Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007046.1 Hibiscus syriacus cultivar Beakdansim tig00018271_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: 76291
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:217 original size:2 final size:2
Alignment explanation
Indices: 210--252 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
200 CATGGGAAGG
210 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
251 AT
1 AT
253 CTCCGGATAC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2459 original size:24 final size:23
Alignment explanation
Indices: 2428--2472 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
2418 TTCATTTCAT
2428 ATTTAATTGGAGTTTGAATTTAA
1 ATTTAATTGGAGTTTGAATTTAA
*
2451 ATTTCAATTTGAGTTTGAATTT
1 ATTT-AATTGGAGTTTGAATTT
2473 TCAATATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.31, C:0.02, G:0.16, T:0.51
Consensus pattern (23 bp):
ATTTAATTGGAGTTTGAATTTAA
Found at i:2461 original size:18 final size:19
Alignment explanation
Indices: 2440--2477 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2430 TTAATTGGAG
2440 TTTGAATTT-AAATTTCAA
1 TTTGAATTTGAAATTTCAA
* *
2458 TTTGAGTTTGAATTTTCAA
1 TTTGAATTTGAAATTTCAA
2477 T
1 T
2478 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTGAATTTGAAATTTCAA
Found at i:4953 original size:23 final size:23
Alignment explanation
Indices: 4927--4977 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
4917 TAAGTAATTA
** *
4927 ACCTATTTTATTATATCAGTGCT
1 ACCTATTACATTATATAAGTGCT
*
4950 ACCTATTACGTTATATAAGTGCT
1 ACCTATTACATTATATAAGTGCT
4973 ACCTA
1 ACCTA
4978 ATATGTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (23 bp):
ACCTATTACATTATATAAGTGCT
Found at i:4985 original size:23 final size:23
Alignment explanation
Indices: 4937--4986 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
4927 ACCTATTTTA
* *
4937 TTATATCAGTGCTACCTATTACG
1 TTATATAAGTGCTACCTAATACG
*
4960 TTATATAAGTGCTACCTAATATG
1 TTATATAAGTGCTACCTAATACG
4983 TTAT
1 TTAT
4987 TGTGCTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (23 bp):
TTATATAAGTGCTACCTAATACG
Found at i:5010 original size:154 final size:150
Alignment explanation
Indices: 4727--5010 Score: 442
Period size: 154 Copynumber: 1.9 Consensus size: 150
4717 CGATCCCAAA
* *
4727 AACATTTTAGGCGTTTACCTAATGTGTTGTAATAACAAATTAAGTAATTAACCTATTTATTATAA
1 AACAATTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGTAATTAACCTATTTATTATAA
* * *
4792 GCGTTACTATTACGTTTTATAAACGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAA
66 GCGCTACTATTACGTTATATAAACGCTACCTAATATGTTATTGTGCTTGATAATATTTCCAGTAA
4857 ATAATCGGTTATGTTATGGT
131 ATAATCGGTTATGTTATGGT
*
4877 AACAATTTAGGTGTTTACCTAATATGTTGTAATAACAAATTAAGTAATTAACCTATTTTATTATA
1 AACAATTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGTAATTAACCTA-TTTATTATA
* ** *
4942 TCAGTGCTACCTATTACGTTATATAAGTGCTACCTAATATGTTATTGTGCTTGATAATATTTTCA
65 --AGCGCTA-CTATTACGTTATATAAACGCTACCTAATATGTTATTGTGCTTGATAATATTTCCA
5007 GTAA
127 GTAA
5011 TTAAACTATT
Statistics
Matches: 120, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
150 52 0.43
151 9 0.08
153 5 0.04
154 54 0.45
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (150 bp):
AACAATTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGTAATTAACCTATTTATTATAA
GCGCTACTATTACGTTATATAAACGCTACCTAATATGTTATTGTGCTTGATAATATTTCCAGTAA
ATAATCGGTTATGTTATGGT
Found at i:5049 original size:23 final size:23
Alignment explanation
Indices: 5022--5072 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
5012 TAAACTATTT
*
5022 ATTATATAAGC-ACTACCTATTAC
1 ATTATATAAGCGA-TACCTAATAC
