Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007954.1 Hibiscus syriacus cultivar Beakdansim tig00110379_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: 289567
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:184828 original size:42 final size:41
Alignment explanation
Indices: 184743--184865 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
184733 GTGAATCGGG
* * * *
184743 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
184785 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
184827 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
184866 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:185258 original size:91 final size:90
Alignment explanation
Indices: 185083--185267 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
185073 ACTTCAAACT
*
185083 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
185148 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
*
185176 TTCAACCAAAAGATAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
185240 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
185267 T
1 T
185268 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 42 0.48
93 18 0.21
95 27 0.31
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:186985 original size:20 final size:19
Alignment explanation
Indices: 186954--187094 Score: 113
Period size: 19 Copynumber: 7.8 Consensus size: 19
186944 TCTTTTGGTT
186954 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
186973 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
186994 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
187013 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** *
187027 GAAATGACTATCGCAACGC
1 GAAATGAAAATCGCAACGA
187046 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
187065 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
187079 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
187095 TGCGATTTTG
Statistics
Matches: 98, Mismatches: 12, Indels: 24
0.73 0.09 0.18
Matches are distributed among these distances:
14 21 0.21
16 4 0.04
17 4 0.04
19 38 0.39
20 29 0.30
21 2 0.02
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:186998 original size:40 final size:37
Alignment explanation
Indices: 186954--187099 Score: 130
Period size: 33 Copynumber: 4.1 Consensus size: 37
186944 TCTTTTGGTT
**
186954 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGACTATCGCAACG-GA-AATGAGAATCGCAACGC
186993 GGAAATGACTATCGCAAC-G--A-GAGAATCGCAACGC
1 -GAAATGACTATCGCAACGGAAATGAGAATCGCAACGC
*
187027 GAAATGACTATCGCAACGCGAAATGAAAATCGCAA--C
1 GAAATGACTATCGCAACG-GAAATGAGAATCGCAACGC
* * *
187063 GAGA-GA--ATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGACTATCGCAACG-GAAATGAGAATCGCAACGC
187098 GA
1 GA
187100 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 4, Indels: 19
0.81 0.03 0.16
Matches are distributed among these distances:
33 43 0.45
34 14 0.15
35 7 0.07
36 4 0.04
37 1 0.01
38 11 0.12
40 15 0.16
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (37 bp):
GAAATGACTATCGCAACGGAAATGAGAATCGCAACGC
Found at i:187112 original size:52 final size:52
Alignment explanation
Indices: 186962--187099 Score: 195
Period size: 52 Copynumber: 2.6 Consensus size: 52
186952 TTGAAATGAA
* * **
186962 AATCGCAACGAGATAATGAGAATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGA-AATGAAAATCGCAACGC-GAAATGAAAATCGCAACGAGAG
**
187016 AATCGCAACGCGAAATGACTATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
*
187068 AATCGCAACGCGAAATGAAAATCGCAATGCGA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGA
187100 TTTTGGTTTC
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
52 49 0.64
53 15 0.20
54 12 0.16
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (52 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:187128 original size:19 final size:19
Alignment explanation
Indices: 187089--187141 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
187079 GAAATGAAAA
* *
187089 TCGCAATGCGATTTTGGTT
1 TCGCATTGCGATTTTGATT
*
187108 TCGCATTGCGATTTTTATT
1 TCGCATTGCGATTTTGATT
* *
187127 TCGCGTTGTGATTTT
1 TCGCATTGCGATTTT
187142 CTCGTTGCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.13, C:0.15, G:0.23, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTGATT
Found at i:187159 original size:33 final size:34
Alignment explanation
Indices: 187113--187176 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
187103 TGGTTTCGCA
** *
187113 TTGCGATTTTTATTT-CGCGTTGTGATTTTCTCG
1 TTGCGATAGTTATTTCCGCGTTGCGATTTTCTCG
187146 TTGCGATAGTTATTTCCGCGTTGCGATTTTC
1 TTGCGATAGTTATTTCCGCGTTGCGATTTTC
187177 ATTCTCGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 13 0.48
34 14 0.52
ACGTcount: A:0.11, C:0.17, G:0.22, T:0.50
Consensus pattern (34 bp):
TTGCGATAGTTATTTCCGCGTTGCGATTTTCTCG
Found at i:187745 original size:20 final size:20
Alignment explanation
Indices: 187693--187764 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
187683 GCTATGTGAA
* *
187693 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTACGTAT
187713 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* *
187733 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
187754 TCGCATTGCGA
1 TCGCATTGCGA
187765 ATTATGAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
19 3 0.07
20 30 0.65
21 13 0.28
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:187778 original size:21 final size:21
Alignment explanation
Indices: 187754--187826 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
187744 TTTTCCTAAT
* *
187754 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
** *
187775 TCGCAACCCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
187795 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
187816 TTGCATTGCGA
1 TCGCAATGCGA
187827 TAGTCAGTAT
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 16 0.40
21 24 0.60
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:187862 original size:21 final size:21
Alignment explanation
Indices: 187836--187890 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
187826 ATAGTCAGTA
* *
187836 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGAATTTACAAAT
