Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005381.1 Hibiscus syriacus cultivar Beakdansim tig00012307_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: 351681
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 2
Found at i:111013 original size:19 final size:18
Alignment explanation
Indices: 110960--111018 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 18
110950 GCAACGAGAG
*
110960 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAA-CAA
* *
110979 AATCGCAACGCAAAACACA
1 AATCGCAATGCGAAACA-A
* *
110998 AATCGCAATACGAAACTA
1 AATCGCAATGCGAAACAA
111016 AAT
1 AAT
111019 TTGCATTGCG
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
18 5 0.16
19 27 0.84
ACGTcount: A:0.51, C:0.22, G:0.14, T:0.14
Consensus pattern (18 bp):
AATCGCAATGCGAAACAA
Found at i:111080 original size:19 final size:19
Alignment explanation
Indices: 111018--111070 Score: 97
Period size: 20 Copynumber: 2.7 Consensus size: 19
111008 CGAAACTAAA
111018 TTTGCATTGCGATTTTCAT
1 TTTGCATTGCGATTTTCAT
111037 TTTCGCATTGCGATTTTCAT
1 TTT-GCATTGCGATTTTCAT
111057 TTTGCATTGCGATT
1 TTTGCATTGCGATT
111071 CTCTCGTTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 14 0.42
20 19 0.58
ACGTcount: A:0.15, C:0.17, G:0.17, T:0.51
Consensus pattern (19 bp):
TTTGCATTGCGATTTTCAT
Found at i:111100 original size:20 final size:20
Alignment explanation
Indices: 111075--111160 Score: 70
Period size: 20 Copynumber: 4.3 Consensus size: 20
111065 GCGATTCTCT
111075 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
111095 CGTTGCGATAG-CCATTTCCG
1 CGTTGCGATAGTCAAATT-CG
* * *
111115 CATTACGATAGTC-ATTTC-
1 CGTTGCGATAGTCAAATTCG
*
111133 CTTGTTGCGATAGTCATATTCG
1 C--GTTGCGATAGTCAAATTCG
111155 CGTTGC
1 CGTTGC
111161 TATTTCCCCG
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
18 1 0.02
19 5 0.10
20 41 0.79
21 4 0.08
22 1 0.02
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:111648 original size:75 final size:73
Alignment explanation
Indices: 111481--111686 Score: 227
Period size: 75 Copynumber: 2.7 Consensus size: 73
111471 CAAAGTCAAA
* * * * *
111481 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCCAAAGGGGGTACCGA-TCACCCCTGAATGG
1 AATTCCAGAATACTCGGAGGGAACCGATT---CCCCATAGGGGGTACCGATTC-CCCCTGAATAG
111545 TTTGGCTCCGAG
62 TTTGGCTCCGAG
* * *
111557 ATTTCCAGAATGCTCGGAGGGAACTGATTCTCCCATAGGGGGTACCGATTCCCCCTTGAATAGTT
1 AATTCCAGAATACTCGGAGGGAACCGATTC-CCCATAGGGGGTACCGATTCCCCC-TGAATAGTT
*
111622 TGGCTCTGAG
64 TGGCTCCGAG
* *
111632 AATTCCAGTATACTCGGAGGGAACCGATTCCCC-TCCAAGGGGTACCGATTCCCCC
1 AATTCCAGAATACTCGGAGGGAACCGATTCCCCAT--AGGGGGTACCGATTCCCCC
111687 CTGTTTAACG
Statistics
Matches: 113, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
73 2 0.02
74 23 0.20
75 63 0.56
76 25 0.22
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.23
Consensus pattern (73 bp):
AATTCCAGAATACTCGGAGGGAACCGATTCCCCATAGGGGGTACCGATTCCCCCTGAATAGTTTG
GCTCCGAG
Found at i:115437 original size:170 final size:171
Alignment explanation
Indices: 115154--115488 Score: 663
Period size: 170 Copynumber: 2.0 Consensus size: 171
115144 GAAGGATTCT
115154 TGTGAATGATGATGTAGGTGTTATAAATACAAATGGCGTTAGATATGAAGTTGGGGAACCGTCAT
1 TGTGAATGATGATGTAGGTGTTATAAATACAAATGGCGTTAGATATGAAGTTGGGGAACCGTCAT
115219 CAAAGGAAGAAACGAAAAATGAGGAAACTCATGATCCTCTTGAGAATCCAACCATTGAAGAAAGG
66 CAAAGGAAGAAACGAAAAATGAGGAAACTCATGATCCTCTTGAGAATCCAACCATTGAAGAAAGG
115284 GAAGTATCTTATCCAAGAGAGTACACTATGTCAAGTTCTTG
131 GAAGTATCTTATCCAAGAGAGTACACTATGTCAAGTTCTTG
115325 TGTGAATGATGATGTAGGTGTTATAAATACAAATGGCGTTAGATATGAAGTT-GGGAACCGTCAT
1 TGTGAATGATGATGTAGGTGTTATAAATACAAATGGCGTTAGATATGAAGTTGGGGAACCGTCAT
115389 CAAAGGAAGAAACGAAAAATGAGGAAACTCATGATCCTCTTGAGAATCCAACCATTGAAGAAAGG
66 CAAAGGAAGAAACGAAAAATGAGGAAACTCATGATCCTCTTGAGAATCCAACCATTGAAGAAAGG
115454 GAAGTATCTTATCCAAGAGAGTACACTATGTCAAG
131 GAAGTATCTTATCCAAGAGAGTACACTATGTCAAG
115489 GGTGGTGAGA
Statistics
Matches: 164, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
170 112 0.68
171 52 0.32
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.24
Consensus pattern (171 bp):
TGTGAATGATGATGTAGGTGTTATAAATACAAATGGCGTTAGATATGAAGTTGGGGAACCGTCAT
CAAAGGAAGAAACGAAAAATGAGGAAACTCATGATCCTCTTGAGAATCCAACCATTGAAGAAAGG
GAAGTATCTTATCCAAGAGAGTACACTATGTCAAGTTCTTG
Found at i:117357 original size:20 final size:21
Alignment explanation
Indices: 117330--117434 Score: 81
Period size: 21 Copynumber: 5.0 Consensus size: 21
117320 CATTTTGGTG
117330 CAGAGGGAATCGATCCCCCC-
1 CAGAGGGAATCGATCCCCCCA
* * * *
117350 CTGAGGGAACCGATTCCCCCT
1 CAGAGGGAATCGATCCCCCCA
** *
117371 TTGAAGGGGAACCGATTCCCCCCA
1 CAG-A-GGGAATCGA-TCCCCCCA
117395 CAG-GGGAATCGATACCCCCCA
1 CAGAGGGAATCGAT-CCCCCCA
*
117416 CAG-GGGAATCGATACCCCC
1 CAGAGGGAATCGATCCCCCC
117435 TGGGGTTCTG
Statistics
Matches: 70, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
20 23 0.33
21 30 0.43
22 1 0.01
23 9 0.13
24 7 0.10
ACGTcount: A:0.25, C:0.37, G:0.25, T:0.13
Consensus pattern (21 bp):
CAGAGGGAATCGATCCCCCCA
Found at i:117401 original size:21 final size:21
Alignment explanation
Indices: 117375--117434 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
117365 CCCCCTTTGA
* *
117375 AGGGGAACCGATTCCCCCCAC
1 AGGGGAATCGATACCCCCCAC
117396 AGGGGAATCGATACCCCCCAC
1 AGGGGAATCGATACCCCCCAC
117417 AGGGGAATCGATACCCCC
1 AGGGGAATCGATACCCCC
117435 TGGGGTTCTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.27, C:0.38, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAATCGATACCCCCCAC
Found at i:120162 original size:75 final size:75
Alignment explanation
Indices: 120005--120212 Score: 287
Period size: 75 Copynumber: 2.8 Consensus size: 75
119995 CAAAGTCAAA
* *
120005 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCCAAAGGGGGTACCGA-TCCCCCCTGAATGG
1 AATTCCAGAATGCTCAGAGGGAACCGATT-CCCCCC-AAGGGGGTACCGATTCCCCCCTGAATAG
120069 TTTGGCTCCGAG
64 TTTGGCTCCGAG
* * * *
120081 ATTTCCAGAATGCTCGGAGGGAACCGATT-CTCCCATAGGGGGTACCGATTCCCCCTTGAATAGT
1 AATTCCAGAATGCTCAGAGGGAACCGATTCCCCCCA-AGGGGGTACCGATTCCCCCCTGAATAGT
120145 TTGGCTCCGAG
65 TTGGCTCCGAG
* * *
120156 AATTCCAGTATACTCAGAGGGAACCGATTCCCCCCAA-GGGGTACCAATTCCCCCCTG
1 AATTCCAGAATGCTCAGAGGGAACCGATTCCCCCCAAGGGGGTACCGATTCCCCCCTG
120213 TTTAACGGTC
Statistics
Matches: 116, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
73 1 0.01
74 34 0.29
75 50 0.43
76 31 0.27
ACGTcount: A:0.23, C:0.31, G:0.25, T:0.22
Consensus pattern (75 bp):
AATTCCAGAATGCTCAGAGGGAACCGATTCCCCCCAAGGGGGTACCGATTCCCCCCTGAATAGTT
TGGCTCCGAG
Found at i:120427 original size:45 final size:46
Alignment explanation
Indices: 120363--120455 Score: 179
Period size: 45 Copynumber: 2.0 Consensus size: 46
120353 GTATTTAAGC
120363 AAGCTTAGAAGCCATTGATCAAAAACAAG-AACATCAAGCAACTAG
1 AAGCTTAGAAGCCATTGATCAAAAACAAGAAACATCAAGCAACTAG
120408 AAGCTTAGAAGCCATTGATCAAAAACAAGAAACATCAAGCAACTAG
1 AAGCTTAGAAGCCATTGATCAAAAACAAGAAACATCAAGCAACTAG
120454 AA
1 AA
120456 TCAAGAGAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 29 0.62
46 18 0.38
ACGTcount: A:0.51, C:0.19, G:0.15, T:0.15
Consensus pattern (46 bp):
AAGCTTAGAAGCCATTGATCAAAAACAAGAAACATCAAGCAACTAG
Found at i:122418 original size:12 final size:12
Alignment explanation
Indices: 122401--122425 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
122391 TCTTCGGGGA
122401 CTTTTTCTTCTT
1 CTTTTTCTTCTT
122413 CTTTTTCTTCTT
1 CTTTTTCTTCTT
122425 C
1 C
122426 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:122634 original size:24 final size:24
Alignment explanation
Indices: 122600--122653 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
122590 CTGAAACATC
122600 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
122624 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
122648 ATCAAA
1 ATCAAA
122654 TTTTGAATAC
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:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:123415 original size:20 final size:20
Alignment explanation
Indices: 123390--123477 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
123380 GTATTATCTT
123390 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
123410 GTTGCGATAGGCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* *
123430 GTTGCGAAAGTCAGTATCGC
1 GTTGCGATAGTCAGAATCGC
* *
123450 GTTGCGAAAGTCAGTATCGC
1 GTTGCGATAGTCAGAATCGC
*
123470 ATTGCGAT
1 GTTGCGAT
123478 TTTCCAAATT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:123552 original size:20 final size:21
Alignment explanation
Indices: 123466--123559 Score: 145
Period size: 21 Copynumber: 4.5 Consensus size: 21
123456 AAAGTCAGTA
123466 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
123487 TCGCATTGCGATTTTTCAAAT
1 TCGCATTGCGATTTTCCAAAT
123508 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* **
123529 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCAAAT
123549 TCGCATTGCGA
1 TCGCATTGCGA
123560 ATTGGGAAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
20 17 0.25
21 51 0.75
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:123571 original size:42 final size:42
Alignment explanation
Indices: 123466--123571 Score: 106
Period size: 42 Copynumber: 2.5 Consensus size: 42
123456 AAAGTCAGTA
** * *
123466 TCGCATTGCGATTTTCCAAATTCGCATTGCGATTTTTCAAAT
1 TCGCATTGCGATTGGCAAAATTCGCATTGCGATTTTACAAAT
** * **
123508 TCGCATTGCGATTTTCCAAATTCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTGGCAAAATTCGCATTGCGATTTTACAAAT
*
123549 TCGCATTGCGAATTGGGAAAATT
1 TCGCATTGCG-ATTGGCAAAATT
123572 GCAACGCGAA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
41 16 0.29
42 40 0.71
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.39
Consensus pattern (42 bp):
TCGCATTGCGATTGGCAAAATTCGCATTGCGATTTTACAAAT
Found at i:124802 original size:2 final size:2
Alignment explanation
Indices: 124797--124847 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
124787 ATTAAAAATA
124797 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
124839 AT AT AT AT A
1 AT AT AT AT A
124848 ACCCAAACAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:128289 original size:2 final size:2
Alignment explanation
Indices: 128282--128323 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
128272 TAAATCTAAA
128282 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
128324 GTATTTACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:130181 original size:55 final size:55
Alignment explanation
Indices: 130113--130648 Score: 548
Period size: 55 Copynumber: 9.8 Consensus size: 55
130103 CAAATGACGA
* * *
130113 GTCCGCTCCCTATTCCTTCAG-GAAGTATA-AGACTCGAACAATCTTCATAAAATGT
1 GTCCGCTCTCTATTCCTTCAGAG-AGTATAGA-ACTCGAACAATCTTCATAAAACGG