*
5045 ATTATATAAGCGATACCTAATAT
1 ATTATATAAGCGATACCTAATAC
5068 ATTAT
1 ATTAT
5073 TGTATTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.41, C:0.16, G:0.06, T:0.37
Consensus pattern (23 bp):
ATTATATAAGCGATACCTAATAC
Found at i:5088 original size:86 final size:87
Alignment explanation
Indices: 4919--5089 Score: 227
Period size: 86 Copynumber: 2.0 Consensus size: 87
4909 TAACAAATTA
* * ** * * * *
4919 AGTAATTAACCTATTTTATTATATCAGTGCTACCTATTACGTTATATAAGTGCTACCTAATATGT
1 AGTAATTAAACTATTTTATTATATAAGCACTACCTATTACATTATATAAGCGATACCTAATATAT
* *
4984 TATTGTGCTTGATAATATTTTC
66 TATTGTACTTAATAATATTTTC
5006 AGTAATTAAACTA-TTTATTATATAAGCACTACCTATTACATTATATAAGCGATACCTAATATAT
1 AGTAATTAAACTATTTTATTATATAAGCACTACCTATTACATTATATAAGCGATACCTAATATAT
* *
5070 TATTGTATTTAATGATATTT
66 TATTGTACTTAATAATATTT
5090 CTAATTAAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
86 60 0.83
87 12 0.17
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (87 bp):
AGTAATTAAACTATTTTATTATATAAGCACTACCTATTACATTATATAAGCGATACCTAATATAT
TATTGTACTTAATAATATTTTC
Found at i:7935 original size:39 final size:39
Alignment explanation
Indices: 7846--7935 Score: 99
Period size: 39 Copynumber: 2.3 Consensus size: 39
7836 ACCATAGGGA
* * * *
7846 CCTGCGTTAAGGTCTTACCCTAAGAACAAAGCAGAGGAG
1 CCTGCGATAAGGACTTACCCTAAGAACAAAGCACAGAAG
* * *
7885 CCTACGATAAGGACTTACCCTAAGCACAAAGCACTGAAG
1 CCTGCGATAAGGACTTACCCTAAGAACAAAGCACAGAAG
* *
7924 CTTGCGGTAAGG
1 CCTGCGATAAGG
7936 TCTTGCAAGT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.18
Consensus pattern (39 bp):
CCTGCGATAAGGACTTACCCTAAGAACAAAGCACAGAAG
Found at i:9739 original size:19 final size:19
Alignment explanation
Indices: 9715--9801 Score: 156
Period size: 19 Copynumber: 4.6 Consensus size: 19
9705 TGCAGAAATG
9715 GTATCGGTACCGTAATAAA
1 GTATCGGTACCGTAATAAA
9734 GTATCGGTACCGTAATAAA
1 GTATCGGTACCGTAATAAA
*
9753 GTATTGGTACCGTAATAAA
1 GTATCGGTACCGTAATAAA
9772 GTATCGGTACCGTAATAAA
1 GTATCGGTACCGTAATAAA
*
9791 GTGTCGGTACC
1 GTATCGGTACC
9802 ATGGTATAGT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 65 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (19 bp):
GTATCGGTACCGTAATAAA
Found at i:11087 original size:81 final size:81
Alignment explanation
Indices: 10359--11052 Score: 1075
Period size: 81 Copynumber: 8.6 Consensus size: 81
10349 ACTATTCCAA
* * * * *
10359 AGTAAAAGATTAATAGTCTAGTTGTGTATTTGATAGAAAGATGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
10424 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
*
10440 AGTAAAAGATTAATAGCCTAGCTATGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
10505 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * *
10521 AGTAAAAGATTAATATCCTAGCTGAGCATTTGACAGAAAGGTGTCAATTATGTCAGTTAGAT-AT
1 AGTAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGA-
10585 AAGGTTAAATACCTTTG
65 AAGGTTAAATACCTTTG
* * *
10602 TGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTTTGCCAGTTAGATGAA
1 AGTAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
* *
10667 AGGTTAAGTACCATTG
66 AGGTTAAATACCTTTG
* * * * *
10683 AGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAATGTGTTAATTTTGCTAGTTAGATGAA
1 AGTAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
10748 AGGTTAAATACATTTG
66 AGGTTAAATACCTTTG
* *
10764 AGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAAATATGCCAGTTAGATGAA
1 AGTAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
10829 ATGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* *
10845 AGTAAAAGATTAATAACCTAGATGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
