Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001442.1 Hibiscus syriacus cultivar Beakdansim tig00002791_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: 60991
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4134 original size:13 final size:13
Alignment explanation
Indices: 4118--4171 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 13
4108 CATAATGAAA
*
4118 ATAAATAAATAGT
1 ATAAATAAATAAT
4131 ATAAATAAAATAAT
1 ATAAAT-AAATAAT
4145 A-AAATAAA-AA-
1 ATAAATAAATAAT
*
4155 ATATATAAA-AAT
1 ATAAATAAATAAT
4167 ATAAA
1 ATAAA
4172 AATGTATGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
10 1 0.03
11 10 0.29
12 7 0.20
13 10 0.29
14 7 0.20
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (13 bp):
ATAAATAAATAAT
Found at i:4165 original size:17 final size:16
Alignment explanation
Indices: 4137--4174 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 16
4127 TAGTATAAAT
4137 AAAATAATAAAATA-A
1 AAAATAATAAAATATA
4152 AAAATATATAAAAATATA
1 AAAATA-AT-AAAATATA
4170 AAAAT
1 AAAAT
4175 GTATGTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
16 2 0.10
17 6 0.30
18 6 0.30
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAATAATAAAATATA
Found at i:5068 original size:283 final size:278
Alignment explanation
Indices: 4562--5115 Score: 1002
Period size: 283 Copynumber: 2.0 Consensus size: 278
4552 AAAAAACAAA
4562 ACGCGGATCCACACGACCGTTTATAAAAATCCGAATAGTTTTTCAAAAACACAAGCATCGGGGAC
1 ACGCGGATCCACAC-ACCGTTTATAAAAATCCGAATAGTTTTTCAAAAACACAAGCATCGGGGAC
4627 TAGATCTACAAAAATAGATCTCGAAAACACCCCGTTCATCGGCCAAAAACACTTCTCTCAGTTTC
65 TAGATCTACAAAAATAGATCTCGAAAACACCCCGTTCATCGGCCAAAAACACTTCTCTCAGTTTC
4692 TTTCGAATCAAAAACAACAAGGGTAAGGAAAAATAACATGCGAAGGTATGAACTTTACCTTTCAA
130 TTTCGAATCAAAAACAACAAGGGTAAGGAAAAATAACATGCGAAGGTATGAACTTTACCTTTCAA
4757 AATATAAATGCTTCGAAAAATGGCTACGAGTTGCTTGTAATTTTTTTGCTTGGTATTTCGTATAT
195 AATATAAATGCTTCGAAAAATGGCTACGAGTTGCTTGTAATTTTTTTGCTTGGTATTTCGTATAT
4822 CCCCTTGCTTGTTGTGTTAC
260 CCCCTTG-TTGTTGTGTTAC
*
4842 ACGCGGATCCACGAC-CCGTTTATAAAAATCCGAATAGTTTTTCAAAAACACAAGCCTCGGGGAC
1 ACGCGGATCCAC-ACACCGTTTATAAAAATCCGAATAGTTTTTCAAAAACACAAGCATCGGGGAC
*
4906 TAGATCTACAAAAATAGATCTCGAAAACGCCCTCGTTCATCGGCCAAAAACACTTCTCTCAGTTT
65 TAGATCTACAAAAATAGATCTCGAAAACACCC-CGTTCATCGGCCAAAAACACTTCTCTCAG-TT
* *
4971 TCTTTTGAATCAAAAACACATCAAGGGTAAGGAAAAATAGCATGCGAAGGTATGAACTTTACCTT
128 TCTTTCGAATCAAAAACA-A-CAAGGGTAAGGAAAAATAACATGCGAAGGTATGAACTTTACCTT
5036 TCAAAATATAAATGCTTCGAAAAATGGCTACGAGTTGCTTGTAATTTTTTTGCTTGGTATTTCGT
191 TCAAAATATAAATGCTTCGAAAAATGGCTACGAGTTGCTTGTAATTTTTTTGCTTGGTATTTCGT
5101 ATATCCCCTTGTTGT
256 ATATCCCCTTGTTGT
5116 GTTACAATAG
Statistics
Matches: 265, Mismatches: 4, Indels: 8
0.96 0.01 0.03
Matches are distributed among these distances:
279 79 0.30
280 41 0.15
281 21 0.08
282 5 0.02
283 119 0.45
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (278 bp):
ACGCGGATCCACACACCGTTTATAAAAATCCGAATAGTTTTTCAAAAACACAAGCATCGGGGACT
AGATCTACAAAAATAGATCTCGAAAACACCCCGTTCATCGGCCAAAAACACTTCTCTCAGTTTCT
TTCGAATCAAAAACAACAAGGGTAAGGAAAAATAACATGCGAAGGTATGAACTTTACCTTTCAAA
ATATAAATGCTTCGAAAAATGGCTACGAGTTGCTTGTAATTTTTTTGCTTGGTATTTCGTATATC
CCCTTGTTGTTGTGTTAC
Found at i:9042 original size:4 final size:4
Alignment explanation
Indices: 9033--9063 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
9023 TTCAACTATG
*
9033 TATT TATT TATT TATT TATA TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TAT
9064 ACATGCATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:16428 original size:182 final size:182
Alignment explanation
Indices: 16121--16570 Score: 720
Period size: 182 Copynumber: 2.5 Consensus size: 182
16111 ACTTTTTTAC
* *
16121 TACCGGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
* * *
16186 TACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACATCTTTTCTTTTAAATTCCAAAAG
66 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACATATTCTCTTTTAAATTCCAAAAG
* * *
16251 TGTCAATACTTACAATAAAGTATCGACACTATCAACATATCCGGTAGCTCTT
131 TGTCAATACATACAATAAAGTATCGACACTATCAACATATCCGATAGCGCTT
*
16303 TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACTTGTTATATTGTTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