**
187857 TCGCATTGC-AATTTACTTAT
1 TCGCATTGCGAATTTACAAAT
187877 TCGCATTGCGAATT
1 TCGCATTGCGAATT
187891 GGGAAAATCG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGAATTTACAAAT
Found at i:187901 original size:21 final size:20
Alignment explanation
Indices: 187877--187929 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
187867 ATTTACTTAT
187877 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATT-GGAAAA
**
187898 TCGCAACGCGAAATTGGAAAA
1 TCGCATTGCG-AATTGGAAAA
187919 TCGCATTGCGA
1 TCGCATTGCGA
187930 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 22 0.81
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:188415 original size:15 final size:17
Alignment explanation
Indices: 188395--188427 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
188385 TTTCTTATAT
188395 TAAAAAT-A-TTATAAA
1 TAAAAATAATTTATAAA
188410 TAAAAATAATTTATAAA
1 TAAAAATAATTTATAAA
188427 T
1 T
188428 TTTGCGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAAATAATTTATAAA
Found at i:188567 original size:19 final size:19
Alignment explanation
Indices: 188543--188579 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
188533 CTAAAAAATA
188543 TTTTTTATTTCTATTTTCG
1 TTTTTTATTTCTATTTTCG
* *
188562 TTTTTTGTTTTTATTTTC
1 TTTTTTATTTCTATTTTC
188580 AGAAAATAAT
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:0.08, C:0.08, G:0.05, T:0.78
Consensus pattern (19 bp):
TTTTTTATTTCTATTTTCG
Found at i:190013 original size:20 final size:20
Alignment explanation
Indices: 189988--190040 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
189978 GGCTGTCCAA
189988 GTGCATCGGTGCACTAGGGT
1 GTGCATCGGTGCACTAGGGT
190008 GTGCATCGGTGCACTAGGGT
1 GTGCATCGGTGCACTAGGGT
190028 GTGCATCGGTGCA
1 GTGCATCGGTGCA
190041 TAAATCAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.15, C:0.21, G:0.40, T:0.25
Consensus pattern (20 bp):
GTGCATCGGTGCACTAGGGT
Found at i:190107 original size:64 final size:63
Alignment explanation
Indices: 190027--190173 Score: 206
Period size: 64 Copynumber: 2.3 Consensus size: 63
190017 TGCACTAGGG
*
190027 TGTGCATCGGTGCATAAATCAACTTCGATGTTTCAAAATAACCAGGGTGCATCGATGCAT-GTCT
1 TGTGCATCGGTGCATAAATCAA-TTCGATGTTTCAAAATAACCAGAGTGCATCGATGCATGGT-T
* * *
190091 TGTGCATCGGTGCATAAAATCAATTCGATGTTTTAAAATAGCTAGAGTGCATCGATGCATGGTT
1 TGTGCATCGGTGCAT-AAATCAATTCGATGTTTCAAAATAACCAGAGTGCATCGATGCATGGTT
* *
190155 TGTGCATTGATGCATAAAT
1 TGTGCATCGGTGCATAAAT
190174 TGCATTCGAA
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
63 4 0.05
64 62 0.83
65 9 0.12
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.32
Consensus pattern (63 bp):
TGTGCATCGGTGCATAAATCAATTCGATGTTTCAAAATAACCAGAGTGCATCGATGCATGGTT
Found at i:191613 original size:57 final size:57
Alignment explanation
Indices: 191525--191645 Score: 224
Period size: 57 Copynumber: 2.1 Consensus size: 57
191515 TATTTTCTCT
*
191525 GCAATGCGATTTTCAAATTCGCAACACTAATTACCGATATAGGTAAACAGTACTATC
1 GCAATGTGATTTTCAAATTCGCAACACTAATTACCGATATAGGTAAACAGTACTATC
*
191582 GCAATGTGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATC
1 GCAATGTGATTTTCAAATTCGCAACACTAATTACCGATATAGGTAAACAGTACTATC
191639 GCAATGT
1 GCAATGT
191646 AAACAGTACT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (57 bp):
GCAATGTGATTTTCAAATTCGCAACACTAATTACCGATATAGGTAAACAGTACTATC
Found at i:191649 original size:20 final size:20
Alignment explanation
Indices: 191624--191664 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
191614 ACCGATATAG
*
191624 GTAAACAGTACTATCGCAAT
1 GTAAACAGTACTATCACAAT
191644 GTAAACAGTACTATCACAAT
1 GTAAACAGTACTATCACAAT
191664 G
1 G
191665 CGATTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (20 bp):
GTAAACAGTACTATCACAAT
Found at i:191707 original size:20 final size:20
Alignment explanation
Indices: 191684--191750 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
191674 AATTCGCAAC
*
191684 GCGATTTTCATATCT-GCGTT
1 GCGATTTACATAT-TAGCGTT
* *
191704 GCGATTTACATATTATCATT
1 GCGATTTACATATTAGCGTT
*
191724 GCGATTTACATATTCGCGTT
1 GCGATTTACATATTAGCGTT
191744 GCGATTT
1 GCGATTT
191751 TGGAACCTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
19 1 0.03
20 39 0.98
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (20 bp):
GCGATTTACATATTAGCGTT
Found at i:197348 original size:19 final size:19
Alignment explanation
Indices: 197318--197373 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
197308 AAAAGAAGAA
*
197318 AATATAATAAAATATAAAT
1 AATAAAATAAAATATAAAT
* * *
197337 GGATAAAA-AAAATACACAT
1 -AATAAAATAAAATATAAAT
197356 AATAAAATAAAATATAAA
1 AATAAAATAAAATATAAA
197374 ACAATGAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
18 6 0.21
19 17 0.61
20 5 0.18
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATATAAAT
Found at i:197489 original size:2 final size:2
Alignment explanation
Indices: 197482--197539 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
197472 ATAATAAATA
197482 AT AT AT AT AT AT AT 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 AT AT AT AT
197524 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
197540 GTAGAATATA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:197625 original size:19 final size:18
Alignment explanation
Indices: 197601--197656 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 18
197591 AGTAATACAT
197601 ATATAATAATAAAAATATA
1 ATATAATAATAAAAA-ATA
197620 ATATAATAGCATAAATAAATA
1 ATATAATA--ATAAA-AAATA
*
197641 ATAATAATAGTAAAAA
1 AT-ATAATAATAAAAA
197657 GTAAAAGGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
19 10 0.31
20 4 0.12
21 10 0.31
22 8 0.25
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.29
Consensus pattern (18 bp):
ATATAATAATAAAAAATA
Found at i:199397 original size:20 final size:20
Alignment explanation
Indices: 199374--199415 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
199364 GAATCCTTCG
199374 TCGTGAAATTGAAATCGAAC
1 TCGTGAAATTGAAATCGAAC
*
199394 TCGTGAAGTTGAAATCGAAC
1 TCGTGAAATTGAAATCGAAC
199414 TC
1 TC
199416 AGAGTTCTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGTGAAATTGAAATCGAAC
Found at i:199861 original size:105 final size:105
Alignment explanation
