Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002307.1 Hibiscus syriacus cultivar Beakdansim tig00004700_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: 66692
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:434 original size:32 final size:32
Alignment explanation
Indices: 379--454 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
369 TCTTCGAGAT
* *
379 ATATGGACAG-TATACCTATGTTCTAAGGAAC
1 ATATGGACAGTTTTACCTAGGTTCTAAGGAAC
** *
410 ATATGGACAGTTTTACCTAGGTTCTTTGGGAC
1 ATATGGACAGTTTTACCTAGGTTCTAAGGAAC
*
442 CTATGGACAGTTT
1 ATATGGACAGTTT
455 CGAGGTTCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
31 10 0.26
32 28 0.74
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (32 bp):
ATATGGACAGTTTTACCTAGGTTCTAAGGAAC
Found at i:11806 original size:46 final size:45
Alignment explanation
Indices: 11707--11877 Score: 256
Period size: 46 Copynumber: 3.8 Consensus size: 45
11697 GATAAACTGG
* * **
11707 AAAATAAGCTTACTAGCTTATGGAAT-AATGACAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGT
11751 AAAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTAT-GGATTAAATGGTAAGTATATTGGT
* *
11797 AAAATAAGCTTACTAGCTTATGGGATTAAATGGTAAGTATTTTGGT
1 AAAATAAGCTTACGAGCTTAT-GGATTAAATGGTAAGTATATTGGT
11843 AAAATAAGCTTACGAGCTTATGGA-TAAATGGTAAG
1 AAAATAAGCTTACGAGCTTATGGATTAAATGGTAAG
11878 AGATTTTATC
Statistics
Matches: 118, Mismatches: 7, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
44 31 0.26
45 7 0.06
46 80 0.68
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.32
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGT
Found at i:12314 original size:33 final size:33
Alignment explanation
Indices: 12277--12342 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
12267 TACTGTAGTA
* *
12277 GTTACTGTAGCAGTGCATCGGTACACTGTTCAC
1 GTTACTGTAACAATGCATCGGTACACTGTTCAC
12310 GTTACTGTAACAATGCATCGGTACACTGTTCAC
1 GTTACTGTAACAATGCATCGGTACACTGTTCAC
12343 TGTTCATGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.30
Consensus pattern (33 bp):
GTTACTGTAACAATGCATCGGTACACTGTTCAC
Found at i:15721 original size:41 final size:41
Alignment explanation
Indices: 15660--15782 Score: 219
Period size: 41 Copynumber: 3.0 Consensus size: 41
15650 CCTAATAAAT
* *
15660 TAGTTGTTAATTCAAGGGAAGATGAAACTCCAAAAGTTCAC
1 TAGTTATTAATTCAATGGAAGATGAAACTCCAAAAGTTCAC
15701 TAGTTATTAATTCAATGGAAGATGAAACTCCAAAAGTTCAC
1 TAGTTATTAATTCAATGGAAGATGAAACTCCAAAAGTTCAC
*
15742 TAGTTATTAATTCAATGGAATATGAAACTCCAAAAGTTCAC
1 TAGTTATTAATTCAATGGAAGATGAAACTCCAAAAGTTCAC
15783 GTAGAATGAA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 79 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (41 bp):
TAGTTATTAATTCAATGGAAGATGAAACTCCAAAAGTTCAC
Found at i:17266 original size:21 final size:21
Alignment explanation
Indices: 17242--17309 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
17232 AATATGTAAA
17242 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
17263 TCGCGTTGCGATTTTGCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
17284 TCACGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
17305 TCGCA
1 TCGCA
17310 ACACGAATCT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.37
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:17330 original size:20 final size:20
Alignment explanation
Indices: 17305--17353 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
17295 TTTTCCAAAT
17305 TCGCAACACGAATCTATAAA
1 TCGCAACACGAATCTATAAA
* * *
17325 TCGCAACGCGAATTTGTAAA
1 TCGCAACACGAATCTATAAA
17345 TCGCAACAC
1 TCGCAACAC
17354 ATACGTCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.39, C:0.27, G:0.14, T:0.20