** * *
130168 GTATGCTCTCTATTCATTCAGAGAGTATA-AGACTTGAACAATCTTCAATAAAACGG
1 GTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTC-ATAAAACGG
*
130224 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGGAA-AATCTTCA-ATAAACAG
1 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTC-GAACAATCTTCATA-AAACGG
* * * * * *
130279 GTCCGCTCCCTATTCTTTTAGAGAGTATAGGACT----CAATCTTTA-ACAAACGT
1 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGG
* *
130330 GTTCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATAAAACGG
1 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGG
**
130385 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAAACAT
1 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGG
* * *
130440 GTTCGCTCTCTATTCTTTCAGAGAGTATAGAACTCGAACAATCTTCATGAAACGG
1 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGG
* **
130495 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACGAACTT
1 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGG
* * * * * * * *
130550 GTCCGCTCCCTCTTTC-TCTAGGGAGTATGGAACTCAAACATATTCTTC-T--TACAG
1 GTCCGCTCTCTATTCCTTC-AGAGAGTATAGAACTCGAACA-A-TCTTCATAAAACGG
*
130604 GTTCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC-ATCTTC
1 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTC
130649 TTCTTACTGG
Statistics
Matches: 404, Mismatches: 58, Indels: 42
0.80 0.12 0.08
Matches are distributed among these distances:
51 46 0.11
52 1 0.00
54 35 0.09
55 267 0.66
56 46 0.11
57 9 0.02
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.30
Consensus pattern (55 bp):
GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGG
Found at i:130471 original size:110 final size:110
Alignment explanation
Indices: 130113--130648 Score: 605
Period size: 110 Copynumber: 4.9 Consensus size: 110
130103 CAAATGACGA
* * * **
130113 GTCCGCTCCCTATTCCTTCAG-GAAGTATA-AGACTCGAACAATCTTCATAAAATGTGTATGCTC
1 GTCCGCTCTCTATTCCTTCAGAG-AGTATAGA-ACTCGAACAATCTTCATAAAACGGGTCCGCTC
* * * *
130176 TCTATTCATTCAGAGAGTATA-AGACTTGAACAATCTTCAATAAAACGG
64 TCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAA-CAAACGT
*
130224 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGGAA-AATCTTCA-ATAAACAGGTCCGCTC
1 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTC-GAACAATCTTCATA-AAACGGGTCCGCTC
* * * * *
130287 CCTATTCTTTTAGAGAGTATAGGACT----CAATCTTTAACAAACGT
64 TCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGT
* *
130330 GTTCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATAAAACGGGTCCGCTCTC
1 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTC
*
130395 TATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACAT
66 TATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGT
* * *
130440 GTTCGCTCTCTATTCTTTCAGAGAGTATAGAACTCGAACAATCTTCATGAAACGGGTCCGCTCTC
1 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTC
* *
130505 TATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACGAACTT
66 TATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGT
* * * * * * * * *
130550 GTCCGCTCCCTCTTTC-TCTAGGGAGTATGGAACTCAAACATATTCTTC-T--TACAGGTTCGCT
1 GTCCGCTCTCTATTCCTTC-AGAGAGTATAGAACTCGAACA-A-TCTTCATAAAACGGGTCCGCT
130611 CTCTATTCCTTCAGAGAGTATAGAACTCGAAC-ATCTTC
63 CTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTC
130649 TTCTTACTGG
Statistics
Matches: 373, Mismatches: 38, Indels: 31
0.84 0.09 0.07
Matches are distributed among these distances:
105 2 0.01
106 82 0.22
107 10 0.03
108 6 0.02
109 43 0.12
110 150 0.40
111 70 0.19
112 10 0.03
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.30
Consensus pattern (110 bp):
GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTC
TATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGT
Found at i:130637 original size:54 final size:54
Alignment explanation
Indices: 130462--131030 Score: 782
Period size: 54 Copynumber: 10.5 Consensus size: 54
130452 TTCTTTCAGA
* *** * * * * *
130462 GAGTATAGAACTCGAACAATCTTCATGAAACGGGTCCGCTCTCTATTCCT-TCAGA
1 GAGTATAGAACTCGAAC-ATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCT-AGG
** ** ** *
130517 GAGTATAGAACTCGAACAATCTTCAACGAACTTGTCCGCTCCCTCTTTCTCTAGG
1 GAGTATAGAACTCGAAC-ATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
* * * * * * * *
130572 GAGTATGGAACTCAAACATATTCTTCTTACAGGTTCGCTCTCTATTCCT-TCAGA
1 GAGTATAGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCT-AGG
*
130626 GAGTATAGAACTCGAACATCTTCTTCTTACTGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATAGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
*
130680 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATAGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
* *
130734 GAGTATGGAACTCGAACATCTTCTTCTTAAGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATAGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
*
130788 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATAGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
* *
130842 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCACTCCCTCTTTCTCTAGG
1 GAGTATAGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
*
130896 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATAGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
130950 GAGTATAGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATAGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
* *
131004 GAGTATGGAACTCGAACATTTTCTTCT
1 GAGTATAGAACTCGAACATCTTCTTCT
131031 GCTTTACTAC
Statistics
Matches: 471, Mismatches: 40, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
53 1 0.00
54 409 0.87
55 60 0.13
56 1 0.00
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (54 bp):
GAGTATAGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
Found at i:130691 original size:108 final size:108
Alignment explanation
Indices: 130381--131030 Score: 806
Period size: 108 Copynumber: 6.0 Consensus size: 108
130371 TCTTCATAAA
* * ** ** **
130381 ACGGGTCCGCTCTCTATTCCT-TCAGAGAGTATAGAACTCGAACAATCTTCAACAAACATGTTCG
1 ACGGGTTCGCTCCCTATTCCTCT-AGAGAGTATAGAACTCGAAC-ATCTTCTTCTTACGGGTTCG
* * * * ***
130445 CT--CTCTATTCTTTCAGAGAGTATAGAACTCGAACAATCTTCATGAA
64 CTCCCTCT-TTCTCT-AGGGAGTATGGAACTCGAAC-ATCTTCTTCTT
* * ** ** ** *
130491 ACGGGTCCGCTCTCTATTCCT-TCAGAGAGTATAGAACTCGAACAATCTTCAACGAACTTGTCCG
1 ACGGGTTCGCTCCCTATTCCTCT-AGAGAGTATAGAACTCGAAC-ATCTTCTTCTTACGGGTTCG
* *
130555 CTCCCTCTTTCTCTAGGGAGTATGGAACTCAAACATATTCTTCTT
64 CTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCTT
* * *
130600 ACAGGTTCGCTCTCTATTCCT-TCAGAGAGTATAGAACTCGAACATCTTCTTCTTACTGGTTCGC
1 ACGGGTTCGCTCCCTATTCCTCT-AGAGAGTATAGAACTCGAACATCTTCTTCTTACGGGTTCGC
130664 TCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCTT
65 TCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCTT
* * * * *
130708 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCTTAAGGGTTCGCT
1 ACGGGTTCGCTCCCTATTCCTCTAGAGAGTATAGAACTCGAACATCTTCTTCTTACGGGTTCGCT
130773 CCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCTT
66 CCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCTT
* * * * *
130816 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCACT
1 ACGGGTTCGCTCCCTATTCCTCTAGAGAGTATAGAACTCGAACATCTTCTTCTTACGGGTTCGCT
130881 CCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCTT
66 CCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCTT
* * *
130924 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTTCTTACGGGTTCGCT
1 ACGGGTTCGCTCCCTATTCCTCTAGAGAGTATAGAACTCGAACATCTTCTTCTTACGGGTTCGCT
*
130989 CCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCT
66 CCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCT
131031 GCTTTACTAC
Statistics
Matches: 502, Mismatches: 35, Indels: 8
0.92 0.06 0.01
Matches are distributed among these distances:
108 365 0.73
109 48 0.10
110 80 0.16
111 5 0.01
112 4 0.01
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.34
Consensus pattern (108 bp):
ACGGGTTCGCTCCCTATTCCTCTAGAGAGTATAGAACTCGAACATCTTCTTCTTACGGGTTCGCT
CCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCTT
Found at i:131103 original size:37 final size:37
Alignment explanation
Indices: 131030--131109 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 37
131020 CATTTTCTTC
* * * *
131030 TGCTTTACTACTTTCTTGTGAAGACTTCTAGATGATT
1 TGCTTCACTACTCTCTCGTGAAGACTTCAAGATGATT
*
131067 TGCTTCACTACTCTCTCGTGAAGACTT-AAGTTTGATT
1 TGCTTCACTACTCTCTCGTGAAGACTTCAAG-ATGATT
131104 TGCTTC
1 TGCTTC
131110 GAAGGTCGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 2 0.05
37 35 0.95
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.44
Consensus pattern (37 bp):
TGCTTCACTACTCTCTCGTGAAGACTTCAAGATGATT
Found at i:131373 original size:37 final size:37
Alignment explanation
Indices: 131322--131446 Score: 135
Period size: 37 Copynumber: 3.4 Consensus size: 37
131312 TTGCTCAAAC
* * * *
131322 ACTCTTCCGAGAAGGCTTAAAAAGGATATGCTTCACT
1 ACTCTTCGGTGAAGGCTTAAAATGGATTTGCTTCACT
***
131359 ACTCTTCGGTGAAGGCTTAGCTTTGG-TTTGCTTCACT
1 ACTCTTCGGTGAAGGCTTA-AAATGGATTTGCTTCACT
** *
131396 ACTCTTTAGTGAAGGCTCAAAATGGATTTGCTTCACT
1 ACTCTTCGGTGAAGGCTTAAAATGGATTTGCTTCACT
*
131433 ACTCTTTGGTGAAG
1 ACTCTTCGGTGAAG
131447 ACTTGGCTTT
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
36 3 0.04
37 67 0.93
38 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (37 bp):
ACTCTTCGGTGAAGGCTTAAAATGGATTTGCTTCACT
Found at i:136330 original size:72 final size:72
Alignment explanation
Indices: 136213--136363 Score: 257
Period size: 72 Copynumber: 2.1 Consensus size: 72
136203 CCCCTAACAG
*
136213 GTTCTTGATCAGTTGCTATCATCACTTTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
1 GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
*
136278 TTCATCT
66 TTCATAT
* *
136285 GTTCTTGATCATTTGCTATCATCACATTGGTTGCACCACTAACATTCAGATTCTCACCCGAAGTC
1 GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
136350 TTCATAT
66 TTCATAT
*
136357 TTTCTTG
1 GTTCTTG
136364 TATAATAGGG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.37
Consensus pattern (72 bp):
GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
TTCATAT
Found at i:137118 original size:55 final size:55
Alignment explanation
Indices: 137024--137154 Score: 181
Period size: 55 Copynumber: 2.4 Consensus size: 55
137014 AACATCTTTA
* ** * *
137024 GGATGTCTTTCTTTGTGGATCGGTCTTCAATCAGTTTCAAATATCTTCATTCATC
1 GGATGTCATTCTTCATGAATCGGTCTTCAATCAGGTTCAAATATCTTCATTCATC
* * *
137079 GGATGTCATTCTTCATGAATCGTTCTTCAGTCAGGTTCAAATTTCTTCATTCATC
1 GGATGTCATTCTTCATGAATCGGTCTTCAATCAGGTTCAAATATCTTCATTCATC
*
137134 GGATGCCATTCTTCATGAATC
1 GGATGTCATTCTTCATGAATC
137155 ATCTGAACGC
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 67 1.00
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.41