Indices: 199679--200189 Score: 925
Period size: 105 Copynumber: 4.9 Consensus size: 105
199669 AAATCGAACT
* *
199679 TGTTTATTGACAACCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
199744 CCTTCGTTGTGAAGTTGAAATTGGCTCCGAATTTGAGAAA
66 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAATCTGAGAAA
199784 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
199849 CCTTCGTTGTGAAGTTGAAATTGACTCTGAATCTGAGAAA
66 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAATCTGAGAAA
*
199889 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTGGAGTCCAATAT
1 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
199954 CCTTCGTTGTGAAGTTGAAATTGACTCTGAATCTGAGAAA
66 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAATCTGAGAAA
*
199994 TGTTTGTTGACAACCAGCGGTCCCTTCTTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
200059 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAAT-TGAGAAA
66 CCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATCTGAGAAA
*
200099 TGTTTGTTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
200164 CCTTCGTTGTGAAGTTGAAATTGGCT
66 CCTTCGTTGTGAAGTTGAAATTGGCT
200190 TTGGGTAAAA
Statistics
Matches: 394, Mismatches: 11, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
105 391 0.99
106 3 0.01
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (105 bp):
TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
CCTTCGTTGTGAAGTTGAAATTGGCTCTGAATCTGAGAAA
Found at i:205166 original size:120 final size:123
Alignment explanation
Indices: 204951--205195 Score: 469
Period size: 120 Copynumber: 2.0 Consensus size: 123
204941 GGGTTTGCTT
204951 GACCTCCATCCTTGTACATTTGGAGAGTCGAGGTCTTGGGATTCTCTTTCCTTCCGCCACAAATG
1 GACCTCCATCCTTGTACATTTGGAGAGTCGAGGTCTTGGGATTCTCTTTCCTTCCGCCACAAATG
205016 TGGCATTCACAAACTCCAAAGAGCGGAACG-ACATTCTACCGCTTCCTCGTCTACTTC
66 TGGCATTCACAAACTCCAAAGAGCGGAACGAACATTCTACCGCTTCCTCGTCTACTTC
205073 GACCTCCATCCTTGTACATTTGGAGAGTCGA-GTCTTGGGA-TCTCTTTCCTTCCGCCACAAATG
1 GACCTCCATCCTTGTACATTTGGAGAGTCGAGGTCTTGGGATTCTCTTTCCTTCCGCCACAAATG
205136 TGGCATTCACAAACTCCAAAGAGCGGAACGAACATTCTACCGCTTCCTCGTCTACTTC
66 TGGCATTCACAAACTCCAAAGAGCGGAACGAACATTCTACCGCTTCCTCGTCTACTTC
205194 GA
1 GA
205196 TGTATGGAGC
Statistics
Matches: 122, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
120 53 0.43
121 38 0.31
122 31 0.25
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (123 bp):
GACCTCCATCCTTGTACATTTGGAGAGTCGAGGTCTTGGGATTCTCTTTCCTTCCGCCACAAATG
TGGCATTCACAAACTCCAAAGAGCGGAACGAACATTCTACCGCTTCCTCGTCTACTTC
Found at i:211329 original size:19 final size:17
Alignment explanation
Indices: 211298--211352 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
211288 AAAAAGAAGA
*
211298 AAAT-ATAATAAAATAT
1 AAATAATAAAAAAATAT
*
211314 AAATGGATAAAAAAA-AT
1 AAAT-AATAAAAAAATAT
211331 ACACATAATAAAAAAATAT
1 A-A-ATAATAAAAAAATAT
211350 AAA
1 AAA
211353 ACAATGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
16 4 0.12
17 4 0.12
18 19 0.59
19 5 0.16
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.22
Consensus pattern (17 bp):
AAATAATAAAAAAATAT
Found at i:211441 original size:11 final size:11
Alignment explanation
Indices: 211421--211457 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
211411 ATAATAGTAA
*
211421 AAATAGTAATG
1 AAATAATAATG
211432 AAATAATAATG
1 AAATAATAATG
211443 AAA-AATAAT-
1 AAATAATAATG
211452 AAATAA
1 AAATAA
211458 AATATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
9 3 0.12
10 8 0.33
11 13 0.54
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (11 bp):
AAATAATAATG
Found at i:214778 original size:3 final size:3
Alignment explanation
Indices: 214770--214809 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
214760 AACCACGCCC
214770 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
214810 GTATATGGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:217034 original size:53 final size:55
Alignment explanation
Indices: 216933--217037 Score: 160
Period size: 54 Copynumber: 1.9 Consensus size: 55
216923 TTATTTCGAC
* * *
216933 AGGTGATAATAATGTATGGCTATGAATATTTCTCGATTTAATATTTGTATGGAGT
1 AGGTGATAATAATGTATGACTAAGAATATTTCTCGAATTAATATTTGTATGGAGT
*
216988 AGGTGGTAATAAT-TATGACTAAGAATATTTCTC-AATTAATATTTGTATGG
1 AGGTGATAATAATGTATGACTAAGAATATTTCTCGAATTAATATTTGTATGG
217038 TGTATGTTGC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
53 16 0.35
54 18 0.39
55 12 0.26
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (55 bp):
AGGTGATAATAATGTATGACTAAGAATATTTCTCGAATTAATATTTGTATGGAGT
Found at i:228463 original size:30 final size:31
Alignment explanation
Indices: 228427--228514 Score: 99
Period size: 31 Copynumber: 2.9 Consensus size: 31
228417 GAAGGACCTA
* *
228427 TCCATATGTTCCGAAGAACTTAGGT-AACTG
1 TCCATATGTCCCGAAGAACATAGGTAAACTG
** *
228457 TCCATATGTCCCGAATTACATAGGTAAATTG
1 TCCATATGTCCCGAAGAACATAGGTAAACTG
*
228488 TCCATATGTCTCGAA-AGACATAGGTAA
1 TCCATATGTCCCGAAGA-ACATAGGTAA
228515 CCCTCGACTC
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
30 21 0.43
31 28 0.57
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (31 bp):
TCCATATGTCCCGAAGAACATAGGTAAACTG
Found at i:232744 original size:30 final size:29
Alignment explanation
Indices: 232693--232780 Score: 88
Period size: 31 Copynumber: 2.9 Consensus size: 29
232683 GAAAGACCTA
* *
232693 TCCATATGTTCCGAAGAACATATG-CAACTG
1 TCCATATG-TCCGAAG-ACATAGGTAAACTG
*
232723 TCCATATGTCGCGAATGACATAGGTAAATTG
1 TCCATATGTC-CGAA-GACATAGGTAAACTG
232754 TCCATATGTCTCGAAAGACATAGGTAA
1 TCCATATGTC-CG-AAGACATAGGTAA
232781 CCCTCCACTC
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
29 2 0.04
30 18 0.36
31 28 0.56
32 2 0.04
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (29 bp):
TCCATATGTCCGAAGACATAGGTAAACTG
Found at i:232759 original size:31 final size:31
Alignment explanation
Indices: 232721--232780 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
232711 CATATGCAAC
*
232721 TGTCCATATGTCGCGAATGACATAGGTAAAT
1 TGTCCATATGTCGCGAAAGACATAGGTAAAT
*
232752 TGTCCATATGTCTCGAAAGACATAGGTAA
1 TGTCCATATGTCGCGAAAGACATAGGTAA
232781 CCCTCCACTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (31 bp):