Consensus pattern (20 bp):
TCGCAACACGAATCTATAAA
Found at i:17368 original size:20 final size:20
Alignment explanation
Indices: 17345--17551 Score: 301
Period size: 20 Copynumber: 10.3 Consensus size: 20
17335 AATTTGTAAA
* *
17345 TCGCAACACATACGTCAAAT
1 TCGCAACACAAAAGTCAAAT
17365 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
17385 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
17405 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
17425 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
17445 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
17465 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* * *
17485 TCGCAACGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* **
17505 TCGTAACACGAATTTGT-AAA-
1 TCGCAACAC-AA-AAGTCAAAT
*
17525 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
17545 TCGCAAC
1 TCGCAAC
17552 GCGGAATTTC
Statistics
Matches: 170, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
18 2 0.01
19 4 0.02
20 157 0.92
21 4 0.02
22 3 0.02
ACGTcount: A:0.45, C:0.25, G:0.12, T:0.17
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:17591 original size:60 final size:60
Alignment explanation
Indices: 17300--17591 Score: 270
Period size: 60 Copynumber: 4.9 Consensus size: 60
17290 TGCGATTTTC
* * * * * * *
17300 CAAATTCGCAACACGAATCT-ATAAATCGCAACGCGAATTTGTAAA-TCGCAACACATACGT
1 CAAATTCGCAACGCGAATGTCA-AATTCGCAACACGAATTT-CAAATTCGCAACACAAAAGT
* * * * **
17360 CAAATTCGCAACACAAAAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGCGAATGTCAAATTCGCAACACGAATTTCAAATTCGCAACACAAAAGT
* * * * **
17420 CAAATTCGCAACACAAAAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGCGAATGTCAAATTCGCAACACGAATTTCAAATTCGCAACACAAAAGT
* * *
17480 CAAATTCGCAACGCG-ATAGTCAAATTCGTAACACGAATTTGTAAA-TCGCAACACAGAAGT
1 CAAATTCGCAACGCGAAT-GTCAAATTCGCAACACGAATTT-CAAATTCGCAACACAAAAGT
* * * *
17540 CAAATTCGCAACGCGGAATTTCAAATTTGCAAC-TGAATTTCAAATTTGCAAC
1 CAAATTCGCAACGC-GAATGTCAAATTCGCAACACGAATTTCAAATTCGCAAC
17592 TAGATTTTTG
Statistics
Matches: 199, Mismatches: 26, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
59 7 0.04
60 174 0.87
61 16 0.08
62 2 0.01
ACGTcount: A:0.43, C:0.24, G:0.13, T:0.20
Consensus pattern (60 bp):
CAAATTCGCAACGCGAATGTCAAATTCGCAACACGAATTTCAAATTCGCAACACAAAAGT
Found at i:17598 original size:19 final size:19
Alignment explanation
Indices: 17555--17592 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
17545 TCGCAACGCG
17555 GAATTTCAAATTTGCAACT
1 GAATTTCAAATTTGCAACT
17574 GAATTTCAAATTTGCAACT
1 GAATTTCAAATTTGCAACT
17593 AGATTTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (19 bp):
GAATTTCAAATTTGCAACT
Found at i:18583 original size:24 final size:24
Alignment explanation
Indices: 18556--18609 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
18546 GTATTCGAAA
18556 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
18580 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
18604 TTTGAT
1 TTTGAT
18610 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:20892 original size:18 final size:18
Alignment explanation
Indices: 20869--20904 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
20859 AAACAAAAGG
*
20869 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
20887 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
20905 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:21311 original size:20 final size:21
Alignment explanation
Indices: 21286--21349 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 21
21276 TTAACACTTA
*
21286 TTTCGCATTGCAAATTTGA-T