Consensus pattern (55 bp):
GGATGTCATTCTTCATGAATCGGTCTTCAATCAGGTTCAAATATCTTCATTCATC
Found at i:137559 original size:46 final size:45
Alignment explanation
Indices: 137472--137559 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 45
137462 TGCAAAAAAT
*
137472 CCTAACCGCATGATATCTAATTCGCATGCTTGTTCGAGAAAATAAA
1 CCTAACCGCATGATATCTAATTCGCATGCTTATTC-AGAAAATAAA
*
137518 CCTAACCGCATGATATCTAGTTCGCATGCATTTATTC-GAAAA
1 CCTAACCGCATGATATCTAATTCGCATGC--TTATTCAGAAAA
137560 ATGAAAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
46 33 0.87
48 5 0.13
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.30
Consensus pattern (45 bp):
CCTAACCGCATGATATCTAATTCGCATGCTTATTCAGAAAATAAA
Found at i:164742 original size:25 final size:25
Alignment explanation
Indices: 164708--164757 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
164698 ATAAGCTAAT
164708 TGCATCAAAGCCAAAAGAGAAAGAG
1 TGCATCAAAGCCAAAAGAGAAAGAG
164733 TGCATCAAAGCCAAAAGAGAAAGAG
1 TGCATCAAAGCCAAAAGAGAAAGAG
164758 CCCGTTACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.16, G:0.24, T:0.08
Consensus pattern (25 bp):
TGCATCAAAGCCAAAAGAGAAAGAG
Found at i:165568 original size:18 final size:19
Alignment explanation
Indices: 165545--165584 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
165535 CAAAATAGGT
165545 ATTTAAATTTACAA-ATAA
1 ATTTAAATTTACAATATAA
* *
165563 ATTTAATTTTATAATATAA
1 ATTTAAATTTACAATATAA
165582 ATT
1 ATT
165585 GATTCAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTAAATTTACAATATAA
Found at i:165859 original size:18 final size:19
Alignment explanation
Indices: 165824--165860 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
165814 CACGGAATGT
165824 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
165844 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
165861 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:167016 original size:13 final size:13
Alignment explanation
Indices: 166998--167032 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
166988 ACATGAGATA
166998 AGTGCTCAAGGCT
1 AGTGCTCAAGGCT
167011 AGTGCTCAAGGCT
1 AGTGCTCAAGGCT
*
167024 AATGCTCAA
1 AGTGCTCAA
167033 TATGAATGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.23
Consensus pattern (13 bp):
AGTGCTCAAGGCT
Found at i:172362 original size:21 final size:21
Alignment explanation
Indices: 172338--172380 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
172328 TCCCCTCCTT
172338 AGCTAACTTGTCCGCCTCCCA
1 AGCTAACTTGTCCGCCTCCCA
172359 AGCTAACTTGTCCGCCTCCCA
1 AGCTAACTTGTCCGCCTCCCA
172380 A
1 A
172381 TTACAAGCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.42, G:0.14, T:0.23
Consensus pattern (21 bp):
AGCTAACTTGTCCGCCTCCCA
Found at i:184367 original size:336 final size:337
Alignment explanation
Indices: 183754--184427 Score: 1341
Period size: 336 Copynumber: 2.0 Consensus size: 337
183744 GAGAAAACAG
183754 AAATGTTTGGTTTTTTATACGTCGGATTGTGATAATGGGGGTAATGTTTGGATGGAAAGAACAGG
1 AAATGTTTGGTTTTTTATACGTCGGATTGTGATAATGGGGGTAATGTTTGGATGGAAAGAACAGG
183819 CCTGTTCATGGCATTGCAACCAAGGATCATAGCATGTGGGAATTCCGTTGCAGCTTTTGCGATGG
66 CCTGTTCATGGCATTGCAACCAAGGATCATAGCATGTGGGAATTCCGTTGCAGCTTTTGCGATGG
183884 CCGTGAGATTCCTTACAGGTCCAGCTGTCATGGCAGCCGCTTCCATTGCTGTTGGCCTTCGTGGC
131 CCGTGAGATTCCTTACAGGTCCAGCTGTCATGGCAGCCGCTTCCATTGCTGTTGGCCTTCGTGGC
183949 GTCCTCTTACGCGTTGCCATTGTCCAGGTCACTCCCACAACTGCATGCATAAATTTATTATCAAG
196 GTCCTCTTACGCGTTGCCATTGTCCAGGTCACTCCCACAACTGCATGCATAAATTTATTATCAAG
184014 ATAATGTTAGTTTACTAAAAACTCCAGAACATTAAATAAACAATTGTAAAATGTGACCAATTAA-
261 ATAATGTTAGTTTACTAAAAACTCCAGAACATTAAATAAACAATTGTAAAATGTGACCAATTAAT
184078 TAATCAAAGAAA
326 TAATCAAAGAAA
184090 AAATGTTTGGTTTTTTATACGTCGGATTGTGATAATGGGGGTAATGTTTGGATGGAAAGAACAGG
1 AAATGTTTGGTTTTTTATACGTCGGATTGTGATAATGGGGGTAATGTTTGGATGGAAAGAACAGG
184155 CCTGTTCATGGCATTGCAACCAAGGATCATAGCATGTGGGAATTCCGTTGCAGCTTTTGCGATGG
66 CCTGTTCATGGCATTGCAACCAAGGATCATAGCATGTGGGAATTCCGTTGCAGCTTTTGCGATGG
184220 CCGTGAGATTCCTTACAGGTCCAGCTGTCATGGCAGCCGCTTCCATTGCTGTTGGCCTTCGTGGC
131 CCGTGAGATTCCTTACAGGTCCAGCTGTCATGGCAGCCGCTTCCATTGCTGTTGGCCTTCGTGGC
184285 GTCCTCTTACGCGTTGCCATTGTCCAGGTCACTCCCACAACTGCATGCATAAATTTATTATCAAG
196 GTCCTCTTACGCGTTGCCATTGTCCAGGTCACTCCCACAACTGCATGCATAAATTTATTATCAAG
184350 ATAATGTTAGTTTACTAAAAACTCCAGAACATTAAATAAACAATTGTAAAATGTGACCAATTAAT
261 ATAATGTTAGTTTACTAAAAACTCCAGAACATTAAATAAACAATTGTAAAATGTGACCAATTAAT
184415 TAATCAAAGAAA
326 TAATCAAAGAAA
184427 A
1 A
184428 TTAATGGAGT
Statistics
Matches: 337, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
336 324 0.96
337 13 0.04
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.30
Consensus pattern (337 bp):
AAATGTTTGGTTTTTTATACGTCGGATTGTGATAATGGGGGTAATGTTTGGATGGAAAGAACAGG
CCTGTTCATGGCATTGCAACCAAGGATCATAGCATGTGGGAATTCCGTTGCAGCTTTTGCGATGG
CCGTGAGATTCCTTACAGGTCCAGCTGTCATGGCAGCCGCTTCCATTGCTGTTGGCCTTCGTGGC
GTCCTCTTACGCGTTGCCATTGTCCAGGTCACTCCCACAACTGCATGCATAAATTTATTATCAAG
ATAATGTTAGTTTACTAAAAACTCCAGAACATTAAATAAACAATTGTAAAATGTGACCAATTAAT
TAATCAAAGAAA
Found at i:186387 original size:12 final size:12
Alignment explanation
Indices: 186357--186414 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
186347 TGGCATGGAG
*
186357 GAAGAGGATGAA
1 GAAGAGAATGAA
*
186369 GACGAGAATGAA
1 GAAGAGAATGAA
* **
186381 TAAGAGAATTTA
1 GAAGAGAATGAA
186393 GAAGAGAATGAA
1 GAAGAGAATGAA
*
186405 GAAGAAAATG
1 GAAGAGAATG
186415 TAGTAGGGGG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.53, C:0.02, G:0.31, T:0.14
Consensus pattern (12 bp):
GAAGAGAATGAA
Found at i:187085 original size:77 final size:77
Alignment explanation
Indices: 186992--187145 Score: 308
Period size: 77 Copynumber: 2.0 Consensus size: 77
186982 AAGTCTATCT
186992 TTTCATTATGGTCTTACTTCTATGTCTTACTTGCCCGACAGAGTTTACTAAAGGTGCCCTATGCT
1 TTTCATTATGGTCTTACTTCTATGTCTTACTTGCCCGACAGAGTTTACTAAAGGTGCCCTATGCT
187057 ATATCTAGTTAA
66 ATATCTAGTTAA
187069 TTTCATTATGGTCTTACTTCTATGTCTTACTTGCCCGACAGAGTTTACTAAAGGTGCCCTATGCT
1 TTTCATTATGGTCTTACTTCTATGTCTTACTTGCCCGACAGAGTTTACTAAAGGTGCCCTATGCT
187134 ATATCTAGTTAA
66 ATATCTAGTTAA
187146 GGGACTCGAC
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (77 bp):
TTTCATTATGGTCTTACTTCTATGTCTTACTTGCCCGACAGAGTTTACTAAAGGTGCCCTATGCT
ATATCTAGTTAA
Found at i:188347 original size:20 final size:20
Alignment explanation
Indices: 188318--188355 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
188308 TTTCCACCAT
*
188318 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
188338 ATGCATCTATATGATCCT
1 ATGCAACTATATGATCCT
188356 TTATTAGCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:192492 original size:9 final size:9
Alignment explanation
Indices: 192478--192502 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
192468 GGTCTTTACT
192478 TTTAATAAA
1 TTTAATAAA
192487 TTTAATAAA
1 TTTAATAAA
192496 TTTAATA
1 TTTAATA
192503 TTTAATCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTTAATAAA
Found at i:193398 original size:2 final size:2
Alignment explanation
Indices: 193386--193419 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
193376 TAATATGATA
193386 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
193420 CACACACACA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:194189 original size:593 final size:572
Alignment explanation
Indices: 192433--194165 Score: 2962
Period size: 594 Copynumber: 3.0 Consensus size: 572
192423 ATAATTATAC
* *
192433 ATTTAGTCTTCATTACTTGCACATTCTATTAATTTGGTCTTTACTTTTAATAAATTTAATAAATT
1 ATTTAGTCTTCATTACTTGCACATTTTATTAATTTGGTCTTTACTTTTAATTAATTTAATAAATT
* * *
192498 TAATATTTAATCAGATTGTGACATGTGTCACTATGAGATTGGATTTTTTCTTAATATTTTTGTTT
66 TAATCTTTAATCAGATTGTGACATGTGTCACCATGGGATTGGATTTTTTCTTAATATTTTTGTTT
*
192563 AATTTAATAAATTTTTCATCCAACTAAATAGTGTCGCGTGTCTCCAAATAAATGAATAAAAAATA
131 AATTTAATAAATTTTTCATCCAACCAAATAGTGTCGCGTGTCTCCAAATAAATGAATAAAAAATA
*
192628 AATTGAATCAATAACTACTGTTGGTGGGATTTGAACCCAAAACATGAGTAAAGGGAGCAA-A---
196 AATTGAATCAATAACTACTGTTGGTGGGATTTGAACCCAAAACATGAGTAGAGGGAGCAACACCC
192689 C-ACCACTTGCCTACACTATTCAAATGACAAACTTATCACAACATAATATATATAGTTAATGACA
261 CAACCACTTGCCTACACTATTCAAATGACAAACTTATCACAACATAATATATATAGTTAATGACA
192753 ATAAAAAAGGGACAATGACCTAATAAGAACTCCAACAAGAAATAATTGAATAATATGATAATATG
326 ATAAAAAAGGGACAATGACCTAATAAGAACTCCAACAAGAAATAATTGAATAATATGATAATATG
192818 ATATATATATATATATACAA-ATATTATGACTGATTAGTATGTGAATGTATTTTATTTATATTTT
391 ATATATATATATATATACAATATATTATGACTGATTAGTATGTGAATGTATTTTATTTATATTTT
*
192882 AAATCATTTTGATAAAAAATAAAAATGATTTTAATATAATATAATTGAAATATAACGAAAAACTT
456 AAATCATTTTAATAAAAAATAAAAATGATTTTAATATAATATAATTGAAATATAACGAAAAACTT
*
192947 TGTTGACTTAAAATTTTCCTGTTAGTTGATGGCTTATCATAGTAAAGATTTT
521 CGTTGACTTAAAATTTTCCTGTTAGTTGATGGCTTATCATAGTAAAGATTTT
192999 ATTTAGTCTTCATTACTTGCACATTTTATTAATTTGGTCTTTACTTTTAATTAATTTAATAAATT
1 ATTTAGTCTTCATTACTTGCACATTTTATTAATTTGGTCTTTACTTTTAATTAATTTAATAAATT
*
193064 TAATCTTTAATCAGATTGTGACATGTGTCACCATGGGATTAGA-TTTTTCTTAATATTTTTGTTT
66 TAATCTTTAATCAGATTGTGACATGTGTCACCATGGGATTGGATTTTTTCTTAATATTTTTGTTT
193128 AATTTAATAAATTTTTCATCCAACCAAATAGTGTCGCGTGTCTCCAAATAAATGAATAAAAAATA
131 AATTTAATAAATTTTTCATCCAACCAAATAGTGTCGCGTGTCTCCAAATAAATGAATAAAAAATA
193193 AATTGAATCAATAACACTACTGTTGGTGGGATTTGAACCCAAAACATGAGTAGAGGGAGCAAACA
196 AATTGAATCAAT-A-ACTACTGTTGGTGGGATTTGAACCCAAAACATGAGTAGAGGGAGC-AACA
193258 CCCCAACCACTTGCCTACACTATTCAAATGACAAACTTATCACAACATAATATATATAGTTAATG
258 CCCCAACCACTTGCCTACACTATTCAAATGACAAACTTATCACAACATAATATATATAGTTAATG
* *
193323 ACAATAAAAAAGGGACAACGACCTAATAAGAACTCCAACATGAAATAATTGAATAATATGATAAT
323 ACAATAAAAAAGGGACAATGACCTAATAAGAACTCCAACAAGAAATAATTGAATAATATGATAAT
*
193388 ATGATATATATATATATATATATATATATATACACACACACAAAATATTATGACTGATTAGTATG
388 ATG------------ATATATATATATATAT--------ACAATATATTATGACTGATTAGTATG
* * *
193453 TGAATTTATTTTATTTATATTTTAAATTATTGTAATAAAAAATAAAAATGATTTTAATATAATAT
433 TGAATGTATTTTATTTATATTTTAAATCATTTTAATAAAAAATAAAAATGATTTTAATATAATAT
193518 AATTGAAATATAACGAAAAACTTCGTTGACTTAAAATTTTCCTGTTAGTTGATGGCTTATCATAG
498 AATTGAAATATAACGAAAAACTTCGTTGACTTAAAATTTTCCTGTTAGTTGATGGCTTATCATAG
193583 TAAAGATTTT
563 TAAAGATTTT
193593 ATTTAGTCTTCATTACTTGCACATTTTATTAATTTGGTCTTTACTTTTAATTAATTTAATAAATT
1 ATTTAGTCTTCATTACTTGCACATTTTATTAATTTGGTCTTTACTTTTAATTAATTTAATAAATT
193658 TAATCTTTAATCAGATTGTGACATGTGTCACCATGGGATTGGATTTTTTCTTAATATTTTTGTTT
66 TAATCTTTAATCAGATTGTGACATGTGTCACCATGGGATTGGATTTTTTCTTAATATTTTTGTTT
* * *
193723 AATTTAATAAATTTTTTATCTAACCAAATAGAGTCGCGTGTCTCCAAATAAATGAATAAAAAATA
131 AATTTAATAAATTTTTCATCCAACCAAATAGTGTCGCGTGTCTCCAAATAAATGAATAAAAAATA
*
193788 AATTAAATCAATAACTACTGTTGGTGGGATTTGAACCCAAAACATGAGTAGAGGGAGCAAGCACC