10910 ATGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * *
10926 AGTAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATTCTAGTTAGATAAA
1 AGTAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
10991 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * * *
11007 AGTAAAAGATTAATGGCCTAGCTGTGTATTAGACAGGAAGGTGTCA
1 AGTAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCA
11053 GTCCTGTAAA
Statistics
Matches: 566, Mismatches: 45, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
80 1 0.00
81 564 1.00
82 1 0.00
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.32
Consensus pattern (81 bp):
AGTAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
AGGTTAAATACCTTTG
Found at i:12156 original size:18 final size:18
Alignment explanation
Indices: 12133--12193 Score: 104
Period size: 18 Copynumber: 3.4 Consensus size: 18
12123 CGTTTTCAAC
12133 CTCCTCCGCCTCACTCTG
1 CTCCTCCGCCTCACTCTG
*
12151 CTCCTCTGCCTCACTCTG
1 CTCCTCCGCCTCACTCTG
*
12169 CTCCTCCACCTCACTCTG
1 CTCCTCCGCCTCACTCTG
12187 CTCCTCC
1 CTCCTCC
12194 AACACCAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.07, C:0.56, G:0.08, T:0.30
Consensus pattern (18 bp):
CTCCTCCGCCTCACTCTG
Found at i:13891 original size:81 final size:81
Alignment explanation
Indices: 13756--14173 Score: 568
Period size: 81 Copynumber: 5.2 Consensus size: 81
13746 GAGAGAAGAA
* * **
13756 CTTTGAGTAAAATATTAATAGCCTAGTTGTGTATTTGACAGAAAGGTGTCAATTATATCAGTTAG
1 CTTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAG
*
13821 ATGTAAGGTTAAATAC
66 ATGAAAGGTTAAATAC
* *
13837 CTTTGAGTAAAAGATTAATAGCCTAGTTATGCATTTGACTGAAAGGTGTCAATTATGCCAGTTAG
1 CTTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAG
13902 ATGAAAGGTTAAATAC
66 ATGAAAGGTTAAATAC
* ** * * *
13918 CTTTGAGTAAAAGATTAACAATCTAGATGTGCATTTGACATAAAGGTGCCAATTATGCCAGTTAG
1 CTTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAG
13983 ATGAAAGGTTAAATAC
66 ATGAAAGGTTAAATAC
* * *
13999 CTTAGAGTAAAATATTAATAGCCTAGTTGTGCATTAGACAGAAAGGTGTCAATTATGCCAGTTAG
1 CTTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAG
14064 ATGAAAGGTTAAATAC
66 ATGAAAGGTTAAATAC
* * * * * * * *
14080 CTTTGAGTAAAAGATTAATGGCCTAGCTGTGTATTGGACATG-AAGGTGCCAATCATGCAAATTA
1 CTTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGACA-GAAAGGTGTCAATTATGCCAGTTA
* * *
14144 GATGAAAGGCTATATGC
65 GATGAAAGGTTAAATAC
*
14161 CTTTGGGTAAAAG
1 CTTTGAGTAAAAG
14174 GCTAAATGCT
Statistics
Matches: 298, Mismatches: 38, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
81 297 1.00
82 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (81 bp):
CTTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAG
ATGAAAGGTTAAATAC
Found at i:16971 original size:2 final size:2
Alignment explanation
Indices: 16964--17004 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
16954 TGCACTGTTG
16964 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17005 TTATTTATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17009 original size:4 final size:4
Alignment explanation
Indices: 17002--17028 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
16992 TATATATATA
17002 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
17029 GGCATTCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:17639 original size:20 final size:20
Alignment explanation
Indices: 17614--17693 Score: 97
Period size: 20 Copynumber: 3.7 Consensus size: 20
17604 TTCATTTATG
17614 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
17634 GCATCCTTTCATGCATTTCATTTAT
1 GCATCCTTTCATGC----C-TTAAT
17659 GTCATCCTTTCATGCCTTAAT
1 G-CATCCTTTCATGCCTTAAT