1 TTTCGCATTGCAAATTTGACC
* *
21306 TTTCGCGTTGCGAATTT-ACC
1 TTTCGCATTGCAAATTTGACC
*
21326 TTTCGCATTACAAATTTGTACC
1 TTTCGCATTGCAAATTTG-ACC
21348 TT
1 TT
21350 CAACAGGTCT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 1 0.03
20 29 0.83
22 5 0.14
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.44
Consensus pattern (21 bp):
TTTCGCATTGCAAATTTGACC
Found at i:21482 original size:66 final size:65
Alignment explanation
Indices: 21400--21571 Score: 249
Period size: 66 Copynumber: 2.6 Consensus size: 65
21390 TTAAAACAAT
21400 AAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATTAAA
1 AAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATC-AATTAAA
21465 C
65 C
* *
21466 AAATCAACTTTTACAAATCAATTAAACAAGC-AAAAAATAATTCTTATTTCCTCATCAATTAAAC
1 AAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTAAAC
21530 AAATCAACTTTCAATGTA-AAATTCAATTAAACAAGCAAAAAA
1 AAATCAAC-TT---T-TACAAA-TCAATTAAACAAGCAAAAAA
21572 GTATACCCCA
Statistics
Matches: 97, Mismatches: 2, Indels: 10
0.89 0.02 0.09
Matches are distributed among these distances:
64 16 0.16
65 25 0.26
66 31 0.32
68 4 0.04
69 16 0.16
70 5 0.05
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.28
Consensus pattern (65 bp):
AAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTAAAC
Found at i:22943 original size:21 final size:21
Alignment explanation
Indices: 22919--23017 Score: 76
Period size: 21 Copynumber: 4.7 Consensus size: 21
22909 GCGGATGGGA
*
22919 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAACGATGAGAGGGG
* * * *
22940 CCTCTTGAAAGGTGGGATGGG
1 CCTCTTGAACGATGAGAGGGG
* * *
22961 CATCTTCG-ATGATGATAGGGG
1 CCTCTT-GAACGATGAGAGGGG
*
22982 CCTCTTGAACGAT-AGGAGGCG
1 CCTCTTGAACGATGA-GAGGGG
*
23003 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
23018 TAGATGCATC
Statistics
Matches: 58, Mismatches: 16, Indels: 7
0.72 0.20 0.09
Matches are distributed among these distances:
20 2 0.03
21 54 0.93
22 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.24
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:23015 original size:42 final size:42
Alignment explanation
Indices: 22911--23020 Score: 125
Period size: 42 Copynumber: 2.6 Consensus size: 42
22901 CTTGAACGGC
* * * *
22911 GGATGGGACCTCTTGAACGATGACAGGGGCCTCTTGAAAGGTG
1 GGATGGG-CCTCTTGAATGATGATAGGGGCCTCTTGAAAGATA
* *
22954 GGATGGGCATCTTCG-ATGATGATAGGGGCCTCTTGAACGATA
1 GGATGGGCCTCTT-GAATGATGATAGGGGCCTCTTGAAAGATA
22996 GGA-GGCGCCTCTTGAATGATGATAG
1 GGATGG-GCCTCTTGAATGATGATAG
23021 ATGCATCGGG
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
41 3 0.05
42 46 0.81
43 8 0.14
ACGTcount: A:0.24, C:0.17, G:0.35, T:0.24
Consensus pattern (42 bp):
GGATGGGCCTCTTGAATGATGATAGGGGCCTCTTGAAAGATA
Found at i:25620 original size:22 final size:22
Alignment explanation
Indices: 25565--25622 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
25555 GATGGAGATA
*
25565 GATGGATTTCGCCGGAGATGGG
1 GATGGATTTCGTCGGAGATGGG
*
25587 GACGGATTTCGTCGGAGATGGG
1 GATGGATTTCGTCGGAGATGGG
*
25609 GATGGATGTCGTCG
1 GATGGATTTCGTCG
25623 TAGAGAGTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.17, C:0.14, G:0.45, T:0.24
Consensus pattern (22 bp):
GATGGATTTCGTCGGAGATGGG
Found at i:25776 original size:20 final size:20
Alignment explanation
Indices: 25731--25877 Score: 156
Period size: 20 Copynumber: 7.3 Consensus size: 20
25721 TGTGTTTCGC
* *
25731 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTG-ACTTCTGT
*
25752 GTTGCGAATTTGACTTCTTT
1 GTTGCGAATTTGACTTCTGT
25772 GTTGCGAATTTGACTATC-GT
1 GTTGCGAATTTGACT-TCTGT
*