196 AATTGAATCAATAACTACTGTTGGTGGGATTTGAACCCAAAACATGAGTAGAGGGAGCAA-CACC
193853 CCAACCACTTGCCTACACTATTCAAATGACAAACTTATCACAACATAATATATATAGTTAATGAC
260 CCAACCACTTGCCTACACTATTCAAATGACAAACTTATCACAACATAATATATATAGTTAATGAC
193918 AATAAAAAAGGGACAATGACCTAATAAGAACTCCAACAAGAAATAATTGAATAATATGATAATAT
325 AATAAAAAAGGGACAATGACCTAATAAGAACTCCAACAAGAAATAATTGAATAATATGATAATAT
193983 GATATATATATATATATA-AATATATTATGACTGATTAGTATGTGAATGTATTTTATTTATATTT
390 GATATATATATATATATACAATATATTATGACTGATTAGTATGTGAATGTATTTTATTTATATTT
*
194047 TAAATCATTTTAATAAAAAATAAAAATGATTTTAATATATTATAATTGAAATATAACGAAAAGA-
455 TAAATCATTTTAATAAAAAATAAAAATGATTTTAATATAATATAATTGAAATATAACGAAAA-AC
* * *
194111 TTCGTTGACTTAAAATTTTCCTGATAGTTGATGACTTATCGTAGTAAAGATTTT
519 TTCGTTGACTTAAAATTTTCCTGTTAGTTGATGGCTTATCATAGTAAAGATTTT
194165 A
1 A
194166 ACTTGTGCAT
Statistics
Matches: 1105, Mismatches: 30, Indels: 58
0.93 0.03 0.05
Matches are distributed among these distances:
565 97 0.09
566 103 0.09
567 44 0.04
568 2 0.00
569 1 0.00
572 156 0.14
573 128 0.12
581 16 0.01
585 16 0.01
592 2 0.00
593 182 0.16
594 264 0.24
595 94 0.09
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (572 bp):
ATTTAGTCTTCATTACTTGCACATTTTATTAATTTGGTCTTTACTTTTAATTAATTTAATAAATT
TAATCTTTAATCAGATTGTGACATGTGTCACCATGGGATTGGATTTTTTCTTAATATTTTTGTTT
AATTTAATAAATTTTTCATCCAACCAAATAGTGTCGCGTGTCTCCAAATAAATGAATAAAAAATA
AATTGAATCAATAACTACTGTTGGTGGGATTTGAACCCAAAACATGAGTAGAGGGAGCAACACCC
CAACCACTTGCCTACACTATTCAAATGACAAACTTATCACAACATAATATATATAGTTAATGACA
ATAAAAAAGGGACAATGACCTAATAAGAACTCCAACAAGAAATAATTGAATAATATGATAATATG
ATATATATATATATATACAATATATTATGACTGATTAGTATGTGAATGTATTTTATTTATATTTT
AAATCATTTTAATAAAAAATAAAAATGATTTTAATATAATATAATTGAAATATAACGAAAAACTT
CGTTGACTTAAAATTTTCCTGTTAGTTGATGGCTTATCATAGTAAAGATTTT
Found at i:194796 original size:14 final size:14
Alignment explanation
Indices: 194777--194806 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
194767 CATTTGATTG
*
194777 AATAAAAATTATTA
1 AATAAAAAATATTA
194791 AATAAAAAATATTA
1 AATAAAAAATATTA
194805 AA
1 AA
194807 AAATCCAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AATAAAAAATATTA
Found at i:208210 original size:8 final size:7
Alignment explanation
Indices: 208186--208227 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
208176 TTTTCATACA
208186 TGCA-TT
1 TGCATTT
208192 TGCATTT
1 TGCATTT
208199 TGCATCTT
1 TGCAT-TT
208207 TGCATTT
1 TGCATTT
* *
208214 TTCATTG
1 TGCATTT
208221 TGCATTT
1 TGCATTT
208228 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:208210 original size:15 final size:14
Alignment explanation
Indices: 208186--208227 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
208176 TTTTCATACA
208186 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
208199 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
208214 TTCATTGTGCATTT
1 TGCATTTTGCATTT
208228 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:208316 original size:26 final size:26
Alignment explanation
Indices: 208287--208345 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
208277 CATTCACATA
*
208287 TTTACATTTGAATTTGCATTTGCATT
1 TTTACATTTGAATTTACATTTGCATT
* * *
208313 TTTACGTTTGTATTTACATTTTCATT
1 TTTACATTTGAATTTACATTTGCATT
208339 TTTACAT
1 TTTACAT
208346 AATTACATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.12, G:0.08, T:0.58
Consensus pattern (26 bp):
TTTACATTTGAATTTACATTTGCATT
Found at i:210319 original size:19 final size:19
Alignment explanation
Indices: 210281--210319 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
210271 TATTATACTC
*
210281 ATCCAGCAAAGAAAATAAA
1 ATCCAGCAAAGAAAAGAAA
*
210300 ATCCAGCAAAGAAAGGAAA
1 ATCCAGCAAAGAAAAGAAA
210319 A
1 A
210320 AAGAAAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.62, C:0.15, G:0.15, T:0.08
Consensus pattern (19 bp):
ATCCAGCAAAGAAAAGAAA
Found at i:210327 original size:7 final size:7
Alignment explanation
Indices: 210315--210388 Score: 62
Period size: 7 Copynumber: 10.0 Consensus size: 7
210305 GCAAAGAAAG
210315 GAAAAAA
1 GAAAAAA
210322 GAAAAAAGA
1 G-AAAAA-A
210331 GGAAAAAA
1 -GAAAAAA
210339 GAAAAAA
1 GAAAAAA
*
210346 -AAGGAAA
1 GAA-AAAA
210353 GAAATAGAA
1 GAAA-A-AA
*
210362 AAAAAAA
1 GAAAAAA
210369 GAAAAAA
1 GAAAAAA
210376 G-AAAAA
1 GAAAAAA
210382 GAAAAAA
1 GAAAAAA
210389 AATTAAATCA
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
6 8 0.15
7 25 0.45
8 10 0.18
9 11 0.20
10 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (7 bp):
GAAAAAA
Found at i:210335 original size:17 final size:17
Alignment explanation
Indices: 210311--210381 Score: 97
Period size: 17 Copynumber: 4.0 Consensus size: 17
210301 TCCAGCAAAG
210311 AAAGGAAAAAAGAAAAA
1 AAAGGAAAAAAGAAAAA
*
210328 AGAGGAAAAAAGAAAAA
1 AAAGGAAAAAAGAAAAA
210345 AAAGGAAAGAAATAGAAAAA
1 AAAGG-AA-AAA-AGAAAAA
*
210365 AAAAGAAAAAAGAAAAA
1 AAAGGAAAAAAGAAAAA
210382 GAAAAAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
17 27 0.56
18 5 0.10
19 5 0.10
20 11 0.23
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.01
Consensus pattern (17 bp):
AAAGGAAAAAAGAAAAA
Found at i:210337 original size:10 final size:9
Alignment explanation
Indices: 210316--210381 Score: 57
Period size: 9 Copynumber: 7.3 Consensus size: 9
210306 CAAAGAAAGG
210316 AAAAA-AGA
1 AAAAAGAGA
210324 AAAAAGAGGA
1 AAAAAGA-GA
*
210334 AAAAAGAAA
1 AAAAAGAGA
210343 AAAAAG-GA
1 AAAAAGAGA
*
210351 AAGAAATAGAA
1 AA-AAAGAG-A
*
210362 AAAAAAAGA
1 AAAAAGAGA
210371 AAAAAGA-A
1 AAAAAGAGA
210379 AAA
1 AAA
210382 GAAAAAAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
8 12 0.25
9 18 0.38
10 15 0.31
11 3 0.06
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.02
Consensus pattern (9 bp):
AAAAAGAGA
Found at i:210366 original size:23 final size:23
Alignment explanation
Indices: 210307--210390 Score: 82
Period size: 23 Copynumber: 3.5 Consensus size: 23
210297 AAAATCCAGC
210307 AAAGAAAGGAAAAAAGAAAAAAGAGGA
1 AAAGAAA--AAAAAAGAAAAAAGA--A
**
210334 AAA-AAGAAAAAAA-AGGAAAGAA
1 AAAGAA-AAAAAAAGAAAAAAGAA
*
210356 ATAGAAAAAAAAAGAAAAAAGAA
1 AAAGAAAAAAAAAGAAAAAAGAA
210379 AAAGAAAAAAAA
1 AAAGAAAAAAAA
210391 TTAAATCAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
22 10 0.21
23 20 0.42
24 6 0.12
25 6 0.12
26 2 0.04
27 4 0.08
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (23 bp):
AAAGAAAAAAAAAGAAAAAAGAA
Found at i:210390 original size:10 final size:10
Alignment explanation
Indices: 210323--210389 Score: 64
Period size: 10 Copynumber: 6.6 Consensus size: 10
210313 AGGAAAAAAG
**
210323 AAAAAAGAGG
1 AAAAAAGAAA
210333 AAAAAAGAAA
1 AAAAAAGAAA
*
210343 AAAAAGGAAA
1 AAAAAAGAAA
* *
210353 GAAATAGAAA
1 AAAAAAGAAA
210363 AAAAAAGAAA
1 AAAAAAGAAA
210373 AAAGAAA-AAGA
1 AAA-AAAGAA-A
210384 AAAAAA
1 AAAAAA
210390 ATTAAATCAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
10 40 0.85
11 7 0.15
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:210390 original size:17 final size:17
Alignment explanation
Indices: 210316--210390 Score: 64
Period size: 17 Copynumber: 4.2 Consensus size: 17
210306 CAAAGAAAGG
210316 AAAAAAGAAAAAAGAGGAAA
1 AAAAAAG-AAAAAGA--AAA
*
210336 AAAGAAA-AAAAAGGAAA
1 AAA-AAAGAAAAAGAAAA
* *
210353 GAAATAGAAAAA-AAAA
1 AAAAAAGAAAAAGAAAA
210369 GAAAAAAGAAAAAGAAAA
1 -AAAAAAGAAAAAGAAAA
210387 AAAA
1 AAAA
210391 TTAAATCAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
16 5 0.11
17 24 0.53
18 4 0.09
19 6 0.13
20 3 0.07
21 3 0.07
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (17 bp):
AAAAAAGAAAAAGAAAA
Found at i:212830 original size:114 final size:114
Alignment explanation
Indices: 212622--212847 Score: 371
Period size: 114 Copynumber: 2.0 Consensus size: 114
212612 AAGTGCCATG
*
212622 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * *
212687 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATT
66 TGATTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATT
*
212736 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * *
212801 TGATTCGGTAGGAACCCCAGAACCGATCATTGGAATTGAAAGATGAA
66 TGATTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAA
212848 CTGCATGATC
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 103 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGATTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATT
Found at i:215448 original size:22 final size:22
Alignment explanation
Indices: 215417--215471 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
215407 ATCTACACTC
**
215417 TTCAAAGATGGTAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
215439 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
215461 TTCAAAGATGA
1 TTCAAAGATGA
215472 AAGCTTTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:216068 original size:113 final size:113
Alignment explanation
Indices: 215871--216417 Score: 685
Period size: 112 Copynumber: 4.9 Consensus size: 113
215861 TTAGCAAAGT
* *
215871 TCAAATCCATCATTCAATGGATCAACA-TTCCAG-GACGAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATTCATCATTCGATGGATCAACATTTCCAGAGA-GAGTTCATAATGAGAAGAACTCATCTG
* *
215934 AATAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* *
215983 TCAAATCCATCATTCGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATTCATCATTCGATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
* *
216048 AGAAGGAAGAAGAATTTCATAATGAGAAGAACTTGTTCAACTTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * ** *
216096 TTAAATTCATCATTTGATGGATCATCATTACCAGTTAGAGTTCATAATGAGAAGAACTCATTTGA
1 TCAAATTCATCATTCGATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
* *
216161 AGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* ** * * * * **
216208 TTAAATTCATCACCCGGTGGATCAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATTCATCATTCGATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
*
216273 AG-AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTT-C
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * *** * *
216319 CCTGAATTCATCACTT-GATGAATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCT
1 TC-AAATTCATCA-TTCGATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCT
*
216383 GAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTT
64 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTT
216418 ATCTGAAGAG
Statistics
Matches: 384, Mismatches: 46, Indels: 10
0.87 0.10 0.02
Matches are distributed among these distances:
111 2 0.01
112 243 0.63
113 137 0.36
114 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (113 bp):
TCAAATTCATCATTCGATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:216394 original size:19 final size:19
Alignment explanation
Indices: 216370--216433 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
216360 TTCATAATGA