17680 GCATCCTTTCATGC
1 GCATCCTTTCATGC
17694 ATTTCATTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
20 27 0.52
21 5 0.10
22 1 0.02
24 1 0.02
25 5 0.10
26 13 0.25
ACGTcount: A:0.19, C:0.29, G:0.10, T:0.42
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:17653 original size:46 final size:46
Alignment explanation
Indices: 17602--17751 Score: 255
Period size: 46 Copynumber: 3.2 Consensus size: 46
17592 TTATTCGTTA
17602 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
17648 ATTTCATTTATGTCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* **
17694 ATTTCATTTATGGTATTTTTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCA-TCCTTTCATGCCTTAATGCATCCTTTCATGC
17741 ATTTCATTTAT
1 ATTTCATTTAT
17752 TGATTCGTTT
Statistics
Matches: 98, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
46 58 0.59
47 40 0.41
ACGTcount: A:0.20, C:0.23, G:0.09, T:0.48
Consensus pattern (46 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:18203 original size:22 final size:21
Alignment explanation
Indices: 18176--18246 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 21
18166 TACCCCTACC
18176 ATGGTATCGATACTTCTATACT
1 ATGGTATCGATAC-TCTATACT
18198 ATGGTA-CTGATAC-CT-TACT
1 ATGGTATC-GATACTCTATACT
* *
18217 CTCGGTATCGATACTACTACACT
1 AT-GGTATCGATACT-CTATACT
18240 ATGGTAT
1 ATGGTAT
18247 TGGTACTCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
19 5 0.12
20 11 0.28
21 2 0.05
22 18 0.45
23 4 0.10
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (21 bp):
ATGGTATCGATACTCTATACT
Found at i:22519 original size:118 final size:116
Alignment explanation
Indices: 22352--22829 Score: 561
Period size: 118 Copynumber: 4.1 Consensus size: 116
22342 GAGAGTTAAC
* * * * *
22352 AATGAGAAGAACTCATCTA-AAAATGAGAAAAAGTTCATAACGAGAAGAACTTGTTCAACCTTTC
1 AATGAGAAGAACTCGTCCACAAGA-GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTC
* *
22416 ACCCAAATCCATCATATAAGGAGGTGGATTAACATTTCAATGAGGAGTTCAT
65 ACTCAAATCCATCACATAAGGAGGTGGATTAACATTTCAATGAGGAGTTCAT
* * * *
22468 AATGAGAAGAACTCGTCCACAAAGGGGAGAAGAAGTTCTTAATGAGAAGAACTTATTCAACTTTT
1 AATGAGAAGAACTCGTCCAC-AA-GAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
* * *
22533 CACTCAAAGT-CATCATATAAGTAGATGGATTAACATTTCAATGAGGAGTTCAT
64 CACTCAAA-TCCATCACATAAGGAGGTGGATTAACATTTCAATGAGGAGTTCAT
* * ** * * *
22586 AATAAGAAGAACTCAT-C-CAAGAGAGACTAAGTTCATAATGAGAAGAACTTGTTCGACATTTCG
1 AATGAGAAGAACTCGTCCACAAGAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTCA
* * * *
22649 TTCAAATCCGTCACATAAAGAGGTGGATTAACATTTCAATGAGGAGTTTAT
66 CTCAAATCCATCACATAAGGAGGTGGATTAACATTTCAATGAGGAGTTCAT
* * * *
22700 ATTGAGAAGAACTCGTCCATGAATAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTTTC
1 AATGAGAAGAACTCGTCCA-CAAGAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTC
* * ** *
22765 ACTCAAATTCATCACATAAGTAGGTGGAACAACATTTTCAATG-GAAGTTCAT
65 ACTCAAATCCATCACATAAGGAGGTGGATTAACA-TTTCAATGAGGAGTTCAT
22817 AATGAGAAGAACT
1 AATGAGAAGAACT
22830 TGGATAATCT
Statistics
Matches: 305, Mismatches: 48, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
113 1 0.00
114 90 0.30
115 3 0.01
116 18 0.06
117 86 0.28
118 106 0.35
119 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (116 bp):
AATGAGAAGAACTCGTCCACAAGAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTCA
CTCAAATCCATCACATAAGGAGGTGGATTAACATTTCAATGAGGAGTTCAT
Found at i:22806 original size:232 final size:231
Alignment explanation
Indices: 22382--22829 Score: 637
Period size: 232 Copynumber: 1.9 Consensus size: 231
22372 AAATGAGAAA
* * *
22382 AAGTTCATAACGAGAAGAACTTGTTCAACCTTTCACCCAAATCCATCATATAAGGAGGTGGATTA