*
16368 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTATTCTCTTTTAAATTCCAAAAG
66 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACATATTCTCTTTTAAATTCCAAAAG
* * *
16433 TTTCGATACATATAATAAAGTATCGACACTATCAACATATCCGATAGCGCTT
131 TGTCAATACATACAATAAAGTATCGACACTATCAACATATCCGATAGCGCTT
* * ** * *
16485 TACCTGTTTTATCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTTTATTGTTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
*
16550 TAGATTTTTATAAAGTATCGA
66 TACATTTTTATAAAGTATCGA
16571 AACTATCAAC
Statistics
Matches: 247, Mismatches: 21, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
182 247 1.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (182 bp):
TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACATATTCTCTTTTAAATTCCAAAAG
TGTCAATACATACAATAAAGTATCGACACTATCAACATATCCGATAGCGCTT
Found at i:16533 original size:20 final size:20
Alignment explanation
Indices: 16483--16536 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
16473 CCGATAGCGC
16483 TTTACCTGTTTTATCATTTA
1 TTTACCTGTTTTATCATTTA
** * * *
16503 TAGACCGGTTTTGTCATTTT
1 TTTACCTGTTTTATCATTTA
16523 TTTACCTGTTTTAT
1 TTTACCTGTTTTAT
16537 TGTTATGGAT
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.15, G:0.11, T:0.57
Consensus pattern (20 bp):
TTTACCTGTTTTATCATTTA
Found at i:19745 original size:199 final size:199
Alignment explanation
Indices: 19393--20425 Score: 1542
Period size: 199 Copynumber: 5.2 Consensus size: 199
19383 GGTTATAATT
* * * * *
19393 ATTATGTTTTTTGATGTTTTTGGGATCGACAATTGTTATAAATGTATCGAAACTTTGTT-GTGCA
1 ATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTT-TTAGTGCA
* * * * *
19457 ATTGGTTCTT-AAATACATTCTAGACAAAAAGTATCGACACTTGTTCCATTTGTGTCGATACTGT
65 CTT-GTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTTT
*
19521 TTGTACACATGTTTTCTCAAAAACCGATACATTTAGACCGGTTATATTGTTAATTTACCTATTAC
129 TTGTACACATGTTTTCTCAAAAACCGATATATTTAGACCGGTTATATTGTTAATTTACCTATTAC
19586 ATTATA
194 ATTATA
*
19592 ATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGCAC
1 ATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCAC
19657 TTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTTTTT
66 TTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTTTTT
* * * * * *
19722 GTACACTTGTTTTATCAAAAACCGGTATATTTAGACCGTTTACA-TGAATAATTTACCTATTACA
131 GTACACATGTTTTCTCAAAAACCGATATATTTAGACCGGTTATATTG-TTAATTTACCTATTACA
19786 TTATA
195 TTATA
*
19791 ATTATGGTTTTCGATGTTTTTAGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCAC
1 ATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCAC
* * * *
19856 TTGGTTCTGAAATACATTCTGGACCAAAAA-TATCGACACTTGTTCTATTTGTGTTGATACTGTT
66 TTGTTTTTGAAATACATTCTGGA-CAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTTTT
* * *
19920 TGTACACCTGTTTTATCAAAAACCGATATATTTAGACCGGTTATATTTTTAATTTACCTATTACA
130 TGTACACATGTTTTCTCAAAAACCGATATATTTAGACCGGTTATATTGTTAATTTACCTATTACA
19985 TTATA
195 TTATA
*
19990 ATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACAC-TTTTAGGGCAC
1 ATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCAC
*
20054 TTGTTTTTGAAATACATTCTGGACAAAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTT
66 TTGTTTTTGAAATACATTCTGGAC-AAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTTTT
* * *
20119 TTTACACCTGTTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATT-TCTAATTTACCTATTA
130 TGTACACATG-TTTTCTCAAAAACCGATATATTTAGACCGGTTATATTGT-TAATTTACCTATTA
20183 CATTATA
193 CATTATA
* *
20190 ATTATAGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCAC
1 ATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCAC
* * *
20255 TTGGTTTTGAAATACATTTTGGACCAAAAGTATCGACACTTGTT-TGATTTGTGTCGATACTTTT
66 TTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCT-ATTTGTGTCGATACTTTT
* * * **
20319 TTTACACATGTTTTCTCAAAAACCGATATATTTAGACCGTTTACA-TGAACAATTTACCTATTAC
130 TGTACACATGTTTTCTCAAAAACCGATATATTTAGACCGGTTATATTG-TTAATTTACCTATTAC
20383 ATTATA
194 ATTATA
* *
20389 ATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTT
1 ATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTT
20426 TTATTTTTGT
Statistics
Matches: 766, Mismatches: 55, Indels: 26
0.90 0.06 0.03
Matches are distributed among these distances:
197 1 0.00
198 46 0.06
199 527 0.69
200 160 0.21
201 32 0.04
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (199 bp):
ATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCAC
TTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTTTTT
GTACACATGTTTTCTCAAAAACCGATATATTTAGACCGGTTATATTGTTAATTTACCTATTACAT
TATA
Found at i:20900 original size:300 final size:300
Alignment explanation
Indices: 20348--20955 Score: 1092
Period size: 300 Copynumber: 2.0 Consensus size: 300
20338 AAACCGATAT
20348 ATTTA-GACCGTTTACATGAACAATTTACCTATTACATTATAATTATGTTTTTCGATGTTTTCGG
1 ATTTAGGACCGTTTACATGAACAATTTACCTATTACATTATAATTATGTTTTTCGATGTTTTCGG
*
20412 GATCGACACTTGTTTTATTTTTGTCGATACATTTTGTACACCTGTTTTCTCAAAAACCCGTATAT
66 GATCGACACTTGTTTTATTTGTGTCGATACATTTTGTACACCTGTTTTCTCAAAAACCCGTATAT
20477 TTGAAAAAGGTAAGTGTTACCTTAGAAATACATTATGGACAAATTCATTATGCACATTATCACTA
131 TTGAAAAAGGTAAGTGTTACCTTAGAAATACATTATGGACAAATTCATTATGCACATTATCACTA
20542 ATGTTGATATTTGAAAAAGGTAAATTGTTACCTTAGAAATGGAATTTGATGTTTTCTCCCGATGC
196 ATGTTGATATTTGAAAAAGGTAAATTGTTACCTTAGAAATGGAATTTGATGTTTTCTCCCGATGC
* *
20607 ATCCATTGAGTAAGTTGTTTTTAGGATGGATGGAATTTCG
261 ATCCATCGAGTAAGTTGTTTTTAGGATGGATGAAATTTCG
* * * *
20647 GTTTCGGACCTTTTACATGAATAATTTACCTATTACATTATAATTATGTTTTTCGATGTTTTCGG
1 ATTTAGGACCGTTTACATGAACAATTTACCTATTACATTATAATTATGTTTTTCGATGTTTTCGG
20712 GATCGACACTTGTTTTATTTGTGTCGATACATTTTGTACACCTGTTTTCTCAAAAACCCGTATAT
66 GATCGACACTTGTTTTATTTGTGTCGATACATTTTGTACACCTGTTTTCTCAAAAACCCGTATAT
* * *
20777 TTGAAAAATGTAAGTGTTACCTTAGAAATACATTATGTACAAATTCATTATGCGCATTATCACTA
131 TTGAAAAAGGTAAGTGTTACCTTAGAAATACATTATGGACAAATTCATTATGCACATTATCACTA
** *
20842 ATGTTGATATTTGAAAAAGGTATGTTGTTACCTTAGAAATGTAATTTGATGTTTTCTCCCGATGC
196 ATGTTGATATTTGAAAAAGGTAAATTGTTACCTTAGAAATGGAATTTGATGTTTTCTCCCGATGC
20907 ATCCATCGAGTAAGTTGTTTTTAGGATGGATGAAATTTCG
261 ATCCATCGAGTAAGTTGTTTTTAGGATGGATGAAATTTCG
20947 ATTTAGGAC
1 ATTTAGGAC
20956 TAAAATTTAC
Statistics
Matches: 293, Mismatches: 15, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
299 3 0.01
300 290 0.99
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.40
Consensus pattern (300 bp):
ATTTAGGACCGTTTACATGAACAATTTACCTATTACATTATAATTATGTTTTTCGATGTTTTCGG
GATCGACACTTGTTTTATTTGTGTCGATACATTTTGTACACCTGTTTTCTCAAAAACCCGTATAT
TTGAAAAAGGTAAGTGTTACCTTAGAAATACATTATGGACAAATTCATTATGCACATTATCACTA
ATGTTGATATTTGAAAAAGGTAAATTGTTACCTTAGAAATGGAATTTGATGTTTTCTCCCGATGC
ATCCATCGAGTAAGTTGTTTTTAGGATGGATGAAATTTCG
Found at i:23337 original size:15 final size:14
Alignment explanation
Indices: 23313--23354 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
23303 ATGAGGTTGT
23313 GGTTGAGAAGAGCTG
1 GGTTGAGAAGAG-TG
*
23328 GGTTGGGAAGAAGTG
1 GGTTGAGAAG-AGTG
23343 GGTTGAGAAGAG
1 GGTTGAGAAGAG
23355 ATTTGAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 2 0.08
15 20 0.83
16 2 0.08
ACGTcount: A:0.29, C:0.02, G:0.50, T:0.19
Consensus pattern (14 bp):
GGTTGAGAAGAGTG
Found at i:23722 original size:14 final size:15
Alignment explanation
Indices: 23699--23731 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
23689 TCTGTTTTCA
23699 ATTTAAACCGG-TAT
1 ATTTAAACCGGTTAT
*
23713 ATTTAGACCGGTTAT
1 ATTTAAACCGGTTAT
23728 ATTT
1 ATTT
23732 CTAATTTACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42
Consensus pattern (15 bp):
ATTTAAACCGGTTAT
Found at i:23989 original size:199 final size:199
Alignment explanation
Indices: 23703--25000 Score: 2159
Period size: 199 Copynumber: 6.5 Consensus size: 199
23693 TTTTCAATTT
*
23703 AAACCGGTATATTTAGACCGGTTATATTTCTAATTTACCTATTACATTATAATTATGGTTTTCGA
1 AAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGGTTTTCGA
* * * *
23768 TATTTCTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTCTGAAATA
66 TGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGCACTTGGTTTTGAAATA
* *
23833 CATTCTGGACCAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTATTTGTACACCTGTTTTC
131 CATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTGTTTGTACACCTGTTTTC
23898 TCAA
196 TCAA
*
23902 AAACCAGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGGTTTTCGA
1 AAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGGTTTTCGA
* * *