216370 GAAGAACTTATCTGAAGAG
1 GAAGAACTTATCTGAAGAG
**
216389 GAAGAA-GAAGTTCAT-AATGA-
1 GAAGAACTTA--TC-TGAA-GAG
216409 GAAGAACTTATCTGAAGAG
1 GAAGAACTTATCTGAAGAG
216428 GAAGAA
1 GAAGAA
216434 GAAGTTCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
18 4 0.12
19 16 0.47
20 10 0.29
21 4 0.12
ACGTcount: A:0.47, C:0.08, G:0.27, T:0.19
Consensus pattern (19 bp):
GAAGAACTTATCTGAAGAG
Found at i:216396 original size:22 final size:22
Alignment explanation
Indices: 216369--216436 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
216359 GTTCATAATG
216369 AGAAGAACTTATCTGAAGAGGA
1 AGAAGAACTTATCTGAAGAGGA
* *
216391 AGAAGAA-GT-TC--ATA-ATG-
1 AGAAGAACTTATCTGA-AGAGGA
216408 AGAAGAACTTATCTGAAGAGGA
1 AGAAGAACTTATCTGAAGAGGA
216430 AGAAGAA
1 AGAAGAA
216437 GTTCATAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
17 7 0.20
18 4 0.11
19 3 0.09
20 3 0.09
21 4 0.11
22 14 0.40
ACGTcount: A:0.49, C:0.07, G:0.26, T:0.18
Consensus pattern (22 bp):
AGAAGAACTTATCTGAAGAGGA
Found at i:216411 original size:39 final size:39
Alignment explanation
Indices: 216357--216456 Score: 200
Period size: 39 Copynumber: 2.6 Consensus size: 39
216347 TTTCCAGAGA
216357 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
216396 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
216435 AAGTTCATAATGAGAAGAACTT
1 AAGTTCATAATGAGAAGAACTT
216457 GTTTAACCTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 61 1.00
ACGTcount: A:0.46, C:0.08, G:0.24, T:0.22
Consensus pattern (39 bp):
AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
Found at i:216415 original size:151 final size:151
Alignment explanation
Indices: 216246--216565 Score: 534
Period size: 151 Copynumber: 2.1 Consensus size: 151
216236 TGCCAGTTAG
*
216246 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCA
***
216311 ACCTTTTCC-CTGAATTCATCACTTGATGAATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGA
66 ACCTTTTCCTC-GAATTCATCACTTGATGAATTAACATTTCCAGAGAAAGTTCATAATGAGAAGA
216375 ACTTATCTGAAGAGGAAGAAGA
130 ACTTATCTGAAGAGGAAGAAGA
* * *
216397 AGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCA
* *
216462 ACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAA
66 ACCTTTTCCTCGAATTCATCACTTGATGAATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAA
216527 CTTATCTGAAGAGGAAGAAGA
131 CTTATCTGAAGAGGAAGAAGA
*
216548 AATTCATAATGAGAAGAA
1 AGTTCATAATGAGAAGAA
216566 TTTGTTTAAC
Statistics
Matches: 158, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
151 157 0.99
152 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.28
Consensus pattern (151 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCA
ACCTTTTCCTCGAATTCATCACTTGATGAATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAA
CTTATCTGAAGAGGAAGAAGA
Found at i:216435 original size:263 final size:264
Alignment explanation
Indices: 216134--216677 Score: 849
Period size: 263 Copynumber: 2.1 Consensus size: 264
216124 TACCAGTTAG
*
216134 AGTTCATAATGAGAAGAACTCATTTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * * * ** *
216199 ACTTTTTGCTTAAATTCATCACCCGGTGGATCAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAA
66 ACCTTTTGCTCAAATTCATCACCCGATGGATCAACAGTGCCAGAGAAAGTTCATAATGAGAAGAA
216264 CTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTCCCTGAATTCA
131 CTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTCCCTGAATTCA
* * *
216329 TCACTTGATGAATT-ATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAA
196 TCACTTGATGAATTAACTTTTT-CAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAA
216392 GAAGA
260 GAAGA
* * *
216397 AGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* ** * * *
216462 ACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAA
66 ACCTTTTGCTCAAATTCATCACCCGATGGATCAACAGTGCCAGAGAAAGTTCATAATGAGAAGAA
* * *
216527 CTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCCTGAATTCA
131 CTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTCCCTGAATTCA
*
216592 TCACTTGATGGATTAACTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAG
196 TCACTTGATGAATTAACTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAG
216657 AAGA
261 AAGA
216661 AGTTCATAATGAGAAGA
1 AGTTCATAATGAGAAGA
216678 GCTTGTTCAA
Statistics
Matches: 255, Mismatches: 24, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
263 222 0.87
264 33 0.13
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.28
Consensus pattern (264 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTTTGCTCAAATTCATCACCCGATGGATCAACAGTGCCAGAGAAAGTTCATAATGAGAAGAA
CTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTCCCTGAATTCA
TCACTTGATGAATTAACTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAG
AAGA
Found at i:216593 original size:112 final size:112
Alignment explanation
Indices: 216396--216692 Score: 497
Period size: 112 Copynumber: 2.6 Consensus size: 112
216386 GAGGAAGAAG
216396 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
216461 AACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGA
66 AACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGA
* *
216508 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTT
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
* *
216573 AACCTTTTGC-CTGAATTCATCACTTGATGGATTAACTTTTTCAGAGA
66 AACCTTTTGCTC-GAATTCATCACTTGATGGATTAACATTTCCAGAGA
* * *
216620 AAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 AAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
216685 CAACCTTT
65 TAACCTTT
216693 GTTTGATGCT
Statistics
Matches: 173, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
111 1 0.01
112 134 0.77
113 38 0.22
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (112 bp):
AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
AACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGA
Found at i:218532 original size:3 final size:3
Alignment explanation
Indices: 218524--218696 Score: 298
Period size: 3 Copynumber: 58.7 Consensus size: 3
218514 TTTTTATCCA
218524 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
218571 TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
218618 TAT TAT CAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
218665 TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
218697 ATTTACATTA
Statistics
Matches: 161, Mismatches: 6, Indels: 6
0.93 0.03 0.03
Matches are distributed among these distances:
2 6 0.04
3 155 0.96
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:219216 original size:15 final size:15
Alignment explanation
Indices: 219196--219230 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
219186 AGAACCGGAG
219196 AGAAAAAAAAAACAA
1 AGAAAAAAAAAACAA
*
219211 AGAAAAGAAAAACAA
1 AGAAAAAAAAAACAA
219226 A-AAAA
1 AGAAAA
219231 CTATACCAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.86, C:0.06, G:0.09, T:0.00
Consensus pattern (15 bp):
AGAAAAAAAAAACAA
Found at i:220040 original size:19 final size:20
Alignment explanation
Indices: 220016--220054 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
220006 AATAATTAGT
*
220016 AATTAGTT-TTATTTTTATA
1 AATTAGTTATTAATTTTATA
220035 AATTAGTTATTAATTTTATA
1 AATTAGTTATTAATTTTATA
220055 TGTCTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
AATTAGTTATTAATTTTATA
Found at i:220145 original size:22 final size:20
Alignment explanation
Indices: 220104--220148 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
220094 ATAGAATTAT
**
220104 TATTTTATTATATTGTTAAA
1 TATTTTATTATATTCATAAA
220124 TATTTTGATATATATTCATAAA
1 TATTTT-AT-TATATTCATAAA
220146 TAT
1 TAT
220149 ATATAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 2 0.10
22 13 0.62
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTTATTATATTCATAAA
Found at i:220874 original size:12 final size:14
Alignment explanation
Indices: 220847--220879 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
220837 ATTTTTATGT
220847 TTTATTTGCAAGTA
1 TTTATTTGCAAGTA
220861 TTTATTT-C-AGTA
1 TTTATTTGCAAGTA
220873 TTTATTT
1 TTTATTT
220880 TTATGTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
13 1 0.05
14 7 0.37
ACGTcount: A:0.24, C:0.06, G:0.09, T:0.61
Consensus pattern (14 bp):
TTTATTTGCAAGTA
Found at i:231437 original size:1 final size:1
Alignment explanation
Indices: 231431--231497 Score: 62
Period size: 1 Copynumber: 67.0 Consensus size: 1
231421 CTTGAAGAAG
* * * * * * **
231431 AAAAAAAGAGAAAAAAGAAAAAAGAAAAAAAAAGAAAAAAAAAGAAAAAAAAAGGAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
231496 AA
1 AA
231498 GGGGTCAAGG
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (1 bp):
A
Found at i:231444 original size:8 final size:7
Alignment explanation
Indices: 231425--231480 Score: 64
Period size: 7 Copynumber: 8.3 Consensus size: 7
231415 ATTATGCTTG
*
231425 AAGAAGA
1 AAGAAAA
231432 AA-AAAA
1 AAGAAAA
*
231438 GAGAAAA
1 AAGAAAA
231445 AAGAAAA
1 AAGAAAA
231452 AAGAAAA
1 AAGAAAA
231459 AA-AAAGA
1 AAGAAA-A
231466 AA-AAAA
1 AAGAAAA
231472 AAGAAAA
1 AAGAAAA
231479 AA
1 AA
231481 AAAGGAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
6 10 0.23
7 33 0.77
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:231448 original size:17 final size:17
Alignment explanation
Indices: 231428--231480 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
231418 ATGCTTGAAG
231428 AAGAAAAAAAGAGAAAA
1 AAGAAAAAAAGAGAAAA
*
231445 AAG-AAAAAAGAAAAAAA
1 AAGAAAAAAAG-AGAAAA
*
231462 AAGAAAAAAAAAGAAAA
1 AAGAAAAAAAGAGAAAA
231479 AA
1 AA
231481 AAAGGAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 7 0.23
17 18 0.58
18 6 0.19
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAGAGAAAA
Found at i:231448 original size:20 final size:18
Alignment explanation
Indices: 231428--231497 Score: 83
Period size: 20 Copynumber: 3.9 Consensus size: 18
231418 ATGCTTGAAG
*
231428 AAGAAAAAAAG-AGAAAA
1 AAGAAAAAAAGAAAAAAA
231445 AAG-AAAAAAGAAAAAAA
1 AAGAAAAAAAGAAAAAAA
231462 AAGAAAAAAAAAGAAAAAAA
1 AAG--AAAAAAAGAAAAAAA
231482 AAGGAAAAAAA-AAAAA
1 AA-GAAAAAAAGAAAAA
231498 GGGGTCAAGG
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
16 7 0.15
17 11 0.23
18 5 0.11
19 7 0.15
20 16 0.34
21 1 0.02
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (18 bp):
AAGAAAAAAAGAAAAAAA
Found at i:231460 original size:24 final size:23
Alignment explanation
Indices: 231428--231498 Score: 101
Period size: 24 Copynumber: 3.1 Consensus size: 23
231418 ATGCTTGAAG
231428 AAGAAAAAAAGAGAAAAAAGAAAA
1 AAGAAAAAAAGAGAAAAAA-AAAA
* *
231452 AAGAAAAAAAAAGAAAAAAAAAG
1 AAGAAAAAAAGAGAAAAAAAAAA
231475 AA-AAAAAAAG-GAAAAAAAAAA
1 AAGAAAAAAAGAGAAAAAAAAAA
231496 AAG
1 AAG
231499 GGGTCAAGGT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 12 0.29
22 7 0.17