1 AAGTTCATAACGAGAAGAACTTGTTCAACATTTCACCCAAATCCATCACATAAAGAGGTGGATTA
* *
22447 ACATTTCAATGAGGAGTTCATAATGAGAAGAACTCGTCCACAAAGGGGAGAAGAAGTTCTTAATG
66 ACATTTCAATGAGGAGTTCATAATGAGAAGAACTCGTCCACAAAGGAGAGAAGAAGTTCATAATG
* * **
22512 AGAAGAACTTATTCAACTTTTCACTCAAAGTCATCATATAAGTAGATGGATTAACATTTCAATGA
131 AGAAGAACTTATTCAACCTTTCACTCAAAGTCATCACATAAGTAGATGGAACAACATTTCAATG-
*
22577 GGAGTTCATAATAAGAAGAACTCATCCAAGAGAGACT
195 GAAGTTCATAATAAGAAGAACTCATCCAAGAGAGACT
* * *** *
22614 AAGTTCATAATGAGAAGAACTTGTTCGACATTTCGTTCAAATCCGTCACATAAAGAGGTGGATTA
1 AAGTTCATAACGAGAAGAACTTGTTCAACATTTCACCCAAATCCATCACATAAAGAGGTGGATTA
* * ** *
22679 ACATTTCAATGAGGAGTTTATATTGAGAAGAACTCGTCCATGAA-TAGAGAAGAAGTTCATAATG
66 ACATTTCAATGAGGAGTTCATAATGAGAAGAACTCGTCCACAAAGGAGAGAAGAAGTTCATAATG
* * * *
22743 AGAAGAACTTGTTCGACCTTTCACTCAAATTCATCACATAAGTAGGTGGAACAACATTTTCAATG
131 AGAAGAACTTATTCAACCTTTCACTCAAAGTCATCACATAAGTAGATGGAACAACA-TTTCAATG
*
22808 GAAGTTCATAATGAGAAGAACT
195 GAAGTTCATAATAAGAAGAACT
22830 TGGATAATCT
Statistics
Matches: 189, Mismatches: 26, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
231 85 0.45
232 104 0.55
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (231 bp):
AAGTTCATAACGAGAAGAACTTGTTCAACATTTCACCCAAATCCATCACATAAAGAGGTGGATTA
ACATTTCAATGAGGAGTTCATAATGAGAAGAACTCGTCCACAAAGGAGAGAAGAAGTTCATAATG
AGAAGAACTTATTCAACCTTTCACTCAAAGTCATCACATAAGTAGATGGAACAACATTTCAATGG
AAGTTCATAATAAGAAGAACTCATCCAAGAGAGACT
Found at i:29558 original size:12 final size:12
Alignment explanation
Indices: 29543--29578 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
29533 TTTAATTCAG
29543 CTTTTCTTTTTT
1 CTTTTCTTTTTT
29555 CTTTTCTTTTTT
1 CTTTTCTTTTTT
29567 CTTTTCTTTTTT
1 CTTTTCTTTTTT
29579 TGCTTAATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (12 bp):
CTTTTCTTTTTT
Found at i:34285 original size:3 final size:3
Alignment explanation
Indices: 34277--34354 Score: 68
Period size: 3 Copynumber: 25.0 Consensus size: 3
34267 TTTTACTTAA
** *
34277 ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT AAAT ATT ATT ATT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT AT-T
* *
34324 ATAT ATAT ATT ATT ATT A-A ATA ATT ATT ATT
1 AT-T AT-T ATT ATT ATT ATT ATT ATT ATT ATT
34355 TACAAACCGG
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
2 1 0.02
3 50 0.78
4 13 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:35252 original size:22 final size:22
Alignment explanation
Indices: 35227--35287 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 22
35217 TAGTCACTAA
35227 TTTTA-ATTATAAGTTTTATTACT
1 TTTTATATT-TAA-TTTTATTACT
35250 TTTTATATTTAATTTTATTA-T
1 TTTTATATTTAATTTTATTACT
*
35271 TTATAT-TTTAATTTTAT
1 TTTTATATTTAATTTTAT
35288 GTTTAAATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 11 0.31
21 6 0.17
22 8 0.22
23 8 0.22
24 3 0.08
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTATATTTAATTTTATTACT
Found at i:36261 original size:16 final size:15
Alignment explanation
Indices: 36240--36274 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
36230 TCTTTCAAAT
36240 TTTTTATTACTTATTA
1 TTTTTA-TACTTATTA
*
36256 TTTTTATACTTTTTA
1 TTTTTATACTTATTA
36271 TTTT
1 TTTT
36275 ATTTATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTATACTTATTA
Found at i:42569 original size:114 final size:114
Alignment explanation
Indices: 42369--42708 Score: 556
Period size: 114 Copynumber: 3.0 Consensus size: 114
42359 AAGTTCCATG
* *
42369 TTCTCGTAGTAGAAATAAGGAGACCCAATAGCATCTTCT-AGAAGTATTCTTTGAGTTATCTGAT
1 TTCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGA-AAGTGTTCTTTGAGTTATCTGAT