25792 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTCTGT
* *
25812 GTTGCGAATTTGACTTTTGG
1 GTTGCGAATTTGACTTCTGT
*
25832 GTTGC-AGATTTGACTATC-GC
1 GTTGCGA-ATTTGACT-TCTGT
*
25852 GTTTCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
*
25872 ATTGCG
1 GTTGCG
25878 GTTTACAAAT
Statistics
Matches: 108, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
19 4 0.04
20 88 0.81
21 16 0.15
ACGTcount: A:0.18, C:0.14, G:0.24, T:0.44
Consensus pattern (20 bp):
GTTGCGAATTTGACTTCTGT
Found at i:25817 original size:60 final size:60
Alignment explanation
Indices: 25727--25877 Score: 198
Period size: 60 Copynumber: 2.5 Consensus size: 60
25717 ATATTGTGTT
* * *
25727 TCGCGTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTTCTT-TGTTGC-GAATTTGACTA
1 TCGCGTTGCGAATTTG-ACTTCTGTGTTGCGAATTTGACTT-TTGGGTTGCAG-ATTTGACTA
* *
25788 TCGTGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTTTGGGTTGCAGATTTGACTA
1 TCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACTTTTGGGTTGCAGATTTGACTA
* *
25848 TCGCGTTTCGAATTTGACTTCTGTATTGCG
1 TCGCGTTGCGAATTTGACTTCTGTGTTGCG
25878 GTTTACAAAT
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
59 2 0.03
60 61 0.77
61 16 0.20
ACGTcount: A:0.18, C:0.15, G:0.25, T:0.43
Consensus pattern (60 bp):
TCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACTTTTGGGTTGCAGATTTGACTA
Found at i:25896 original size:60 final size:61
Alignment explanation
Indices: 25727--25905 Score: 161
Period size: 60 Copynumber: 3.0 Consensus size: 61
25717 ATATTGTGTT
* * * **
25727 TCGCGTTGCGAATTTGAAATTCAGTGTTGCGAATTTGAC-TTCTTTGTTGCG-AATTTGACTA
1 TCGCGTTGCGAATTTG-ACTTCTGTATTGCGAATTTGACATTC-GCGTTGCGAAATTTGACTA
* * * * * * *
25788 TCGTGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTTTGGGTTGC-AGATTTGACTA
1 TCGCGTTGCGAATTTGACTTCTGTATTGCGAATTTGACATTCGCGTTGCGAAATTTGACTA
* *
25848 TCGCGTTTCGAATTTGACTTCTGTATTGCG-GTTT-ACAAATTCGCGTTGCGAAATTTGA
1 TCGCGTTGCGAATTTGACTTCTGTATTGCGAATTTGAC--ATTCGCGTTGCGAAATTTGA
25906 AATTGGGTTG
Statistics
Matches: 96, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
58 2 0.02
59 3 0.03
60 67 0.70
61 24 0.25
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.42
Consensus pattern (61 bp):
TCGCGTTGCGAATTTGACTTCTGTATTGCGAATTTGACATTCGCGTTGCGAAATTTGACTA
Found at i:25915 original size:20 final size:20
Alignment explanation
Indices: 25892--25945 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
25882 ACAAATTCGC
*
25892 GTTGCGAAATTTGAAATTGG
1 GTTGCGAAATTGGAAATTGG
25912 GTTGCGAAATTGGAAATTGG
1 GTTGCGAAATTGGAAATTGG
25932 GTTGCGAAATTGGA
1 GTTGCGAAATTGGA
25946 GTTCGCGTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.30, C:0.06, G:0.33, T:0.31
Consensus pattern (20 bp):
GTTGCGAAATTGGAAATTGG
Found at i:25955 original size:20 final size:19
Alignment explanation
Indices: 25885--25959 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 19
25875 GCGGTTTACA
*
25885 AATTCGCGTTGCGAAATTTGA
1 AATT-GCGTTGCGAAA-TTGG
*
25906 AATTGGGTTGCGAAATTGG
1 AATTGCGTTGCGAAATTGG
*
25925 AAATTGGGTTGCGAAATTGG
1 -AATTGCGTTGCGAAATTGG
*
25945 AGTTCGCGTTGCGAA
1 AATT-GCGTTGCGAA
25960 TTTGTTGGTC
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
19 6 0.12
20 38 0.79
21 4 0.08
ACGTcount: A:0.27, C:0.11, G:0.32, T:0.31
Consensus pattern (19 bp):
AATTGCGTTGCGAAATTGG
Found at i:29276 original size:25 final size:25
Alignment explanation
Indices: 29248--29318 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 25
29238 GGAGGTTGTG
*
29248 ATTTGGGATTTAGAG-TTCGAGTATA
1 ATTTGGGATTTAG-GTTTAGAGTATA
* * *
29273 ATTTGAAGATTAAGGTTTAGGGTATA
1 ATTTG-GGATTTAGGTTTAGAGTATA