TGTCCATATGTCGCGAAAGACATAGGTAAAT
Found at i:234399 original size:18 final size:18
Alignment explanation
Indices: 234361--234401 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
234351 AAATGGTACT
*
234361 GATACCCAAAAAAATATC
1 GATACCCAAAAAAATACC
* *
234379 GATACCCAAAGAGATACC
1 GATACCCAAAAAAATACC
234397 GATAC
1 GATAC
234402 TACTTTACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.24, G:0.12, T:0.15
Consensus pattern (18 bp):
GATACCCAAAAAAATACC
Found at i:234443 original size:20 final size:21
Alignment explanation
Indices: 234414--234453 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
234404 CTTTACATAG
234414 TAGTACCGATACCAT-AGGCA
1 TAGTACCGATACCATCAGGCA
*
234434 TAGTATCGATACCATCAGGC
1 TAGTACCGATACCATCAGGC
234454 CCTAACGGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.23
Consensus pattern (21 bp):
TAGTACCGATACCATCAGGCA
Found at i:238675 original size:12 final size:12
Alignment explanation
Indices: 238658--238698 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
238648 TTGACTGCAC
*
238658 TATTTATTTATG
1 TATTTATATATG
*
238670 TATTTATATATT
1 TATTTATATATG
*
238682 TATTCATATATG
1 TATTTATATATG
238694 TATTT
1 TATTT
238699 TATTTTATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.63
Consensus pattern (12 bp):
TATTTATATATG
Found at i:244252 original size:30 final size:30
Alignment explanation
Indices: 244218--244275 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
244208 TGTTTCCAAC
244218 ATGGGTATATTCAATTTCTTTTTTCATGAA
1 ATGGGTATATTCAATTTCTTTTTTCATGAA
244248 ATGGGTATATTCAATTTCTTTTTTCATG
1 ATGGGTATATTCAATTTCTTTTTTCATG
244276 TTTTTCTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.52
Consensus pattern (30 bp):
ATGGGTATATTCAATTTCTTTTTTCATGAA
Found at i:250890 original size:23 final size:24
Alignment explanation
Indices: 250863--250908 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
250853 TGTAAGTGAT
*
250863 TATTAATTTT-TTTGTTT-TTTTTA
1 TATT-ATTTTATTTATTTATTTTTA
250886 TATTATTTTATTTATTTATTTTT
1 TATTATTTTATTTATTTATTTTT
250909 CTTTTTGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 10 0.50
24 5 0.25
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (24 bp):
TATTATTTTATTTATTTATTTTTA
Found at i:250995 original size:20 final size:23
Alignment explanation
Indices: 250948--250996 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 23
250938 AATCTATGTC
*
250948 TTTGTGACATGTTTTTCTCTACT
1 TTTGTGACATGTGTTTCTCTACT
*
250971 CTTGTGACAT-TGTTT-T-TACT
1 TTTGTGACATGTGTTTCTCTACT
250991 TTTGTG
1 TTTGTG
250997 GCACGTTCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 9 0.39
21 1 0.04
22 4 0.17
23 9 0.39
ACGTcount: A:0.12, C:0.14, G:0.16, T:0.57
Consensus pattern (23 bp):
TTTGTGACATGTGTTTCTCTACT
Found at i:251374 original size:60 final size:60
Alignment explanation
Indices: 251297--251478 Score: 179
Period size: 60 Copynumber: 3.0 Consensus size: 60
251287 TCATACGTCT
* * * *
251297 TCAATCTATGACCATCATTTTAAATTGGTTCATAAACTTTTAAATATTTCAATTTCATCC
1 TCAAACTATGACTATCATTTTAAATTGGTTCCTAAACTTTTGAATATTTCAATTTCATCC
* ** *
251357 TTAAACTATGACTATCATTTTAAATT-AATCCTCAAACTTTTGAATATTTCATTTTCATCC
1 TCAAACTATGACTATCATTTTAAATTGGTTCCT-AAACTTTTGAATATTTCAATTTCATCC
* * * ** * * *
251417 CCAAAATGTGA-TATTCATTCAAAATTGGTCCCTAAACTTTTTGAATTTTTCAATTTTATCC
1 TCAAACTATGACTA-TCATTTTAAATTGGTTCCTAAAC-TTTTGAATATTTCAATTTCATCC
251478 T
1 T
251479 AAATTATATG
Statistics
Matches: 97, Mismatches: 21, Indels: 7
0.78 0.17 0.06
Matches are distributed among these distances:
59 5 0.05
60 69 0.71
61 23 0.24
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.44
Consensus pattern (60 bp):
TCAAACTATGACTATCATTTTAAATTGGTTCCTAAACTTTTGAATATTTCAATTTCATCC
Found at i:251735 original size:59 final size:59
Alignment explanation
Indices: 251618--251792 Score: 196
Period size: 59 Copynumber: 2.9 Consensus size: 59
251608 TATGGGGATG
* * * * * *
251618 AAATTAGAA-GATCTAAAAGTTTAGGGACCAATTTAGAATGAGATTCATAGTTTG-GGTTA
1 AAATTAGAATG-TTTAAAAGTTTA-AGACTAATTTAGAATAAGAGTCATAATTTGAGGTTA
*
251677 AAATTGGAATGTTTAAAAGTTTAAGACTAATTTAGAATAAGAGTCATAATTTGAGGTTA
1 AAATTAGAATGTTTAAAAGTTTAAGACTAATTTAGAATAAGAGTCATAATTTGAGGTTA
* *
251736 AAATTAGAGTGTTTAAAAGTTTAAGCACTAGTTTA-AGATAAG-GATCATAATTTGAGG
1 AAATTAGAATGTTTAAAAGTTTAAG-ACTAATTTAGA-ATAAGAG-TCATAATTTGAGG
251793 GCATATGATG
Statistics
Matches: 101, Mismatches: 10, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
58 25 0.25
59 49 0.49
60 27 0.27
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.34
Consensus pattern (59 bp):
AAATTAGAATGTTTAAAAGTTTAAGACTAATTTAGAATAAGAGTCATAATTTGAGGTTA
Found at i:254602 original size:2 final size:2
Alignment explanation
Indices: 254595--254626 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
254585 TATTTGAGAT
254595 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
254627 GTTAATGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:254926 original size:20 final size:20
Alignment explanation
Indices: 254903--254949 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
254893 GTTTCCAAAT
254903 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
*
254923 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATATGTAAA
254943 TCGCAAC
1 TCGCAAC
254950 ACATAAGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:254986 original size:20 final size:20
Alignment explanation
Indices: 254957--255070 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
254947 AACACATAAG
*
254957 TCAAAATCGCAACGCG-TTT
1 TCAAATTCGCAACGCGATTT
*
254976 TCTAAATTCGCAACGTGATTT
1 TC-AAATTCGCAACGCGATTT
* * *
254997 ACAAATTCGCAACACTGAATT
1 TCAAATTCGCAACGC-GATTT
*
255018 TCAAATTCGCAACTCGATTT
1 TCAAATTCGCAACGCGATTT
* *
255038 TCGAATTCGCAACACGAATTT
1 TCAAATTCGCAACGCG-ATTT
*
255059 T-AATTTCGCAAC
1 TCAAATTCGCAAC
255071 AGGTTTTATT
Statistics
Matches: 78, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.03
20 50 0.64
21 26 0.33
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (20 bp):
TCAAATTCGCAACGCGATTT
Found at i:255029 original size:41 final size:40
Alignment explanation
Indices: 254974--255070 Score: 124
Period size: 41 Copynumber: 2.4 Consensus size: 40