* *
42433 CTGGTTTGGTATGAACCTCAAAACCAATCATTGGATTTGAAAGATGAATT
65 CTGGTTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATT
*
42483 TTCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATC
1 TTCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATC
42548 TGGTTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATT
* *
42597 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TTCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATC
* * * * *
42662 TGGTTCGGTAGGAACCCCAGAACTAATCATTAGAATTGAAAGATGAA
66 TGGTTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAA
42709 CTGCATGATC
Statistics
Matches: 212, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
114 211 1.00
115 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (114 bp):
TTCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATT
Found at i:44755 original size:50 final size:54
Alignment explanation
Indices: 44623--44780 Score: 209
Period size: 54 Copynumber: 3.0 Consensus size: 54
44613 TAATTGAGAA
* *
44623 ATCTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGCTTTACGAAC
1 ATCTGAGCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
* *
44677 ATCTGAGCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTAC-ATC
1 ATCTGAGCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
***
44730 -TC-GA-CAGAAACCACAGGAAAA-GATGAATGCACTGTCAAATGTTTTACGAAC
1 ATCTGAGCAGAAACCACA-GAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
44781 TTGCTATTCT
Statistics
Matches: 93, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
50 33 0.35
51 9 0.10
52 2 0.02
53 2 0.02
54 47 0.51
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (54 bp):
ATCTGAGCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
Found at i:46047 original size:186 final size:185
Alignment explanation
Indices: 45730--46098 Score: 659
Period size: 186 Copynumber: 2.0 Consensus size: 185
45720 CCAATCAACA
45730 TGTTATTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATG
1 TGTTATTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATG
45795 AAATTGTTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTTACTTAGTAAACTATTTCCCACATC
66 AAATTGTTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTTACTTAGTAAACTATTTCCCACATC
*
45860 TGTAAGTCCTGCAGTGCATGATGTTTCTAAAAAGCCTTCGAGAGCTTTTTGATAT
131 TGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATAT
**
45915 TGTTATTTTGAAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTTTATCTTTTCT-AAAAT
1 TGTTATTTTG-AAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAAT
* *
45979 GAAATTGTTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTTTACTTATTAAACTATTTCCTACA
65 GAAATTGTTGAAAAGTAAGAAAACGATTTCCTTAG-TTTTTTTACTTAGTAAACTATTTCCCACA
*
46044 TCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGAT
129 TCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGAT
46099 GTTTTCAAAG
Statistics
Matches: 176, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
185 50 0.28
186 126 0.72
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (185 bp):
TGTTATTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATG
AAATTGTTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTTACTTAGTAAACTATTTCCCACATC
TGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATAT
Found at i:46242 original size:75 final size:75
Alignment explanation
Indices: 46042--46444 Score: 700
Period size: 75 Copynumber: 5.3 Consensus size: 75
46032 CTATTTCCTA
46042 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
46107 AGCCTTAGGGT
66 A-CCTTAGGGT
*
46118 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