23967 TGTTTTTAGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTCTGAAATA
66 TGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGCACTTGGTTTTGAAATA
* *
24032 CATTATGGACCAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTGTTTGTACACCTGTTTTC
131 CATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTGTTTGTACACCTGTTTTC
24097 TCAA
196 TCAA
*
24101 AAGCCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGGTTTTCGA
1 AAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGGTTTTCGA
24166 TGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGCACTTGGTTTTGAAATA
66 TGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGCACTTGGTTTTGAAATA
* *
24231 CATTCTGGACAAAAAGTATCGACACTTGTTCGATTTGTGTCGATATTGTTTGTACACCTGTTTTC
131 CATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTGTTTGTACACCTGTTTTC
24296 TCAA
196 TCAA
* *
24300 AAATCGGTATATTTAGAACGGTTATATTGCTAATTTACCTATTACATTATAATTATGGTTTTCGA
1 AAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGGTTTTCGA
* *
24365 TGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGTACTTGTTTTTGAAATA
66 TGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGCACTTGGTTTTGAAATA
*
24430 CATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTTTTTGTACACCTGTTTTT
131 CATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTGTTTGTACACCTG-TTTT
*
24495 ATCAA
195 CTCAA
* * * * *
24500 AAACCGGTATATTTAGACTGTTTACA-TGAATAATTTACCTATTACATTATAATTATGTTTTTCG
1 AAACCGGTATATTTAGACCGGTTATATTG-CTAATTTACCTATTACATTATAATTATGGTTTTCG
* *
24564 ATGTTTTCGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGCACTTGTTTTTGAAAT
65 ATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGCACTTGGTTTTGAAAT
* *
24629 ACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACT-TTTTTACACATGTTTT
130 ACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTGTTTGTACACCTGTTTT
24693 CTCAA
195 CTCAA
*
24698 AAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGTTTTTCGA
1 AAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGGTTTTCGA
* * *
24763 TGTTTTCGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGTACTTGTTTTTGAAATA
66 TGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGCACTTGGTTTTGAAATA
* * * * *
24828 CATTATGGACAAAAAGTATCGACACTTGTTCTATTCGTGTCGATATTTTTTTTACACCTGTTTTC
131 CATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTGTTTGTACACCTGTTTTC
24893 TCAA
196 TCAA
* *
24897 AAACCGGTATATTTAGACCGGTTATAATGCTAATTTACCTATGACATTATAATTATGGTTTTCGA
1 AAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGGTTTTCGA
* * *
24962 TATTTTTGGGATGGACACTTGTTATAAATGTATCGACAC
66 TGTTTTTGGGATCGACACTTGTTACAAATGTATCGACAC
25001 ATAAGTTTAC
Statistics
Matches: 1042, Mismatches: 53, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
198 174 0.17
199 695 0.67
200 173 0.17
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (199 bp):
AAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGGTTTTCGA
TGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGCACTTGGTTTTGAAATA
CATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTGTTTGTACACCTGTTTTC
TCAA
Found at i:25393 original size:18 final size:19
Alignment explanation
Indices: 25346--25394 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
25336 TTACATTCAC
*
25346 ATACAAAATTATAAATCGT
1 ATACAAAATTAAAAATCGT
*
25365 ATACAAAATTAAAAATCTT
1 ATACAAAATTAAAAATCGT
25384 ATAC-AAATTAA
1 ATACAAAATTAA
25395 CCATGCATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
18 7 0.25
19 21 0.75
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTAAAAATCGT
Found at i:26894 original size:21 final size:18
Alignment explanation
Indices: 26856--26894 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
26846 TTCTCCTCAT
26856 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
*
26874 TTCCTCCATCTTCTCTTC
1 TTCCTCCATCTTTTCTTC
26892 TTC
1 TTC
26895 AAATTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.05, C:0.41, G:0.00, T:0.54
Consensus pattern (18 bp):
TTCCTCCATCTTTTCTTC
Found at i:27320 original size:9 final size:9
Alignment explanation
Indices: 27303--27350 Score: 60
Period size: 9 Copynumber: 5.3 Consensus size: 9
27293 CTTACTCATT
*
27303 CTCCACTGC
1 CTCCTCTGC
27312 CTCCTCTGC
1 CTCCTCTGC
* *