23 5 0.12
24 18 0.43
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (23 bp):
AAGAAAAAAAGAGAAAAAAAAAA
Found at i:231471 original size:34 final size:33
Alignment explanation
Indices: 231428--231498 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 33
231418 ATGCTTGAAG
*
231428 AAGAAAAAAAGAGAAAAAAGAAA-AAAGAAAAAAA
1 AAGAAAAAAAAAGAAAAAA-AAAGAAA-AAAAAAA
231462 AAGAAAAAAAAAGAAAAAAAAAGGAAAAAAAAAA
1 AAGAAAAAAAAAGAAAAAAAAA-GAAAAAAAAAA
231496 AAG
1 AAG
231499 GGGTCAAGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
33 3 0.09
34 28 0.82
35 3 0.09
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (33 bp):
AAGAAAAAAAAAGAAAAAAAAAGAAAAAAAAAA
Found at i:231494 original size:11 final size:10
Alignment explanation
Indices: 231448--231494 Score: 85
Period size: 10 Copynumber: 4.6 Consensus size: 10
231438 GAGAAAAAAG
231448 AAAAAAGAAA
1 AAAAAAGAAA
231458 AAAAAAGAAA
1 AAAAAAGAAA
231468 AAAAAAGAAA
1 AAAAAAGAAA
231478 AAAAAAGGAAA
1 AAAAAA-GAAA
231489 AAAAAA
1 AAAAAA
231495 AAAGGGGTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 26 0.72
11 10 0.28
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:231842 original size:16 final size:16
Alignment explanation
Indices: 231823--231865 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
231813 ATTTCAAGTG
*
231823 CAATTTATTTGAGATT
1 CAATTTATTTGAAATT
*
231839 CAATTCATTTTTGAAATT
1 CAATT--TATTTGAAATT
231857 CAATTTATT
1 CAATTTATT
231866 CTTTTCTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
16 8 0.36
18 14 0.64
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (16 bp):
CAATTTATTTGAAATT
Found at i:232595 original size:52 final size:51
Alignment explanation
Indices: 232420--232723 Score: 563
Period size: 51 Copynumber: 5.9 Consensus size: 51
232410 TATGTGCTCA
232420 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
232471 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
* *
232522 ATAGCATCTTTTGGAAGTGTTCTTTGAGGTATCTGATCTGGTTAGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAAC
232574 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
232625 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
* *
232676 AAAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAAG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAG
232724 TGTTCTTTGA
Statistics
Matches: 246, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
51 197 0.80
52 49 0.20
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.37
Consensus pattern (51 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
Found at i:232612 original size:103 final size:102
Alignment explanation
Indices: 232420--233104 Score: 856
Period size: 104 Copynumber: 6.4 Consensus size: 102
232410 TATGTGCTCA
232420 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGG
232485 AAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
66 AAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
* *
232522 ATAGCATCTTTTGGAAGTGTTCTTTGAGGTATCTGATCTGGTTAGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAGCATCTTCTG
232587 GAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
65 GAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
*
232625 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACAAAGCATCTTCTGG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGG
* **
232690 AAGTGTTCTTTGAGTTATCTGATCTGGTTGGAAGTGTTC
66 AAGTGTTCTTTGAGTTATCTGATCTGGTTAGAA--GAAC
* * *
232729 TTTGAGTTATCTGATCTGGTTGGAAGAACATAGCATCTTCTGGAAGTGT-TCT--T-TGAGTTAT
1 -AT-AG-CATCT--TC----TGGAAG----T-G-TTCTT-T-G-AGT-TATCTGATCTG-G----
* *
232790 CTGATCTGGTTAGAAGAACAAAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
42 ---------TTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA
232855 CAGAAC
98 -AGAAC
*
232861 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAGCATCTTCTG
232926 GAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
65 GAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAAC
*
232965 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAGCATCTTCTG
233030 GAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
65 GAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
*
233068 ATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
233105 TTGATTGGAC
Statistics
Matches: 521, Mismatches: 20, Indels: 83
0.83 0.03 0.13
Matches are distributed among these distances:
102 94 0.18
103 145 0.28
104 155 0.30
105 1 0.00
106 2 0.00
107 4 0.01
109 2 0.00
113 7 0.01
114 6 0.01
115 1 0.00
116 3 0.01
117 7 0.01
118 2 0.00
119 7 0.01
120 3 0.01
121 1 0.00
122 6 0.01
123 7 0.01
127 2 0.00
129 4 0.01
130 2 0.00
131 1 0.00
132 2 0.00
133 56 0.11
134 1 0.00
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (102 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGG
AAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
Found at i:232700 original size:154 final size:154
Alignment explanation
Indices: 232420--232718 Score: 571
Period size: 154 Copynumber: 1.9 Consensus size: 154
232410 TATGTGCTCA
232420 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGG
* *
232485 AAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTTTGGAAGTGTTCTTTGAG
66 AAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACAAAGCATCTTCTGGAAGTGTTCTTTGAG
232550 GTATCTGATCTGGTTAGACAGAAC
131 GTATCTGATCTGGTTAGACAGAAC
232574 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGG
232639 AAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACAAAGCATCTTCTGGAAGTGTTCTTTGAG
66 AAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACAAAGCATCTTCTGGAAGTGTTCTTTGAG
*
232704 TTATCTGATCTGGTT
131 GTATCTGATCTGGTT
232719 GGAAGTGTTC
Statistics
Matches: 142, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
154 142 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.38
Consensus pattern (154 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGG
AAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACAAAGCATCTTCTGGAAGTGTTCTTTGAG
GTATCTGATCTGGTTAGACAGAAC
Found at i:232722 original size:31 final size:31
Alignment explanation
Indices: 232687--232754 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
232677 AAGCATCTTC
232687 TGGAAGTGTTCTTTGAGTTATCTGATCTGGT
1 TGGAAGTGTTCTTTGAGTTATCTGATCTGGT
232718 TGGAAGTGTTCTTTGAGTTATCTGATCTGGT
1 TGGAAGTGTTCTTTGAGTTATCTGATCTGGT
232749 TGGAAG
1 TGGAAG
232755 AACATAGCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.18, C:0.09, G:0.31, T:0.43
Consensus pattern (31 bp):
TGGAAGTGTTCTTTGAGTTATCTGATCTGGT
Found at i:232737 original size:82 final size:82
Alignment explanation
Indices: 232636--232805 Score: 313
Period size: 82 Copynumber: 2.1 Consensus size: 82
232626 TAGCATCTTC
232636 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACAAAGCATCTTCTGGAAGTGTTCTTT
1 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACAAAGCATCTTCTGGAAGTGTTCTTT
232701 GAGTTATCTGATCTGGT
66 GAGTTATCTGATCTGGT
* *
232718 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAAGAACATAGCATCTTCTGGAAGTGTTCTTT
1 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACAAAGCATCTTCTGGAAGTGTTCTTT
232783 GAGTTATCTGATCTGGT
66 GAGTTATCTGATCTGGT
*
232800 TAGAAG
1 TGGAAG
232806 AACAAAGCAT
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 85 1.00
ACGTcount: A:0.23, C:0.12, G:0.26, T:0.39
Consensus pattern (82 bp):
TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACAAAGCATCTTCTGGAAGTGTTCTTT
GAGTTATCTGATCTGGT
Found at i:232823 original size:133 final size:133
Alignment explanation
Indices: 232585--232854 Score: 531
Period size: 133 Copynumber: 2.0 Consensus size: 133
232575 TAGCATCTTC
232585 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTT
1 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTT
232650 GAGTTATCTGATCTGGTTAGAAGAACAAAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
66 GAGTTATCTGATCTGGTTAGAAGAACAAAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
232715 GGT
131 GGT
*
232718 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAAGAACATAGCATCTTCTGGAAGTGTTCTTT
1 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTT
232783 GAGTTATCTGATCTGGTTAGAAGAACAAAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
66 GAGTTATCTGATCTGGTTAGAAGAACAAAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
232848 GGT
131 GGT
232851 TGGA
1 TGGA
232855 CAGAACATAG
Statistics
Matches: 136, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 136 1.00
ACGTcount: A:0.24, C:0.13, G:0.26, T:0.38
Consensus pattern (133 bp):
TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTT
GAGTTATCTGATCTGGTTAGAAGAACAAAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
GGT
Found at i:232842 original size:184 final size:186
Alignment explanation
Indices: 232532--232906 Score: 691
Period size: 184 Copynumber: 2.0 Consensus size: 186
232522 ATAGCATCTT
232532 TTGGAAGTGTTCTTTGAGGTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAGTGTTCT
1 TTGGAAGTGTTCTTTGAGGTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAGTGTTCT
*
232597 TTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
66 TTGAGTTATCTGATCTGGTTAGAAGAACAAAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
232662 CTGGTTAGA-AGAACAAAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
131 CTGGTTAGACAGAACAAAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
* *
232717 TTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-AGAACATAGCATCTTCTGGAAGTGTTCT
1 TTGGAAGTGTTCTTTGAGGTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAGTGTTCT
232781 TTGAGTTATCTGATCTGGTTAGAAGAACAAAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
66 TTGAGTTATCTGATCTGGTTAGAAGAACAAAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
* *
232846 CTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
131 CTGGTTAGACAGAACAAAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
232902 TTGGA
1 TTGGA
232907 CAGAACATAG
Statistics
Matches: 184, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
184 100 0.54
185 84 0.46
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (186 bp):
TTGGAAGTGTTCTTTGAGGTATCTGATCTGGTTAGACAGAACATAGCATCTTCTGGAAGTGTTCT
TTGAGTTATCTGATCTGGTTAGAAGAACAAAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
CTGGTTAGACAGAACAAAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
Found at i:232882 original size:52 final size:52
Alignment explanation
Indices: 232718--233115 Score: 712
Period size: 52 Copynumber: 7.7 Consensus size: 52
232708 CTGATCTGGT
232718 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-AGAACATAGCATCTTC
1 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTC
* *
232769 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACAAAGCATCTTC
1 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTC
232820 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTC
1 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTC
232872 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTC
1 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTC
*
232924 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTC
1 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTC
232976 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTC
1 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTC
* *
233028 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAGCATTTTC
1 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTC
* *
233079 TGGAAGTGTTCTTTGAGTTATCTGATTTGATTGGACA
1 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACA
233116 TAATCAAGCA
Statistics
Matches: 334, Mismatches: 11, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
51 130 0.39
52 204 0.61
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37
Consensus pattern (52 bp):
TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTC
Found at i:233949 original size:16 final size:16
Alignment explanation
Indices: 233890--233950 Score: 50
Period size: 16 Copynumber: 3.5 Consensus size: 16
233880 ATTTCCAGAG
*
233890 GAAGAGTTCATAATGA
1 GAAGAATTCATAATGA
* *
233906 GAAGAACTCATCATCTGAAA
1 GAAGAATTCAT-A-ATG--A
233926 GGAAGAATTCATAATGA
1 -GAAGAATTCATAATGA
233943 GAAGAATT
1 GAAGAATT
233951 TGTTCAACCT
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
16 17 0.49
17 2 0.06
18 2 0.06
19 2 0.06
20 2 0.06
21 10 0.29
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.23
Consensus pattern (16 bp):
GAAGAATTCATAATGA
Found at i:233992 original size:113 final size:115
Alignment explanation
Indices: 233742--234405 Score: 1022
Period size: 114 Copynumber: 5.8 Consensus size: 115
233732 CAAAGATTCA
*
233742 AATTCATCAATTTGATGGATCATTC-TTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCATCAT
1 AATTCATCAAATTGATGGATCA-TCATTTCCAGAGGAA-AGTTCATAATGAGAAGAACTCATCAT
233806 CTGAAGAAGGAAGAAGTTCATAAT--GAAGAATTTGTTCAACCTTTTGCTTG
64 CTGAAGAAGGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
233856 AATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCATCATC
1 AATTCATCAAATTGATGGATCATCATTTCCAGAGGAA-AGTTCATAATGAGAAGAACTCATCATC
233921 TG-A-AAGGAAGAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
65 TGAAGAAGGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
233969 AATTCATCAAATTGATGGATCATCATTTCCAGAGG-AAGTTCATAATGAGAAGAACTCATCATCT
1 AATTCATCAAATTGATGGATCATCATTTCCAGAGGAAAGTTCATAATGAGAAGAACTCATCATCT
234033 GAAGAAGAAGAAGAAGTTCATAATGA-AAGAATTTGTTCAACCTTTTGCTTG
66 GAAGAAG--GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
*
234084 AATTCATCAAATTGATGGATCATCATTTCCAGA-GAAGAGTTCATAATGAGAAGAACTCGTCATC
1 AATTCATCAAATTGATGGATCATCATTTCCAGAGGAA-AGTTCATAATGAGAAGAACTCATCATC
234148 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTGCTTG
65 TGAAGAA-G--GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
*
234201 AATTCATC-AATTGATGGATCATCATTTCCAGAGG-AAGTTCATAATGAGAAGAACTCGTCATCT
1 AATTCATCAAATTGATGGATCATCATTTCCAGAGGAAAGTTCATAATGAGAAGAACTCATCATCT
234264 GAA-AAGGAAGAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
66 GAAGAAGG-A-AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
* * * *
234315 AATTCATC-AGTTGATGGATCAACATTACCAG-GTAAAGTTCATAATGAGAAGAA--C-TCATCT
1 AATTCATCAAATTGATGGATCATCATTTCCAGAGGAAAGTTCATAATGAGAAGAACTCATCATCT
*
234375 GAAGAAGGAAAAAAGTTCATAATGAGAAGAA
66 GAAGAAGG-AAGAAGTTCATAATGAGAAGAA
234406 CTCATCAAGA
Statistics
Matches: 525, Mismatches: 7, Indels: 39
0.92 0.01 0.07
Matches are distributed among these distances:
111 67 0.13
112 19 0.04
113 101 0.19
114 121 0.23
115 96 0.18
116 68 0.13
117 37 0.07
118 16 0.03
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (115 bp):
AATTCATCAAATTGATGGATCATCATTTCCAGAGGAAAGTTCATAATGAGAAGAACTCATCATCT
GAAGAAGGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
Found at i:234296 original size:231 final size:232
Alignment explanation
Indices: 233742--234405 Score: 1048
Period size: 231 Copynumber: 2.9 Consensus size: 232
233732 CAAAGATTCA
233742 AATTCATCAATTTGATGGATCATTC-TTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCATCAT
1 AATTCATCAA-TTGATGGATCA-TCATTTCCAGAGG-A-AGTTCATAATGAGAAGAACTCATCAT
233806 CTGAAGAAGG-A-AGAAGTTCATAAT--GAAGAATTTGTTCAACCTTTTGCTTGAATTCATCAAA
62 CTGAAGAAGGAAGAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCAAA
233867 TTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCATCATCTG-A-AA-G--
127 TTGATGGATCATCATTTCCAGA-GAAGAGTTCATAATGAGAAGAACTC-TCATCTGAAGAAGGAA
233927 GAAGAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
190 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
233969 AATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCATCTG
1 AATTCATC-AATTGATGGATCATCATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCATCTG
234034 AAGAA-GAAGAAGAAGTTCATAATGA-AAGAATTTGTTCAACCTTTTGCTTGAATTCATCAAATT
65 AAGAAGGAAG-AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCAAATT
234097 GATGGATCATCATTTCCAGAGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAA
129 GATGGATCATCATTTCCAGAGAAGAGTTCATAATGAGAAGAACTC-TCATCTGAAGAAGGAAGAA
234162 GAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTGCTTG
193 GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
*
234201 AATTCATCAATTGATGGATCATCATTTCCAGAGGAAGTTCATAATGAGAAGAACTCGTCATCTGA
1 AATTCATCAATTGATGGATCATCATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCATCTGA
*
234266 A-AAGGAAGAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATC-AGTTGA
66 AGAAGGAAGAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCAAATTGA
* *
234329 TGGATCAACATTACCAG-GTAA-AGTTCATAATGAGAAGAA--CTCATCTGAAGAAGGAA-AA-A
131 TGGATCATCATTTCCAGAG-AAGAGTTCATAATGAGAAGAACTCTCATCTGAAGAAGGAAGAAGA
234388 AGTTCATAATGAGAAGAA
195 AGTTCATAATGAGAAGAA
234406 CTCATCAAGA
Statistics
Matches: 416, Mismatches: 5, Indels: 35
0.91 0.01 0.08
Matches are distributed among these distances:
224 20 0.05
225 37 0.09
226 19 0.05
227 75 0.18
228 61 0.15
229 21 0.05
230 40 0.10
231 94 0.23
232 22 0.05
233 27 0.06
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (232 bp):
AATTCATCAATTGATGGATCATCATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCATCTGA
AGAAGGAAGAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCAAATTGA
TGGATCATCATTTCCAGAGAAGAGTTCATAATGAGAAGAACTCTCATCTGAAGAAGGAAGAAGAA
GTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
Found at i:234666 original size:3 final size:3
Alignment explanation
Indices: 234653--234823 Score: 274
Period size: 3 Copynumber: 57.7 Consensus size: 3
234643 TTTTTATCCA
234653 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
234699 TAT CAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
234747 CAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
234795 TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
234824 ATTTACATTA
Statistics
Matches: 154, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
2 4 0.03
3 150 0.97
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:235841 original size:17 final size:19
Alignment explanation
Indices: 235819--235854 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
235809 AATAATTAGT
235819 AATTAGT-TT-ATTTTATA
1 AATTAGTATTAATTTTATA
235836 AATTAGTATTAATTTTATA
1 AATTAGTATTAATTTTATA
235855 TGTCTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 2 0.12
19 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (19 bp):
AATTAGTATTAATTTTATA
Found at i:241360 original size:31 final size:31
Alignment explanation
Indices: 241325--241386 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
241315 CAGACCGTCT
241325 TGTTTAATACGACTTATGGGTAAGTAATGTA
1 TGTTTAATACGACTTATGGGTAAGTAATGTA
241356 TGTTTAATACGACTTATGGGTAAGTAATGTA
1 TGTTTAATACGACTTATGGGTAAGTAATGTA
241387 AGTTGCCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.39
Consensus pattern (31 bp):
TGTTTAATACGACTTATGGGTAAGTAATGTA
Found at i:260938 original size:33 final size:33
Alignment explanation
Indices: 260896--261064 Score: 275
Period size: 33 Copynumber: 5.1 Consensus size: 33
260886 CCCTCACCTC
*
260896 CTCAACTTTCAGTTTTTCTTCCACTTTGGAGTT
1 CTCAACTTTCCGTTTTTCTTCCACTTTGGAGTT
* *
260929 CTCAACTTTCTGTGTTTCTTCCACTTTGGAGTT
1 CTCAACTTTCCGTTTTTCTTCCACTTTGGAGTT
* * *
260962 CTCAGCTTTCTGTGTTTCTTCCACTTTGGAGTT
1 CTCAACTTTCCGTTTTTCTTCCACTTTGGAGTT
260995 CTCAACTTTCCGTTTTTCTTCCACTTTGGAGTT
1 CTCAACTTTCCGTTTTTCTTCCACTTTGGAGTT
*
261028 CTCAACTTTCCGTTTTTCTTCCACTTTGCAGTT
1 CTCAACTTTCCGTTTTTCTTCCACTTTGGAGTT
261061 CTCA
1 CTCA
261065 GTCTGCAACA
Statistics
Matches: 129, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 129 1.00
ACGTcount: A:0.12, C:0.27, G:0.13, T:0.48
Consensus pattern (33 bp):
CTCAACTTTCCGTTTTTCTTCCACTTTGGAGTT
Found at i:268986 original size:114 final size:114
Alignment explanation
Indices: 268786--268994 Score: 330
Period size: 114 Copynumber: 1.8 Consensus size: 114
268776 ACTATTTTAC
* *
268786 TGTTAATAGTATTTTGGATGATAACATTATCTGTATTTTGAAAATCAGGTTCTCAAATATAATTA
1 TGTTAATAGTATTTTGAATGATAACATTATCGGTATTTTGAAAATCAGGTTCTCAAATATAATTA
** *
268851 TATTTCTAATTGAGTGAACTTTTGTTCTGGAAGTTCAATTAAAAGCTAA
66 TATTTCTAATCAAGTGAACTTTTGCTCTGGAAGTTCAATTAAAAGCTAA
* * *
268900 TGTTACTAGTATTTTGAATGATAACATTATCGGT-TTCTTGAAAATCGGGTTCTCAACTATAATT
1 TGTTAATAGTATTTTGAATGATAACATTATCGGTATT-TTGAAAATCAGGTTCTCAAATATAATT
268964 ATATTTCTAATCAAGTGAACTTTTGCTCTGG
65 ATATTTCTAATCAAGTGAACTTTTGCTCTGG
268995 TAGCTTAACT
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
113 2 0.02
114 84 0.98
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (114 bp):
TGTTAATAGTATTTTGAATGATAACATTATCGGTATTTTGAAAATCAGGTTCTCAAATATAATTA
TATTTCTAATCAAGTGAACTTTTGCTCTGGAAGTTCAATTAAAAGCTAA
Found at i:271892 original size:16 final size:17
Alignment explanation
Indices: 271867--271905 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
271857 TCTGAAAATG
*
271867 TTAAAGAATTATTT-AA
1 TTAAATAATTATTTAAA
*
271883 TTAAATAATTCTTTAAA
1 TTAAATAATTATTTAAA
271900 TTAAAT
1 TTAAAT
271906 TAAAACAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (17 bp):
TTAAATAATTATTTAAA
Found at i:272773 original size:6 final size:6
Alignment explanation
Indices: 272744--272793 Score: 70
Period size: 6 Copynumber: 8.8 Consensus size: 6
272734 TGAGAGTTGA
*
272744 TCAAAT T-AAAT T-AAAT T-GAAT TCAAAT TCAAAT TCAAAT TCAAAT
1 TCAAAT TCAAAT TCAAAT TCAAAT TCAAAT TCAAAT TCAAAT TCAAAT
272789 TCAAA
1 TCAAA
272794 CAAAAATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
5 14 0.34