29299 ATTTGGGATTTAAGGTTTAG
1 ATTTGGGATTT-AGGTTTAG
29319 GTGTTTAGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
25 10 0.27
26 27 0.73
ACGTcount: A:0.30, C:0.01, G:0.28, T:0.41
Consensus pattern (25 bp):
ATTTGGGATTTAGGTTTAGAGTATA
Found at i:29297 original size:26 final size:26
Alignment explanation
Indices: 29268--29319 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
29258 TAGAGTTCGA
29268 GTATAATTTGAAGA-TTAAGGTTTAGG
1 GTATAATTTG-AGATTTAAGGTTTAGG
*
29294 GTATAATTTGGGATTTAAGGTTTAGG
1 GTATAATTTGAGATTTAAGGTTTAGG
29320 TGTTTAGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 2 0.08
26 22 0.92
ACGTcount: A:0.31, C:0.00, G:0.29, T:0.40
Consensus pattern (26 bp):
GTATAATTTGAGATTTAAGGTTTAGG
Found at i:32260 original size:43 final size:43
Alignment explanation
Indices: 32199--32305 Score: 205
Period size: 43 Copynumber: 2.5 Consensus size: 43
32189 TATTTTATAA
32199 AGCAAAAACATTCTGGAAAAATATATTTATTTATCGTTGTAAC
1 AGCAAAAACATTCTGGAAAAATATATTTATTTATCGTTGTAAC
32242 AGCAAAAACATTCTGGAAAAATATATTTATTTATCGTTGTAAC
1 AGCAAAAACATTCTGGAAAAATATATTTATTTATCGTTGTAAC
*
32285 AGCAAAAACATTCTGAAAAAA
1 AGCAAAAACATTCTGGAAAAA
32306 AAAACACATT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 63 1.00
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.31
Consensus pattern (43 bp):
AGCAAAAACATTCTGGAAAAATATATTTATTTATCGTTGTAAC
Found at i:32316 original size:19 final size:19
Alignment explanation
Indices: 32288--32343 Score: 89
Period size: 18 Copynumber: 3.0 Consensus size: 19
32278 TTGTAACAGC
32288 AAAA-ACATTCTGAAAAAA
1 AAAACACATTCTGAAAAAA
32306 AAAACACATTCTG-AAAAA
1 AAAACACATTCTGAAAAAA
32324 AAAACACATTCTGGAAAAAA
1 AAAACACATTCT-GAAAAAA
32344 CAAATTAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
18 21 0.60
19 9 0.26
20 5 0.14
ACGTcount: A:0.62, C:0.14, G:0.07, T:0.16
Consensus pattern (19 bp):
AAAACACATTCTGAAAAAA
Found at i:34264 original size:22 final size:22
Alignment explanation
Indices: 34239--34286 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
34229 ACAACACCAT
34239 CATACACCAAGTATGTCAATTA
1 CATACACCAAGTATGTCAATTA
*
34261 CATACATCAAGTATGTCAATTA
1 CATACACCAAGTATGTCAATTA
34283 CATA
1 CATA
34287 TATAGTGCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (22 bp):
CATACACCAAGTATGTCAATTA
Found at i:43948 original size:22 final size:22
Alignment explanation
Indices: 43922--44000 Score: 92
Period size: 23 Copynumber: 3.7 Consensus size: 22
43912 TTGGTGCAGA
*
43922 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTTGAAG
*
43944 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-TTGAAG
*
43967 GGGAACCGATTCCCCC-T--AG
1 GGGAACCGATACCCCCTTGAAG
*
43986 GGGAATCGATACCCC
1 GGGAACCGATACCCC
44001 ATTGGGGTTC
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
19 15 0.29
21 1 0.02
22 14 0.27
23 22 0.42
ACGTcount: A:0.24, C:0.32, G:0.27, T:0.18
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:43964 original size:23 final size:23
Alignment explanation
Indices: 43922--43983 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
43912 TTGGTGCAGA
* *
43922 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
43944 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
43967 GGGAACCGATTCCCCCT
1 GGGAACCGATTCCCCCT
43984 AGGGGAATCG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
22 14 0.38
23 23 0.62
ACGTcount: A:0.23, C:0.32, G:0.26, T:0.19
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:44007 original size:19 final size:19
Alignment explanation
Indices: 43965--44007 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
43955 CCCCCTTTGA