27321 CTCATCTAC
1 CTCCTCTGC
27330 CTCCTCTGC
1 CTCCTCTGC
*
27339 CTCCTCTAC
1 CTCCTCTGC
27348 CTC
1 CTC
27351 ATTGACAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.08, C:0.54, G:0.06, T:0.31
Consensus pattern (9 bp):
CTCCTCTGC
Found at i:27334 original size:18 final size:18
Alignment explanation
Indices: 27311--27350 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
27301 TTCTCCACTG
27311 CCTCCTCTGCCTCATCTA
1 CCTCCTCTGCCTCATCTA
*
27329 CCTCCTCTGCCTCCTCTA
1 CCTCCTCTGCCTCATCTA
27347 CCTC
1 CCTC
27351 ATTGACAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.07, C:0.55, G:0.05, T:0.33
Consensus pattern (18 bp):
CCTCCTCTGCCTCATCTA
Found at i:27611 original size:22 final size:21
Alignment explanation
Indices: 27583--27639 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 21
27573 AACCTACATT
*
27583 TATAATAAAAGTTATCATTTTA
1 TATAATAAAA-CTATCATTTTA
27605 TATAATAATTATACTATCATTTTA
1 TATAATAA--A-ACTATCATTTTA
*
27629 TATAAAAAAAC
1 TATAATAAAAC
27640 AAAAACATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
21 2 0.07
22 9 0.30
24 18 0.60
25 1 0.03
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (21 bp):
TATAATAAAACTATCATTTTA
Found at i:28174 original size:21 final size:20
Alignment explanation
Indices: 28144--28186 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
28134 CTTACTCCTA
28144 TCAACGATCCAAACCCCATT
1 TCAACGATCCAAACCCCATT
*
28164 TCAACTGATCCAAACCTCATT
1 TCAAC-GATCCAAACCCCATT
28185 TC
1 TC
28187 CCTCAGCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.33, C:0.37, G:0.05, T:0.26
Consensus pattern (20 bp):
TCAACGATCCAAACCCCATT
Found at i:28627 original size:18 final size:18
Alignment explanation
Indices: 28604--28642 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28594 TACTGTCAAC
28604 ATTTAAAATTTGTAAT-CA
1 ATTTAAAATTT-TAATCCA
*
28622 ATTTAAAGTTTTAATCCA
1 ATTTAAAATTTTAATCCA
28640 ATT
1 ATT
28643 ACCATTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (18 bp):
ATTTAAAATTTTAATCCA
Found at i:28940 original size:19 final size:20
Alignment explanation
Indices: 28893--28941 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
28883 CATTTATACA
28893 ACCTA-AAATATCATTTTCT
1 ACCTATAAATATCATTTTCT
28912 ACCTAT-AATATCATTTT-T
1 ACCTATAAATATCATTTTCT
28930 ACCTATAAATAT
1 ACCTATAAATAT
28942 TAACTAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.25
19 21 0.75
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.43
Consensus pattern (20 bp):
ACCTATAAATATCATTTTCT
Found at i:29567 original size:182 final size:181
Alignment explanation
Indices: 29325--30527 Score: 1612
Period size: 182 Copynumber: 6.6 Consensus size: 181
29315 TACGCGTACT
* * * * * *
29325 TATTAAAGTATCGACACTTTCAACATATCCGATATCTATTTACCAGTTTTGTCA-TTTTGAGACC
1 TATTAAATTATCGACACTTTCAATATATCCGGTAACT-TTTTCCGGTTTTGTCATTTTTGAGACC
* * *
29389 GATTTTATAATATTTTTACCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACAC
65 G-TTTTATCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACAC
* * *
29454 TTTTTAAGTGCTATAACTTCTTCTCTTTTAAATTAAGAAAGTGTCGATACTTA
129 TTTATAAGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* * *
29507 TATTAAATTATCGACAATTTTAACATATCCGGTAACTTTTTCCGGTTTTGTCATTTTTGAGACCT
1 TATTAAATTATCGACACTTTCAATATATCCGGTAACTTTTTCCGGTTTTGTCATTTTTGAGACC-
* *
29572 GTTTTATCATATTTTTACATGTTATATTGGTAAGGATCGATACATTTTCATAAAGTGTCGACACT
65 GTTTTATCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACT
* * *
29637 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTAA
130 TTATAAGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* * *
29689 TATTAAATTATCGACACTTTCAATATGTCCGGCAACTTTTTCCGGTTTTTTCATTTTTGAGACCG
1 TATTAAATTATCGACACTTTCAATATATCCGGTAACTTTTTCCGGTTTTGTCATTTTTGAGACC-
* ** *
29754 GTTTTATCATATTTTTACATGTTATATTGTTATGGATCGATATATTTTTTTAAAGTATCGACACT
65 GTTTTATCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACT
* *
29819 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTTTCGATACTTA
130 TTATAAGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* * * * *
29871 TATTAAATTATCGACACTTTCAATATATCCGGTAGCGTTTTACTGGTTTTGTCAATTTTGTGACA
1 TATTAAATTATCGACACTTTCAATATATCCGGTAAC-TTTTTCCGGTTTTGTCATTTTTGAGAC-
* *
29936 TGTTTTATCATATTTGTACATGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACAC
64 CGTTTTATCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACAC
* *
30001 TTTATAAGCGCAATAACTTTTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
129 TTTATAAGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* * * * *
30054 TATTAAATTATCGACACTTTTAACATATTCGGTAACTTTTTCCGGTTTTGTCATTTTTTAGACAT
1 TATTAAATTATCGACACTTTCAATATATCCGGTAACTTTTTCCGGTTTTGTCATTTTTGAGAC-C
* * * * *
30119 GTTTTATCATATTTTTACCTGTTATATTGGTAAT-GATCGATATATTTTAATAAAGTGTTGACAC
65 GTTTTATCATATTTTTACATGTTATATT-GTTATGGATCGATACATTTTCATAAAGTGTCGACAC
* * * *
30183 TTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTTAGAAAGTGTCGATACTAA
129 TTTATAAGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
*
30236 TATTAAATTATCGACACTTTCAATATATCCGGTAACTTTTTCCGGTTTTGTCATTTTTTAGACCA
1 TATTAAATTATCGACACTTTCAATATATCCGGTAACTTTTTCCGGTTTTGTCATTTTTGAGACC-
* * *
30301 GTTTTATCATATTTTTACATGTTATATTGTTGTGGATCGACATATATTTT--TAAAGTATCGACA
65 GTTTTATCATATTTTTACATGTTATATTGTTATGGATCG--ATACATTTTCATAAAGTGTCGACA
* * *
30364 CTTTATAAGTGCTATAA---CTTCTCTTTTAAATTTAGAAAGTTTCGATACTTA
128 CTTTATAAGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* * *
30415 TATTAAATTATCGACACTTTCAATATATCCGGTAACGTTTTACCGATTTTGTCA-TTTTGGGACC
1 TATTAAATTATCGACACTTTCAATATATCCGGTAAC-TTTTTCCGGTTTTGTCATTTTTGAGACC
* * * * * * *
30479 GGTTTTGTCATATTTGTACCTGTAATATTGCTATGGAGCGATCCATTTT
65 -GTTTTATCATATTTTTACATGTTATATTGTTATGGATCGATACATTTT
30528 TCATTTGTAT
Statistics
Matches: 912, Mismatches: 99, Indels: 25
0.88 0.10 0.02
Matches are distributed among these distances:
177 7 0.01
179 108 0.12
180 15 0.02
181 17 0.02
182 589 0.65
183 167 0.18
184 9 0.01
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (181 bp):
TATTAAATTATCGACACTTTCAATATATCCGGTAACTTTTTCCGGTTTTGTCATTTTTGAGACCG
TTTTATCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACTT
TATAAGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
Found at i:30093 original size:365 final size:362
Alignment explanation
Indices: 29325--30520 Score: 1659
Period size: 365 Copynumber: 3.3 Consensus size: 362
29315 TACGCGTACT
* * * *
29325 TATTAAAGTATCGACACTTTCAACATATCCGATATCTATTTACCAGTTTTGTCATTTTGAGACCG
1 TATTAAATTATCGACACTTTCAACATATCCGGTAACT-TTTACCGGTTTTGTCATTTTGAGACCG
* * * * *
29390 ATTTTATAATATTTTTACCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACT
65 GTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATATATTTTAATAAAGTGTCGACACT
* *
29455 TTTTAAGTGCTATAACTTCTTCTCTTTTAAATTAAGAAAGTGTCGATACTTATATTAAATTATCG
130 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTAAGAAAGTGTCGATACTTATATTAAATTATCG
* * * * * *
29520 ACAATTTTAACATATCCGGTAACTTTTTCCGGTTTTGTCATTTTTGAGACCTGTTTTATCATATT
195 ACACTTTCAATATATCCGGTAACTTTTTCCGGTTTTGTCAATTTTGTGACATGTTTTATCATATT
* * * *
29585 TTTACATGTTATATTGGTAAGGATCGATACATTTTCATAAAGTGTCGACACTTTTTAGGCGCTAT
260 TTTACATGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACTTTATAAGCGCTAT
*
29650 AACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTAA
325 AACTT-TTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* * * * *
29689 TATTAAATTATCGACACTTTCAATATGTCCGGCAACTTTTTCCGGTTTTTTCATTTTTGAGACCG
1 TATTAAATTATCGACACTTTCAACATATCCGGTAACTTTTACCGGTTTTGTCA-TTTTGAGACCG
* ** *
29754 GTTTTATCATATTTTTACATGTTATATTGTTATGGATCGATATATTTTTTTAAAGTATCGACACT
65 GTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATATATTTTAATAAAGTGTCGACACT
* * *
29819 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTTTCGATACTTATATTAAATTATCG
130 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTAAGAAAGTGTCGATACTTATATTAAATTATCG
* * *
29884 ACACTTTCAATATATCCGGTAGCGTTTTACTGGTTTTGTCAATTTTGTGACATGTTTTATCATAT
195 ACACTTTCAATATATCCGGTAAC-TTTTTCCGGTTTTGTCAATTTTGTGACATGTTTTATCATAT
* *
29949 TTGTACATGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACTTTATAAGCGCAA
259 TTTTACATGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACTTTATAAGCGCTA
30014 TAACTTTTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
324 TAAC-TTTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* * * * **
30054 TATTAAATTATCGACACTTTTAACATATTCGGTAACTTTTTCCGGTTTTGTCATTTTTTAGACAT