46183 ACCTTCGGGT
66 ACCTTAGGGT
* **
46193 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
46258 ACCTTCGGGT
66 ACCTTAGGGT
**
46268 CATCTGTAAGTCCTATAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
46333 AGCCTTAGGGT
66 A-CCTTAGGGT
46344 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
46408 AACCTTAGGGT
65 AACCTTAGGGT
46419 CATCTGTAAGTCCTGCAGTGCATGAT
1 CATCTGTAAGTCCTGCAGTGCATGAT
46445 TTTTTAAGAC
Statistics
Matches: 313, Mismatches: 12, Indels: 5
0.95 0.04 0.02
Matches are distributed among these distances:
75 190 0.61
76 123 0.39
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (75 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
ACCTTAGGGT
Found at i:46344 original size:151 final size:150
Alignment explanation
Indices: 46042--46444 Score: 700
Period size: 151 Copynumber: 2.7 Consensus size: 150
46032 CTATTTCCTA
46042 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
46107 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 A-CCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
46172 AATGTTTTCAAACCTTCGGGT
130 AATGTTTTCAAACCTTAGGGT
* **
46193 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* ** *
46258 ACCTTCGGGTCATCTGTAAGTCCTATAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
66 ACCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTA
46323 ATGTTTTCAAAGCCTTAGGGT
131 ATGTTTTCAAA-CCTTAGGGT
46344 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
46408 AACCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGAT
65 AACCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGAT
46445 TTTTTAAGAC
Statistics
Matches: 236, Mismatches: 14, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
150 84 0.36
151 152 0.64
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (150 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
ACCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTA
ATGTTTTCAAACCTTAGGGT
Found at i:46609 original size:3 final size:3
Alignment explanation
Indices: 46601--46688 Score: 85
Period size: 3 Copynumber: 30.0 Consensus size: 3
46591 TTTTACTTAA
** *
46601 ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT ATT ATT AAAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT
* *
46647 ATT A-T ATT A-T ATAT ATT A-T ATT ATT ATT A-A ATA ATT ATT ATT
1 ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
46689 TACAAACCGG
Statistics
Matches: 71, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
2 7 0.10
3 59 0.83
4 5 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:46688 original size:25 final size:26
Alignment explanation
Indices: 46600--46688 Score: 101
Period size: 25 Copynumber: 3.4 Consensus size: 26
46590 ATTTTACTTA
*
46600 AATTATTATTAAAATTATTATTATTAT
1 AATTATTATTAATATTATTATTA-TAT
*
46627 TATTATTATTAAATATTATTATTATAT
1 AATTATTATT-AATATTATTATTATAT
* *
46654 TA-TATATATT-ATATTATTATTAAAT
1 AATTAT-TATTAATATTATTATTATAT
46679 AATTATTATT
1 AATTATTATT
46689 TACAAACCGG
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
25 19 0.35
26 6 0.11
27 18 0.33
28 12 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
AATTATTATTAATATTATTATTATAT
Found at i:47491 original size:35 final size:35
Alignment explanation
Indices: 47448--47525 Score: 147
Period size: 35 Copynumber: 2.2 Consensus size: 35
47438 GAGGGAAGCT
47448 AGAGAGAAGGCAGAGAATTCTGGTTCTCTCATTAG
1 AGAGAGAAGGCAGAGAATTCTGGTTCTCTCATTAG
*
47483 AGAGAGAAGGCAGAGAATTCTGGTTCTCTCGTTAG
1 AGAGAGAAGGCAGAGAATTCTGGTTCTCTCATTAG
47518 AGAGAGAA
1 AGAGAGAA
47526 CCAGAAGAGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.33, C:0.13, G:0.31, T:0.23