254964 CGCAACGCGT
254974 TTTCTAAATTCGCAACGT-GATTTACAAATTCGCAACACTGAA
1 TTTC-AAATTCGCAAC-TCGATTTACAAATTCGCAACAC-GAA
* *
255016 TTTCAAATTCGCAACTCGATTTTCGAATTCGCAACACGAA
1 TTTCAAATTCGCAACTCGATTTACAAATTCGCAACACGAA
* *
255056 TTTTAATTTCGCAAC
1 TTTCAAATTCGCAAC
255071 AGGTTTTATT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
40 17 0.34
41 29 0.58
42 4 0.08
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (40 bp):
TTTCAAATTCGCAACTCGATTTACAAATTCGCAACACGAA
Found at i:255071 original size:20 final size:19
Alignment explanation
Indices: 255002--255090 Score: 74
Period size: 20 Copynumber: 4.5 Consensus size: 19
254992 GATTTACAAA
* *
255002 TTCGCAACACTGAATTTCAAA
1 TTCGCAACAC-G-ATTTTAAT
*
255023 TTCGCAACTCGATTTTCGAA-
1 TTCGCAACACGATTTT--AAT
255043 TTCGCAACACGAATTTTAAT
1 TTCGCAACACG-ATTTTAAT
* *
255063 TTCGCAACA-GGTTTTATT
1 TTCGCAACACGATTTTAAT
255081 TTCGCAACAC
1 TTCGCAACAC
255091 AAATGTTTTG
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
18 15 0.26
19 7 0.12
20 20 0.34
21 16 0.28
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (19 bp):
TTCGCAACACGATTTTAAT
Found at i:255878 original size:12 final size:12
Alignment explanation
Indices: 255857--255890 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
255847 ACCACATTTC
*
255857 CAATACCAAACA
1 CAATATCAAACA
255869 CAATATCAAACA
1 CAATATCAAACA
*
255881 CAATCTCAAA
1 CAATATCAAA
255891 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:256043 original size:24 final size:24
Alignment explanation
Indices: 256016--256069 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
256006 ATATTCGAAA
256016 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
256040 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
256064 TTTGAT
1 TTTGAT
256070 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:258345 original size:12 final size:12
Alignment explanation
Indices: 258330--258364 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
258320 AGAAAAAAGA
258330 AATCAAAATCGC
1 AATCAAAATCGC
*
258342 AATCAAAATCCC
1 AATCAAAATCGC
*
258354 AATCACAATCG
1 AATCAAAATCG
258365 ACTTCACCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.49, C:0.29, G:0.06, T:0.17
Consensus pattern (12 bp):
AATCAAAATCGC
Found at i:258839 original size:25 final size:25
Alignment explanation
Indices: 258796--258847 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
258786 AAATCAATTA
* * *
258796 AACATTGTTGTGTGTACATTATTTG
1 AACATTGTTATGGGAACATTATTTG
258821 AACATTGTTATGGGAACATTATTTG
1 AACATTGTTATGGGAACATTATTTG
258846 AA
1 AA
258848 AAATAATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (25 bp):
AACATTGTTATGGGAACATTATTTG
Found at i:259252 original size:18 final size:18
Alignment explanation
Indices: 259231--259266 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
259221 GTAATTGGAG
259231 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
259249 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
259267 AATAAATTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:259274 original size:24 final size:24
Alignment explanation
Indices: 259223--259275 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
259213 TTTCATATGT
* * *
259223 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
259247 AATTTGAGTTTGAATTTCAAA-ATA
1 AATTTGAGTTTGAATTT-AAATATA
259271 AATTT
1 AATTT
259276 CGACTCCACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.45
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:260447 original size:6 final size:6
Alignment explanation
Indices: 260436--260476 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
260426 AAGAAAAAGG
*
260436 AAATCA AAATCA AAATCA CAATCA AAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATC
260477 CCAATCACAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.63, C:0.20, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:260482 original size:12 final size:12
Alignment explanation
Indices: 260436--260483 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
260426 AAGAAAAAGG
*
260436 AAATCAAAATCA
1 AAATCACAATCA
260448 AAATCACAATCA
1 AAATCACAATCA
*
260460 AAATCAAAATCA
1 AAATCACAATCA
*
260472 AAATCCCAATCA
1 AAATCACAATCA
260484 CAACCGGCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.60, C:0.23, G:0.00, T:0.17
Consensus pattern (12 bp):
AAATCACAATCA
Found at i:260716 original size:13 final size:13
Alignment explanation
Indices: 260700--260734 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
260690 TCAAATTCAA
260700 AACGCAAAATCGC
1 AACGCAAAATCGC
*
260713 AACGTGAAAATCGC
1 AACG-CAAAATCGC
260727 AACGCAAA
1 AACGCAAA
260735 TTTGACTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.49, C:0.26, G:0.17, T:0.09
Consensus pattern (13 bp):
AACGCAAAATCGC
Found at i:260914 original size:64 final size:64
Alignment explanation
Indices: 260813--260965 Score: 236
Period size: 64 Copynumber: 2.4 Consensus size: 64
260803 AATTTAAAAC
*
260813 AACAAATCAACTTTTACAAATTAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATCA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATCA
*** * * *
260877 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATCA
260941 AACAAATCAAC-TTTACAAATCAATT
1 AACAAATCAACTTTTACAAATCAATT
260966 TTTACAAATA
Statistics
Matches: 82, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
63 14 0.17
64 68 0.83
ACGTcount: A:0.52, C:0.18, G:0.02, T:0.29
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATCA
Found at i:260958 original size:13 final size:14
Alignment explanation
Indices: 260942--260974 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
260932 CATCAATTAA
260942 ACAAATCAA-CTTT
1 ACAAATCAATCTTT
*
260955 ACAAATCAATTTTT
1 ACAAATCAATCTTT
260969 ACAAAT
1 ACAAAT
260975 ACATCAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.33
Consensus pattern (14 bp):
ACAAATCAATCTTT
Found at i:262329 original size:21 final size:21
Alignment explanation
Indices: 262300--262405 Score: 97
Period size: 21 Copynumber: 5.0 Consensus size: 21
262290 GAACGGTGGG
*
262300 AGGGACCTCTTGAATGATGACA
1 AGGG-CCTCTTGAACGATGACA
* **
262322 AGGGCCTCTTGAACGGTGGGA