1 TATTAAATTATCGACACTTTCAACATATCCGGTAACTTTTACCGGTTTTGTCA-TTTTGAGACCG
* *
30119 GTTTTATCATATTTTTACCTGTTATATTGGTAAT-GATCGATATATTTTAATAAAGTGTTGACAC
65 GTTTTATCATATTTTTACCTGTTATATT-GTTATGGATCGATATATTTTAATAAAGTGTCGACAC
* *
30183 TTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTTAGAAAGTGTCGATACTAATATTAAATTATC
129 TTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTAAGAAAGTGTCGATACTTATATTAAATTATC
*
30248 GACACTTTCAATATATCCGGTAACTTTTTCCGGTTTTGTC-ATTTTTTAGACCA-GTTTTATCAT
194 GACACTTTCAATATATCCGGTAACTTTTTCCGGTTTTGTCAATTTTGT-GA-CATGTTTTATCAT
* * * *
30311 ATTTTTACATGTTATATTGTTGTGGATCGACATATATTTT--TAAAGTATCGACACTTTATAAGT
257 ATTTTTACATGTTATATTGTTATGGATCG--ATACATTTTCATAAAGTGTCGACACTTTATAAGC
* *
30374 GCTATAAC--TTCTCTTTTAAATTTAGAAAGTTTCGATACTTA
320 GCTATAACTTTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* * *
30415 TATTAAATTATCGACACTTTCAATATATCCGGTAACGTTTTACCGATTTTGTCATTTTGGGACCG
1 TATTAAATTATCGACACTTTCAACATATCCGGTAAC-TTTTACCGGTTTTGTCATTTTGAGACCG
* * * * *
30480 GTTTTGTCATATTTGTACCTGTAATATTGCTATGGAGCGAT
65 GTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGAT
30521 CCATTTTTCA
Statistics
Matches: 738, Mismatches: 84, Indels: 23
0.87 0.10 0.03
Matches are distributed among these distances:
360 3 0.00
361 102 0.14
362 15 0.02
363 19 0.03
364 259 0.35
365 326 0.44
366 14 0.02
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (362 bp):
TATTAAATTATCGACACTTTCAACATATCCGGTAACTTTTACCGGTTTTGTCATTTTGAGACCGG
TTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATATATTTTAATAAAGTGTCGACACTT
TTTAGGCGCTATAACTTCTTCTCTTTTAAATTAAGAAAGTGTCGATACTTATATTAAATTATCGA
CACTTTCAATATATCCGGTAACTTTTTCCGGTTTTGTCAATTTTGTGACATGTTTTATCATATTT
TTACATGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACTTTATAAGCGCTATA
ACTTTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
Found at i:30484 original size:20 final size:21
Alignment explanation
Indices: 30456--30494 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
30446 GTAACGTTTT
30456 ACCGATTTTGTCAT-TTTGGG
1 ACCGATTTTGTCATATTTGGG
*
30476 ACCGGTTTTGTCATATTTG
1 ACCGATTTTGTCATATTTG
30495 TACCTGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (21 bp):
ACCGATTTTGTCATATTTGGG
Found at i:34217 original size:20 final size:20
Alignment explanation
Indices: 34192--34232 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
34182 TTCTTGATTT
34192 TACTGTAGTAG-TATCGATAC
1 TACTGTAG-AGATATCGATAC
34212 TACTGTAGAGATATCGATAC
1 TACTGTAGAGATATCGATAC
34232 T
1 T
34233 CATTTTGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.34
Consensus pattern (20 bp):
TACTGTAGAGATATCGATAC
Found at i:34302 original size:20 final size:20
Alignment explanation
Indices: 34274--34330 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
34264 TACTATTCAT
* *
34274 TATTGTTCACATAGTATCGG
1 TATTATTCACACAGTATCGG
**
34294 TATTATTCATGCAGTATCGG
1 TATTATTCACACAGTATCGG
* *
34314 TACTATTCATACAGTAT
1 TATTATTCACACAGTAT
34331 AATACTATTC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (20 bp):
TATTATTCACACAGTATCGG
Found at i:45691 original size:16 final size:15
Alignment explanation
Indices: 45665--45694 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
45655 TCAGAATATA
45665 AAGAAAAGAAAAAAG
1 AAGAAAAGAAAAAAG
45680 AAGAAGAAGAAAAAA
1 AAGAA-AAGAAAAAA
45695 CATTATGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAGAAAAGAAAAAAG
Found at i:46778 original size:51 final size:51
Alignment explanation
Indices: 46723--46840 Score: 164
Period size: 51 Copynumber: 2.3 Consensus size: 51
46713 AGGTTTCATG
* *
46723 TCACTCGAGATATCTTCCCTCGAAGCTCAAAAACATTTCAACAATTTTATC
1 TCACTCGAGATAACTTCCCTAGAAGCTCAAAAACATTTCAACAATTTTATC
* * *
46774 TCACTCGAGATAACTTCCCTAGGAGCTCAAAATCATTTTAACAATTTTATC
1 TCACTCGAGATAACTTCCCTAGAAGCTCAAAAACATTTCAACAATTTTATC
* * *
46825 TCGCTCAAGATTACTT
1 TCACTCGAGATAACTT
46841 TTCTTAAAAC
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.32, C:0.25, G:0.09, T:0.33
Consensus pattern (51 bp):
TCACTCGAGATAACTTCCCTAGAAGCTCAAAAACATTTCAACAATTTTATC
Found at i:46848 original size:139 final size:137
Alignment explanation
Indices: 46612--46899 Score: 389
Period size: 139 Copynumber: 2.1 Consensus size: 137