6 27 0.66
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.34
Consensus pattern (6 bp):
TCAAAT
Found at i:272800 original size:18 final size:18
Alignment explanation
Indices: 272762--272800 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
272752 AATTAAATTG
***
272762 AATTCAAATTCAAATTCA
1 AATTCAAATTCAAACAAA
272780 AATTCAAATTCAAACAAA
1 AATTCAAATTCAAACAAA
272798 AAT
1 AAT
272801 ATATTAAACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.28
Consensus pattern (18 bp):
AATTCAAATTCAAACAAA
Found at i:281799 original size:26 final size:26
Alignment explanation
Indices: 281763--281818 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
281753 CCACTTCCAT
281763 AATACGATTCATGTGTTTGCCTATTG
1 AATACGATTCATGTGTTTGCCTATTG
*
281789 AATATGATTCATGTGTTTGCCTATTG
1 AATACGATTCATGTGTTTGCCTATTG
281815 AATA
1 AATA
281819 GATGCTCTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (26 bp):
AATACGATTCATGTGTTTGCCTATTG
Found at i:284140 original size:20 final size:20
Alignment explanation
Indices: 284104--284141 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
284094 ATCTTATTCC
**
284104 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
284124 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
284142 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:289068 original size:6 final size:6
Alignment explanation
Indices: 289058--289109 Score: 70
Period size: 6 Copynumber: 8.8 Consensus size: 6
289048 AAACTAAAGA
* * *
289058 TACAAT CACAAT CACAAT TACAAT TATAAT TACAAT TACAAT TACAA-
1 TACAAT TACAAT TACAAT TACAAT TACAAT TACAAT TACAAT TACAAT
289105 TACAA
1 TACAA
289110 CATCTAATCG
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
5 5 0.12
6 37 0.88
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (6 bp):
TACAAT
Found at i:289679 original size:23 final size:23
Alignment explanation
Indices: 289649--289741 Score: 168
Period size: 23 Copynumber: 4.0 Consensus size: 23
289639 TTATAAGATA
*
289649 ATGTTCATCCCTTTGCCAATAAT
1 ATGTTCATCCCTATGCCAATAAT
*
289672 ATGTTCATCCCTTTGCCAATAAT
1 ATGTTCATCCCTATGCCAATAAT
289695 ATGTTCATCCCTATGCCAATAAT
1 ATGTTCATCCCTATGCCAATAAT
289718 ATGTTCATCCCTATGCCAATAAT
1 ATGTTCATCCCTATGCCAATAAT
289741 A
1 A
289742 ATAATAATAA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
23 69 1.00
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.37
Consensus pattern (23 bp):
ATGTTCATCCCTATGCCAATAAT
Found at i:302090 original size:20 final size:20
Alignment explanation
Indices: 302041--302077 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
302031 ATTAGGATAT
302041 ATTA-TTTGTTAAGTTAACC
1 ATTAGTTTGTTAAGTTAACC
*
302060 ATTTGTTTGTTAAGTTAA
1 ATTAGTTTGTTAAGTTAA
302078 TTGTTAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (20 bp):
ATTAGTTTGTTAAGTTAACC
Found at i:306502 original size:13 final size:13
Alignment explanation
Indices: 306484--306508 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
306474 TTCACAATTT
306484 TTTTTAAAAAATA
1 TTTTTAAAAAATA
306497 TTTTTAAAAAAT
1 TTTTTAAAAAAT
306509 TCATCAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTTTAAAAAATA
Found at i:306756 original size:3 final size:3
Alignment explanation
Indices: 306748--306793 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
306738 ACTATCCAAC
306748 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
306794 GTCCCTCACG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:307954 original size:41 final size:42
Alignment explanation
Indices: 307897--307976 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
307887 GGAATGATAG
*
307897 TTAAAGAATAAAAAAA-TAAAATTATTTTATGTTAATATTTA
1 TTAAAGAATAAAAAAATTAAAATTATTTTATGTCAATATTTA
*
307938 TTAAAGAATACAAAAATTAAAATTATTTTATGTCAATAT
1 TTAAAGAATAAAAAAATTAAAATTATTTTATGTCAATAT
307977 GTATATGATT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 15 0.42
42 21 0.58
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (42 bp):
TTAAAGAATAAAAAAATTAAAATTATTTTATGTCAATATTTA
Found at i:315512 original size:2 final size:2
Alignment explanation
Indices: 315507--315534 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
315497 ACTTTTTTAA
315507 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
315535 TCAAATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:315746 original size:24 final size:25
Alignment explanation
Indices: 315702--315748 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
315692 TATTTAATAG
315702 TAATATTTAATTATTTTAATTGAAT
1 TAATATTTAATTATTTTAATTGAAT
315727 TAATA-TT-ATTATTTTTAATTGA
1 TAATATTTAATTA-TTTTAATTGA
315749 GGGTGATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.19
24 12 0.57
25 5 0.24
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (25 bp):
TAATATTTAATTATTTTAATTGAAT
Found at i:321402 original size:36 final size:36
Alignment explanation
Indices: 321350--321456 Score: 205
Period size: 36 Copynumber: 3.0 Consensus size: 36
321340 TTTCCATATT
321350 GGTATATCATATACAAAGTTTCTCGATAAAGATAGG
1 GGTATATCATATACAAAGTTTCTCGATAAAGATAGG
*
321386 GGTACATCATATACAAAGTTTCTCGATAAAGATAGG
1 GGTATATCATATACAAAGTTTCTCGATAAAGATAGG
321422 GGTATATCATATACAAAGTTTCTCGATAAAGATAG
1 GGTATATCATATACAAAGTTTCTCGATAAAGATAG
321457 TGTTTTTTGT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 69 1.00
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (36 bp):
GGTATATCATATACAAAGTTTCTCGATAAAGATAGG
Found at i:326037 original size:19 final size:19
Alignment explanation
Indices: 325999--326040 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
325989 TATTTGTTAT
325999 TTTTGTTATTTTTTACTTTC
1 TTTTGTTATTTTTTA-TTTC
326019 TTTTGTTATTTTCTT-TTTC
1 TTTTGTTATTTT-TTATTTC
326038 TTT
1 TTT
326041 ATTACATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.33
20 12 0.57
21 2 0.10
ACGTcount: A:0.07, C:0.10, G:0.05, T:0.79
Consensus pattern (19 bp):
TTTTGTTATTTTTTATTTC
Found at i:329616 original size:16 final size:16
Alignment explanation
Indices: 329595--329627 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
329585 TACTATTCAT
*
329595 GTGAATAGTGAATTTC
1 GTGAATAGTGAAATTC
329611 GTGAATAGTGAAATTC
1 GTGAATAGTGAAATTC
329627 G
1 G
329628 GTCGGCGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.33
Consensus pattern (16 bp):
GTGAATAGTGAAATTC
Found at i:342857 original size:21 final size:20
Alignment explanation
Indices: 342833--342944 Score: 84
Period size: 21 Copynumber: 5.3 Consensus size: 20
342823 ATAATTCGCA
342833 TTGCGATAGTCCAAGTTCGAG
1 TTGCGATAGTCCAAGTTCG-G
* * *
342854 TTGCTATTTATTACAAGTTC-G
1 TTGCGA--TAGTCCAAGTTCGG
* *
342875 TTGAGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCG-G
* *
342896 TTGCGATTTATTCCAAATTC-G
1 TTGCGA--TAGTCCAAGTTCGG
342917 TTGCGATAGTCCAAGTTCGTG
1 TTGCGATAGTCCAAGTTCG-G
342938 TTGCGAT
1 TTGCGAT
342945 TTATTTCGCG
Statistics
Matches: 69, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
19 19 0.28
21 31 0.45
23 19 0.28
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCCAAGTTCGG
Found at i:342899 original size:42 final size:42
Alignment explanation
Indices: 342837--342949 Score: 163
Period size: 42 Copynumber: 2.7 Consensus size: 42
342827 TTCGCATTGC
* *
342837 GATAGTCCAAGTTCGAGTTGCTATTTATTACAAGTTCGTTGA
1 GATAGTCCAAGTTCGAGTTGCGATTTATTACAAATTCGTTGA
* * * *
342879 GATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
1 GATAGTCCAAGTTCGAGTTGCGATTTATTACAAATTCGTTGA
*
342921 GATAGTCCAAGTTCGTGTTGCGATTTATT
1 GATAGTCCAAGTTCGAGTTGCGATTTATT
342950 TCGCGATAGT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (42 bp):
GATAGTCCAAGTTCGAGTTGCGATTTATTACAAATTCGTTGA
Found at i:342966 original size:33 final size:33
Alignment explanation
Indices: 342919--342982 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
342909 CAAATTCGTT
*
342919 GCGATAGTCCAAGTTCGTGTTGCGATTTATTTC
1 GCGATAGTCCAAGTTCGCGTTGCGATTTATTTC
* *
342952 GCGATAGTCGAAGTTCGCGTTTCGATTTATT
1 GCGATAGTCCAAGTTCGCGTTGCGATTTATT
342983 CCAAATTCGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (33 bp):
GCGATAGTCCAAGTTCGCGTTGCGATTTATTTC
Found at i:343111 original size:5 final size:5
Alignment explanation
Indices: 343090--343123 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
343080 AGACACGTAT
343090 GACCAC GACCAC GACCC GACCC GACCC GACCC GA
1 GACC-C GACC-C GACCC GACCC GACCC GACCC GA
343124 GACGAGACGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.64
6 10 0.36
ACGTcount: A:0.26, C:0.53, G:0.21, T:0.00
Consensus pattern (5 bp):
GACCC
Found at i:343129 original size:5 final size:5
Alignment explanation
Indices: 343121--343159 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
343111 CGACCCGACC
* *
343121 CGAGA CGAGA CGAGA CGACA CGACA CGAGA CGAGA CGAG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAG
343160 CGGCGGCGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.38, C:0.26, G:0.36, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:343672 original size:9 final size:9
Alignment explanation
Indices: 343642--343692 Score: 54
Period size: 9 Copynumber: 6.0 Consensus size: 9
343632 TCCCGTCACG
343642 GGTCGTGGT
1 GGTCGTGGT
* * *
343651 CGTGGTCGT
1 GGTCGTGGT
343660 GGTCGTGGT
1 GGTCGTGGT
343669 GGTC---GT
1 GGTCGTGGT
343675 GGTCGTGGT
1 GGTCGTGGT
343684 GGTCGTGGT
1 GGTCGTGGT
343693 AATACGTGTC
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
6 6 0.18
9 27 0.82
ACGTcount: A:0.00, C:0.14, G:0.53, T:0.33
Consensus pattern (9 bp):
GGTCGTGGT
Found at i:343672 original size:15 final size:15
Alignment explanation
Indices: 343652--343692 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
343642 GGTCGTGGTC
343652 GTGGTCGTGGTCGTG
1 GTGGTCGTGGTCGTG
343667 GTGGTCGTGGTCGTG
1 GTGGTCGTGGTCGTG
343682 GTGGTCGTGGT
1 GTGGTCGTGGT
343693 AATACGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.00, C:0.12, G:0.54, T:0.34
Consensus pattern (15 bp):
GTGGTCGTGGTCGTG
Found at i:343692 original size:6 final size:6
Alignment explanation
Indices: 343642--343683 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
343632 TCCCGTCACG
343642 GGTCGT GGTCGT GGTCGT GGTCGT -G--GT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
343684 GGTCGTGGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 2 0.06
4 1 0.03
5 1 0.03
6 29 0.88
ACGTcount: A:0.00, C:0.14, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:347403 original size:17 final size:16
Alignment explanation
Indices: 347381--347412 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
347371 ATATATATTT
347381 ATATAAAATGTAATATA
1 ATATAAAAT-TAATATA
347398 ATATAAAATTAATAT
1 ATATAAAATTAATAT
347413 TATAATCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
ATATAAAATTAATATA
Done.