1 AGGGCCTCTTGAACGATGACA
* * *
262343 GGGGCCTCTTGAAGGATGATA
1 AGGGCCTCTTGAACGATGACA
* **
262364 GGGGCCTCTTGAACGAT-AGG
1 AGGGCCTCTTGAACGATGACA
262384 AGAGGCCTCTTGAACGATGACA
1 AG-GGCCTCTTGAACGATGACA
262406 GGTGCTTCAG
Statistics
Matches: 67, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
20 2 0.03
21 60 0.90
22 5 0.07
ACGTcount: A:0.25, C:0.19, G:0.35, T:0.21
Consensus pattern (21 bp):
AGGGCCTCTTGAACGATGACA
Found at i:262351 original size:42 final size:42
Alignment explanation
Indices: 262285--262405 Score: 161
Period size: 42 Copynumber: 2.9 Consensus size: 42
262275 GTGAATCGGG
* * *
262285 CTCTCGAACGGTGGGAGGGACCTCTTGAATGATGACAAGGGC
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGACAAGGGC
* * *
262327 CTCTTGAACGGTGGGAGGGGCCTCTTGAAGGATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGACAAGGGC
* * *
262369 CTCTTGAACGATAGGAGAGGCCTCTTGAACGATGACA
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGACA
262406 GGTGCTTCAG
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.24, C:0.20, G:0.36, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGACAAGGGC
Found at i:262765 original size:63 final size:63
Alignment explanation
Indices: 262698--262840 Score: 155
Period size: 63 Copynumber: 2.3 Consensus size: 63
262688 CGTAGAGTGG
* *
262698 CTACCTCATCACGTAAA-GTAGATACCTCACCACG-TAAAGCACCATTGTCATCGCGTAAAACAT
1 CTACCTCATCACGTAAAGGTAG-TACCTCACCACGCCAAA-CACCATTGTCATCACGTAAAACAT
* * * * * **
262761 CTACCTCACCACGTAAAGGTCGTACCTCATCACGCCATACACCATTGTCTTCACGTAAAGTAT
1 CTACCTCATCACGTAAAGGTAGTACCTCACCACGCCAAACACCATTGTCATCACGTAAAACAT
* *
262824 CGACCTCCTCACGTAAA
1 CTACCTCATCACGTAAA
262841 ATATTAACCT
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
63 61 0.92
64 5 0.08
ACGTcount: A:0.31, C:0.33, G:0.13, T:0.23
Consensus pattern (63 bp):
CTACCTCATCACGTAAAGGTAGTACCTCACCACGCCAAACACCATTGTCATCACGTAAAACAT
Found at i:262850 original size:21 final size:21
Alignment explanation
Indices: 262811--262860 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
262801 ACCATTGTCT
* * *
262811 TCACGTAAAGTATCGACCTCC
1 TCACGTAAAATATCAACCTCA
*
262832 TCACGTAAAATATTAACCTCA
1 TCACGTAAAATATCAACCTCA
*
262853 TTACGTAA
1 TCACGTAA
262861 CTCCCCTAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.28
Consensus pattern (21 bp):
TCACGTAAAATATCAACCTCA
Found at i:265062 original size:20 final size:20
Alignment explanation
Indices: 265034--265083 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
265024 AAACGCGCTT
*
265034 TGCGAATTTGACTTCTGTGT
1 TGCGAATTTGACTTCTGTGC
*
265054 TGTGAATTTGACTTCTGTGC
1 TGCGAATTTGACTTCTGTGC
265074 TGCGAATTTG
1 TGCGAATTTG
265084 GAAAATTGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.16, C:0.14, G:0.26, T:0.44
Consensus pattern (20 bp):
TGCGAATTTGACTTCTGTGC
Found at i:265109 original size:21 final size:21
Alignment explanation
Indices: 265075--265115 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
265065 CTTCTGTGCT
* *
265075 GCGAATTTGGAAAATTGCAAC
1 GCGAATTCGGAAAATCGCAAC
*
265096 GCGAATTCGTAAAATCGCAA
1 GCGAATTCGGAAAATCGCAA
265116 TTCGATTTAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (21 bp):
GCGAATTCGGAAAATCGCAAC
Found at i:269342 original size:93 final size:93
Alignment explanation
Indices: 269183--269368 Score: 363
Period size: 93 Copynumber: 2.0 Consensus size: 93
269173 TTTTGGCCAC
269183 TCGTCTTTAAAAAATTAGTGCTGATGTTGATGTCTCATCATAAGATCATGTCACATCATGATTGA
1 TCGTCTTTAAAAAATTAGTGCTGATGTTGATGTCTCATCATAAGATCATGTCACATCATGATTGA
269248 AAAATAATTTAAAATGTCATATTAACAT
66 AAAATAATTTAAAATGTCATATTAACAT
*
269276 TCGTCTTTAAAAAATTAGTGCTGATGTTGATGTCTCATCATAAGATCATGTCACGTCATGATTGA
1 TCGTCTTTAAAAAATTAGTGCTGATGTTGATGTCTCATCATAAGATCATGTCACATCATGATTGA
269341 AAAATAATTTAAAATGTCATATTAACAT
66 AAAATAATTTAAAATGTCATATTAACAT
269369 ATTTCTTAAT
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (93 bp):
TCGTCTTTAAAAAATTAGTGCTGATGTTGATGTCTCATCATAAGATCATGTCACATCATGATTGA
AAAATAATTTAAAATGTCATATTAACAT
Found at i:269531 original size:36 final size:37
Alignment explanation
Indices: 269491--269563 Score: 130
Period size: 36 Copynumber: 2.0 Consensus size: 37
269481 GTGGGGTAAC
*
269491 CAAATAGTTAATTTATACTGAATAAAAAAA-ATGTAT
1 CAAATAGTTAATTTACACTGAATAAAAAAATATGTAT
269527 CAAATAGTTAATTTACACTGAATAAAAAAATATGTAT
1 CAAATAGTTAATTTACACTGAATAAAAAAATATGTAT
269564 GAATTATGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 29 0.83
37 6 0.17
ACGTcount: A:0.52, C:0.07, G:0.08, T:0.33
Consensus pattern (37 bp):
CAAATAGTTAATTTACACTGAATAAAAAAATATGTAT
Found at i:274761 original size:2 final size:2
Alignment explanation
Indices: 274754--274778 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
274744 TTTTACAGTT
274754 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 T
274779 TGAAGTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:276969 original size:2 final size:2
Alignment explanation
Indices: 276964--277004 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
276954 GTGTGTGTGT
276964 GA GA GA GA GA GA GA GA GA GA GA G- GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
277005 TCATCAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:277318 original size:18 final size:18
Alignment explanation
Indices: 277280--277318 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
277270 TATATTATAA
*
277280 TTATATTTTTTTGTATTT
1 TTATATTTTTTTGTATGT
277298 TTATATTTTTTT-TATAGT
1 TTATATTTTTTTGTAT-GT
277316 TTA
1 TTA
277319 AATTGATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (18 bp):
TTATATTTTTTTGTATGT
Found at i:277395 original size:38 final size:38
Alignment explanation
Indices: 277310--277397 Score: 106
Period size: 38 Copynumber: 2.3 Consensus size: 38
277300 ATATTTTTTT
* * * *
277310 TATAGTTTAAATTGATATAATTCATTTTTTAAATTTAT
1 TATAGTTTAAATTGATATAATTCATTGTATAAATTGAG
*
277348 TATAGTTTAAATTGATATAATTCA-TGTATAAGTATGAG
1 TATAGTTTAAATTGATATAATTCATTGTATAAAT-TGAG
*
277386 TATAATTTAAAT
1 TATAGTTTAAAT
277398 ATTATATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
37 6 0.14
38 37 0.86
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (38 bp):
TATAGTTTAAATTGATATAATTCATTGTATAAATTGAG
