CATCTGTAAGTCCTGCAGTGCATGA-GTTTCCAAAAAGCCTTGGGAGC-TTTTGATGTTTTCAAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTGGGAGCTTTTTGATGTTTTCAAA
60146 GCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
66 G-CTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
60211 ATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTTC
130 ATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTTC
60276 GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTCCA
195 GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTCCA
60341 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
260 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA-CCTTAGGGT
60383 CATCTGTAAGT-CTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT-GGGAGCTTTTTGATGTTTTCAA
60447 AGCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCGAAAAAGCCTTCGGGAGCTTTTT
65 AGCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTT
60512 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTT
129 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTT
*
60576 CGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGGTGTTTC
194 CGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATG-TTC
* *
60641 CAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAAACCTTCGTGT
258 C-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAACCTTAGGGT
*
60684 CATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTAGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT-GGGAGCTTTTTGATGTTTTC--
* * * * *
60749 AAACCTTCGGGTCATCTGTAA-CCCTTCAGTGCATGATGTTTTCAAA
63 AAAGCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAA
60795 CATTTCCATC
Statistics
Matches: 392, Mismatches: 11, Indels: 16
0.94 0.03 0.04
Matches are distributed among these distances:
299 12 0.03
300 27 0.07
301 133 0.34
302 166 0.42
303 35 0.09
304 19 0.05
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (300 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTGGGAGCTTTTTGATGTTTTCAAA
GCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGA
TGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCG
GGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTCCAA
AAGCCTTCGGGAGCTTTTTGATGTTTTCAAACCTTAGGGT
Found at i:61975 original size:21 final size:20
Alignment explanation
Indices: 61949--61992 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
61939 GATTTCTGGG
* *
61949 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCC-TT
61970 CAAGGGGAACCGATACCCTT
1 CAAGGGGAACCGATACCCTT
61990 CAA
1 CAA
61993 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (20 bp):
CAAGGGGAACCGATACCCTT
Done.