Consensus pattern (35 bp):
AGAGAGAAGGCAGAGAATTCTGGTTCTCTCATTAG
Found at i:47535 original size:37 final size:35
Alignment explanation
Indices: 47448--47536 Score: 115
Period size: 35 Copynumber: 2.5 Consensus size: 35
47438 GAGGGAAGCT
* *
47448 AGAGAGAAGGCAGAGAATTCTGGTTCTCTCATTAG
1 AGAGAGAAAGAAGAGAATTCTGGTTCTCTCATTAG
* * *
47483 AGAGAGAAGGCAGAGAATTCTGGTTCTCTCGTTAG
1 AGAGAGAAAGAAGAGAATTCTGGTTCTCTCATTAG
47518 AGAGAGAACCAGAAGAGAA
1 AGAGAGAA--AGAAGAGAA
47537 AAATGAGAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
35 42 0.86
37 7 0.14
ACGTcount: A:0.36, C:0.13, G:0.30, T:0.20
Consensus pattern (35 bp):
AGAGAGAAAGAAGAGAATTCTGGTTCTCTCATTAG
Found at i:47954 original size:22 final size:22
Alignment explanation
Indices: 47929--47987 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 22
47919 TAGTCACTAA
47929 TTTTA-ATTATAAGTTTTATTACT
1 TTTTATATT-TAA-TTTTATTACT
47952 TTTTATATTTAATTTTATTA-T
1 TTTTATATTTAATTTTATTACT
*
47973 TTATAT-TTTAATTTT
1 TTTTATATTTAATTTT
47988 GTATGTTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
20 9 0.26
21 6 0.18
22 8 0.24
23 8 0.24
24 3 0.09
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTTATATTTAATTTTATTACT
Found at i:56895 original size:15 final size:15
Alignment explanation
Indices: 56875--56916 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
56865 AAGTTTCGAT
56875 GCCCTTGGAGTCTTC
1 GCCCTTGGAGTCTTC
*
56890 GCCCTTGGAGCCTTC
1 GCCCTTGGAGTCTTC
56905 GCCCTTGGAGTC
1 GCCCTTGGAGTC
56917 CTCTAGCAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.07, C:0.36, G:0.29, T:0.29
Consensus pattern (15 bp):
GCCCTTGGAGTCTTC
Found at i:61168 original size:19 final size:19
Alignment explanation
Indices: 61144--61204 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
61134 AAACCGAAAC
61144 CGGTTTTTTCGGTTCGGTT
1 CGGTTTTTTCGGTTCGGTT
*
61163 CGGTTTTTT---TAACGGTT
1 CGGTTTTTTCGGT-TCGGTT
*
61180 CGGGTTTTTCGGTTCGGTT
1 CGGTTTTTTCGGTTCGGTT
61199 CGGTTT
1 CGGTTT
61205 ATCGGTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 1 0.03
17 13 0.38
19 19 0.56
20 1 0.03
ACGTcount: A:0.03, C:0.15, G:0.31, T:0.51
Consensus pattern (19 bp):
CGGTTTTTTCGGTTCGGTT
Found at i:61203 original size:18 final size:18
Alignment explanation
Indices: 61148--61211 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 18
61138 CGAAACCGGT
61148 TTTTTCGGTTCGGTTCGG
1 TTTTTCGGTTCGGTTCGG
61166 TTTTT---TTAACGGTTCGGG
1 TTTTTCGGTT--CGGTTC-GG
61184 TTTTTCGGTTCGGTTCGG
1 TTTTTCGGTTCGGTTCGG
*
61202 TTTATCGGTT
1 TTTTTCGGTT
61212 TTTCAATAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
15 2 0.05
17 6 0.15
18 23 0.59
19 6 0.15
21 2 0.05
ACGTcount: A:0.05, C:0.14, G:0.30, T:0.52
Consensus pattern (18 bp):
TTTTTCGGTTCGGTTCGG
Found at i:69533 original size:30 final size:28
Alignment explanation
Indices: 69499--69555 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
69489 GTCTTATTTT
* *
69499 TGTTTGAAATTGTATGGTTTTTTATTAGTA
1 TGTTTAAAATT-TATGG-TTATTATTAGTA
*
69529 TGTTTAAAATTTATTGTTATTATTAGT
1 TGTTTAAAATTTATGGTTATTATTAGT
69556 TGAAATTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 10 0.42
29 4 0.17
30 10 0.42
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (28 bp):
TGTTTAAAATTTATGGTTATTATTAGTA
Found at i:74605 original size:4 final size:4
Alignment explanation
Indices: 74596--74630 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
74586 ACTGTTCAAC
74596 TATT TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TATT TAT
74631 ACATGCATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Done.