Found at i:279431 original size:23 final size:23
Alignment explanation
Indices: 279405--279452 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
279395 ATAAAGTACA
*
279405 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
279428 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
279451 AT
1 AT
279453 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:280200 original size:18 final size:18
Alignment explanation
Indices: 280177--280213 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
280167 GCCGAAATAT
280177 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
280195 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
280213 A
1 A
280214 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:280442 original size:23 final size:23
Alignment explanation
Indices: 280416--280480 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
280406 ATGCGAGATA
280416 GATACCTATTACATTATATAAAC
1 GATACCTATTACATTATATAAAC
**
280439 GATACCTATTACATTATATAAGG
1 GATACCTATTACATTATATAAAC
* *
280462 GCTACCTATTACATCATAT
1 GATACCTATTACATTATAT
280481 GTTTACCTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.35
Consensus pattern (23 bp):
GATACCTATTACATTATATAAAC
Found at i:280862 original size:21 final size:20
Alignment explanation
Indices: 280832--280885 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
280822 GATAGACACT
*
280832 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
280853 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
280876 TTACATTATA
1 TTACATTATA
280886 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:280873 original size:23 final size:23
Alignment explanation
Indices: 280847--280909 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
280837 ATATAACCAT
280847 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
280870 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
280893 TACCTATTACATCATAT
1 TACCTATTACATTATAT
280910 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:281217 original size:429 final size:431
Alignment explanation
Indices: 280418--281436 Score: 1976
Period size: 429 Copynumber: 2.4 Consensus size: 431
280408 GCGAGATAGA
280418 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
*
280483 TTACCTATTATATTGAAAGTGTACATACTTTTTATAAAAAGGATCGATAC-TTTTTTAAAA-TTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
280546 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
*
280611 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTA
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTA
280676 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
261 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
280741 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
326 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
280806 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAT
391 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAT
280847 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
280912 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
280977 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATA-TGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
*
281041 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTT
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTA
281106 AATTTAATAATAATATATACCGTAACGT-AAAAATAAATCATTAGACGCCTATAATTACTAAATT
261 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
281170 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
326 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
281235 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAT
391 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAT
281276 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
281341 TTACCTATTATATTGAAAGTGTCCATACTTTTTAT-AAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
281405 TGTAATTTATGTTTCAATTTTTTTAACAGTGT
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGT
281437 ACTGCGAATT
Statistics
Matches: 585, Mismatches: 3, Indels: 5
0.99 0.01 0.01
Matches are distributed among these distances:
428 61 0.10
429 356 0.61
430 111 0.19
431 57 0.10
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (431 bp):
TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
ATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTA
AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAT
Found at i:281291 original size:21 final size:20
Alignment explanation
Indices: 281261--281314 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
281251 GATAGACACT
*
281261 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
281282 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
281305 TTACATTATA
1 TTACATTATA
281315 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:281302 original size:23 final size:23
Alignment explanation
Indices: 281276--281338 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
281266 ATATAACCAT
281276 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
281299 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
281322 TACCTATTACATCATAT
1 TACCTATTACATTATAT
281339 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:284202 original size:183 final size:184
Alignment explanation
Indices: 283894--284562 Score: 1263
Period size: 183 Copynumber: 3.7 Consensus size: 184
283884 TTTTAAATGG
* *
283894 TATGGACATAAAGTACCGACACAATATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
283959 TAA-AACGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
284023 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
284077 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
284142 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCT-TTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
*
284206 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
284260 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
284325 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTA-GGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
284389 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
284443 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