* *
43965 AGGGGAACCGATTCCCCCT
1 AGGGGAACCGATACCCCAT
*
43984 AGGGGAATCGATACCCCAT
1 AGGGGAACCGATACCCCAT
*
44003 TGGGG
1 AGGGG
44008 TTCTGGTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.28, G:0.33, T:0.16
Consensus pattern (19 bp):
AGGGGAACCGATACCCCAT
Found at i:52537 original size:23 final size:23
Alignment explanation
Indices: 52511--52557 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
52501 CATTTTGCCC
52511 TTAATGAAACTTAATATTTACCT
1 TTAATGAAACTTAATATTTACCT
52534 TTAATGAAACTTAATATTTACCT
1 TTAATGAAACTTAATATTTACCT
52557 T
1 T
52558 AATACCAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.45
Consensus pattern (23 bp):
TTAATGAAACTTAATATTTACCT
Found at i:61825 original size:13 final size:13
Alignment explanation
Indices: 61805--61842 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
61795 TTTTACCGGA
61805 TAAAAAACCGGTT
1 TAAAAAACCGGTT
*
61818 TGAAAAACC-G-T
1 TAAAAAACCGGTT
61829 TAAAAAACCGGTT
1 TAAAAAACCGGTT
61842 T
1 T
61843 TTATCCGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
11 9 0.43
12 2 0.10
13 10 0.48
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.24
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:64160 original size:21 final size:21
Alignment explanation
Indices: 64136--64175 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
64126 TTTATTTTAT
64136 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
64157 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
64176 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:64223 original size:33 final size:33
Alignment explanation
Indices: 64170--64268 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
64160 TTTGTTTCAA
64170 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
64202 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
64235 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
64268 T
1 T
64269 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:64297 original size:13 final size:13
Alignment explanation
Indices: 64254--64308 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
64244 TTGGAAGTAT
64254 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
64267 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
64281 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
64294 TTAAGTATTTGAA
1 TTAAGTATTTCAA
64307 TT
1 TT
64309 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:64712 original size:15 final size:15
Alignment explanation
Indices: 64692--64738 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
64682 ATTAAAATCA
*
64692 GTTTTTTTATAACCG
1 GTTTTTTTAAAACCG
*
64707 GTTTTTTAAAAAAACCG
1 GTTTTTT--TAAAACCG
64724 GTTTTTTTAAAACCG
1 GTTTTTTTAAAACCG
64739 AAACCGGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 14 0.52
17 13 0.48
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.45
Consensus pattern (15 bp):
GTTTTTTTAAAACCG
Found at i:64747 original size:21 final size:18
Alignment explanation
Indices: 64702--64735 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
64692 GTTTTTTTAT
64702 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
64719 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
64736 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:64855 original size:15 final size:17
Alignment explanation
Indices: 64829--64860 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
64819 TTCTATGAGA
64829 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
64845 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
64861 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Done.