46602 GAAAATCATT
* ** *
46612 TCAAAAACATTTCAAAATTTTTATCTCGCTCAAGATAGTTTCCCTAAATCTCAAATCATTTCAAC
1 TCAAAAACATTTCAAAATTTTTATCTCACTCAAGATAACTTCCCTAAAGCTCAAATCATTTCAAC
* ** * * *
46677 AATTTTATCCCACTCGAGATTGTTTTTCTTAAAACAAGGTTTCATGTCACTCGAGATATCTTCCC
66 AATTTTATCCCACTCAAGATTACTTTTCTTAAAACAAGATTTCATCTCACTCGAGATAGCTTCCC
46742 TCGAAGC
131 TCGAAGC
* * *
46749 TCAAAAACATTTCAACAA-TTTTATCTCACTCGAGATAACTTCCCTAGGAGCTCAAAATCATTTT
1 TCAAAAACATTTCAA-AATTTTTATCTCACTCAAGATAACTTCCCTA-AAGCTC-AAATCATTTC
* *
46813 AACAATTTTATCTCGCTCAAGATTACTTTTCTTAAAACAAGATTTCATCTCACTCGAGATAGCTT
63 AACAATTTTATCCCACTCAAGATTACTTTTCTTAAAACAAGATTTCATCTCACTCGAGATAGCTT
46878 CCCTCGAAGC
128 CCCTCGAAGC
* *
46888 TTAAAATCATTT
1 TCAAAAACATTT
46900 ATTTTTCAAC
Statistics
Matches: 131, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
137 39 0.30
138 6 0.05
139 86 0.66
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (137 bp):
TCAAAAACATTTCAAAATTTTTATCTCACTCAAGATAACTTCCCTAAAGCTCAAATCATTTCAAC
AATTTTATCCCACTCAAGATTACTTTTCTTAAAACAAGATTTCATCTCACTCGAGATAGCTTCCC
TCGAAGC
Found at i:50921 original size:62 final size:63
Alignment explanation
Indices: 50851--50972 Score: 192
Period size: 62 Copynumber: 2.0 Consensus size: 63
50841 ACGAGTCGAG
* * * *
50851 TTTAACGAGCAATGAGTCAAGTTGAGCAGCAAATTTTTTTAACAATC-CGAGTCGAGCACAAT
1 TTTAACGAGCAACGAGTCAAGTCGAGCAGCAAAATTTTTTAACAAGCACGAGTCGAGCACAAT
*
50913 TTTAACGAGCAACGAGTCAAGTCGAGCAGCAAAATTTTTTAATAAGCACGAGTCGAGCAC
1 TTTAACGAGCAACGAGTCAAGTCGAGCAGCAAAATTTTTTAACAAGCACGAGTCGAGCAC
50973 TGTCCAACTT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
62 42 0.78
63 12 0.22
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (63 bp):
TTTAACGAGCAACGAGTCAAGTCGAGCAGCAAAATTTTTTAACAAGCACGAGTCGAGCACAAT
Found at i:58132 original size:81 final size:84
Alignment explanation
Indices: 58025--58188 Score: 228
Period size: 81 Copynumber: 2.0 Consensus size: 84
58015 GATTAAGATG
* * *
58025 GAAATATTAATGCTGATCTATCTCCTTCTGCGAT-GAATCGAGC-TAA-GTTGAACAAGTTCTTC
1 GAAATACTAATGATGATCTATCTCCTTCTGCGATAGAATCGAGCAAAAGGTTGAACAAGTTCTTC
*
58087 AGA-TATTGAACTTCTTCTA
66 AGATTA-TAAACTTCTTCTA
* * *
58106 GAAATACTAATGATGCTCTATTTCCTTCTGCGATAGAATCGAGCAAAAGGTTGAATAAGTTCTTC
1 GAAATACTAATGATGATCTATCTCCTTCTGCGATAGAATCGAGCAAAAGGTTGAACAAGTTCTTC
58171 AGATTATAAACTTCTTCT
66 AGATTATAAACTTCTTCT
58189 TCCTCTTATG
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
81 30 0.42
82 9 0.12
83 2 0.03
84 29 0.40
85 2 0.03
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (84 bp):
GAAATACTAATGATGATCTATCTCCTTCTGCGATAGAATCGAGCAAAAGGTTGAACAAGTTCTTC
AGATTATAAACTTCTTCTA
Found at i:58248 original size:123 final size:123
Alignment explanation
Indices: 58094--58479 Score: 514
Period size: 123 Copynumber: 3.2 Consensus size: 123
58084 TTCAGATATT
* ** * * * * *
58094 GAACTTCTTCTAGAAATACTAATGATGCTCTATTTCCTTCTGCGATAGAATCGAGCAAAAGGTTG
1 GAACTCCTTCTAGAAATGTTGATGCTACTCTATCTCCTTCTGCAATAGAATCGAGCAAAAGGTTG
* *
58159 AATAAGTTCTTCAGATTATAAACTTCTTCTTCCTCTT-ATGATGAGTTCTTCTTATTAT
66 AATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCA-GATGAGTTCTTCTTATTAC
* * * *
58217 GAACTCCTTCTGGAAATGTTGATGCTACTCTATCTCCTTCTGTAATAGAATCAAGCAAAATGTTG
1 GAACTCCTTCTAGAAATGTTGATGCTACTCTATCTCCTTCTGCAATAGAATCGAGCAAAAGGTTG
* * *
58282 AATAAGTTCTTTAGATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTT-AT-TTAC
66 AATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTAC
* * * * *
58338 GAACTCCTTTTAGAAATGTTAATGTTGCTCTATCTCCTT-TGCAATAGAGTCGAGC-AAAGGTTG
1 GAACTCCTTCTAGAAATGTTGATGCTACTCTATCTCCTTCTGCAATAGAATCGAGCAAAAGGTTG
*
58401 AATAA-TTCTTCATATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTAC
66 AATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTAC
58458 GAACTCCTTCTAGAAATGTTGA
1 GAACTCCTTCTAGAAATGTTGA
58480 AACATTCTGC
Statistics
Matches: 228, Mismatches: 32, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
118 41 0.18
119 13 0.06
120 37 0.16
121 37 0.16
122 1 0.00
123 98 0.43
124 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.40
Consensus pattern (123 bp):
GAACTCCTTCTAGAAATGTTGATGCTACTCTATCTCCTTCTGCAATAGAATCGAGCAAAAGGTTG
AATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTAC
Done.