**
284508 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTTTATTATAAT
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
284563 GTTGAAAGTG
Statistics
Matches: 477, Mismatches: 7, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
183 426 0.89
184 51 0.11
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (184 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
Found at i:285929 original size:3 final size:3
Alignment explanation
Indices: 285921--286001 Score: 81
Period size: 3 Copynumber: 27.0 Consensus size: 3
285911 ACTTGTTTGG
* * * **
285921 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * *
285969 AGC TTC ATC GTC ATC ATC ATC ATC ATC GTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
286002 TTTATCGTCA
Statistics
Matches: 61, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.25, C:0.35, G:0.06, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:285944 original size:18 final size:18
Alignment explanation
Indices: 285921--286022 Score: 78
Period size: 18 Copynumber: 5.7 Consensus size: 18
285911 ACTTGTTTGG
285921 ATCATCATCTTCATCATC
1 ATCATCATCTTCATCATC
* *
285939 ATCATCATCATCGTCATC
1 ATCATCATCTTCATCATC
* ** * *
285957 ATCTTCATCGCCAGCTTC
1 ATCATCATCTTCATCATC
* *
285975 ATCGTCATCATCATCATC
1 ATCATCATCTTCATCATC
* * *
285993 ATCGTCATCTTTATCGTC
1 ATCATCATCTTCATCATC
* *
286011 AGCTTCATCTTC
1 ATCATCATCTTC
286023 TGCGACCGAT
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.23, C:0.33, G:0.07, T:0.37
Consensus pattern (18 bp):
ATCATCATCTTCATCATC
Found at i:285988 original size:42 final size:42
Alignment explanation
Indices: 285929--286019 Score: 137
Period size: 42 Copynumber: 2.2 Consensus size: 42
285919 GGATCATCAT
*
285929 CTTCATCATCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
* * * *
285971 CTTCATCGTCATCATCATCATCATCGTCATCTTTATCGTCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
286013 CTTCATC
1 CTTCATC
286020 TTCTGCGACC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.22, C:0.34, G:0.08, T:0.36
Consensus pattern (42 bp):
CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
Found at i:288229 original size:198 final size:197
Alignment explanation
Indices: 287482--289389 Score: 3377
Period size: 199 Copynumber: 9.7 Consensus size: 197
287472 TTTAAATTAG
*
287482 TATCGACACAAA-TATATTAGTGTCGACACATTATTTAGACATATTCTCTCAT-AAACCGGTAT-
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
287544 ATTGTACCGGTTAGATTGAAAAATTACATATTACA-TATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * * *
287608 CGACACGTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG-GAAA
131 CGACAC-TTTTTATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAAA
287672 AAA
195 AAA
*
287675 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
287740 ATTGTACCGGTTAGATTGAAAAATTACATATTA-ATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * * *
287804 CGACACTTTTTATATGGATCGACACTTTATGGGTGCACCTTGTTTTTTATTCATTCTGGGAAAAA
131 CGACACTTTTTATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAAAA
287869 AA
196 AA
*
287871 -ATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATT-TCTTATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
287934 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
287999 CGACACTTTTTATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAAAA
131 CGACACTTTTTATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGG-AAAAA
288064 AAA
195 AAA
288067 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
288132 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
288197 CGACACTTTTATATATGGATCGACAC-TTATTGATGCACCTTGTTTTTAATTCA-TCTGG-AAAA
131 CGACACTTTT-TATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAAA
288259 AAA
195 AAA
288262 TATCGACACAAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTAT
1 TATCGACAC-AAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTAT
288327 AATTGTACCGGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
65 AATTGTACC-GGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
* *
288392 ATCGACACTTTTTTATATATGGATCGACACTTTA-TGGTGCACCTTGTTTTTAATTCATTCTGGG
129 ATCGACAC--TTTT-TATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGA
288456 AAAAAAA
191 AAAAAAA
288463 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
288528 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
288593 CGACACTTTTTATATGGATCGACAC-TTATTGATGCACCTTGTTTTTAATTCATTATGGAAAAAA
131 CGACACTTTTTATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAAAA
288657 AA
196 AA
288659 TATCGACACAAACTATATTAGTGTCGACACATTA-TTAGACTTATTCTCTCAT-AAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
288722 ATTGTA-CGGTTAGATTAAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
66 ATTGTACCGGTTAGATT-AAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
288786 TCGACACTTTTTATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAAA
130 TCGACACTTTTTATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGG--AAA
288851 AAAAA
193 AAAAA
288856 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
288921 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
288986 CGAC-CTTTTTTATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAAA
131 CGACAC-TTTTTATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCT-GGAAAA
289050 AAAA
194 AAAA
289054 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
289119 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
289184 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACAC-TTTT-TATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
289249 AAAA
194 AAAA
289253 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
289318 ATTGTA-CGGTTAGATTAAAAAATTACATATTACATT-TACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
289381 CGACACTTT
131 CGACACTTT
289390 ATTGATGCAC
Statistics
Matches: 1664, Mismatches: 22, Indels: 55
0.96 0.01 0.03
Matches are distributed among these distances:
193 22 0.01
194 179 0.11
195 262 0.16
196 231 0.14
197 192 0.12
198 308 0.19
199 325 0.20
200 129 0.08
201 16 0.01
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (197 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAAAA
AA
Done.