Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000426.1 Hibiscus syriacus cultivar Beakdansim tig00000778_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: 3165331
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 15
Found at i:238718 original size:19 final size:18
Alignment explanation
Indices: 238696--238776 Score: 70
Period size: 14 Copynumber: 4.8 Consensus size: 18
238686 CAAAATCGCA
238696 TTGCGATTTTCATTTAGCG
1 TTGCGATTTTCATTT-GCG
*
238715 TTGCGA--TTC-TCT-CG
1 TTGCGATTTTCATTTGCG
238729 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTT-GCG
*
238748 TTGCGA--TTC-TCT-CG
1 TTGCGATTTTCATTTGCG
238762 TTGCGATTTTCATTT
1 TTGCGATTTTCATTT
238777 CTCTCGTTGC
Statistics
Matches: 50, Mismatches: 4, Indels: 18
0.69 0.06 0.25
Matches are distributed among these distances:
14 16 0.32
16 10 0.20
17 10 0.20
19 14 0.28
ACGTcount: A:0.11, C:0.21, G:0.20, T:0.48
Consensus pattern (18 bp):
TTGCGATTTTCATTTGCG
Found at i:238777 original size:33 final size:33
Alignment explanation
Indices: 238696--238818 Score: 156
Period size: 33 Copynumber: 3.5 Consensus size: 33
238686 CAAAATCGCA
*
238696 TTGCGATTTTCATTTAGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
238729 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
238762 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
238803 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
238819 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 10
0.87 0.02 0.11
Matches are distributed among these distances:
33 44 0.55
34 2 0.03
35 6 0.08
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.03
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:238780 original size:21 final size:21
Alignment explanation
Indices: 238754--238818 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
238744 CGCGTTGCGA
238754 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
238775 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
238795 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
238816 TTC
1 TTC
238819 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:240803 original size:92 final size:93
Alignment explanation
Indices: 240509--240881 Score: 709
Period size: 93 Copynumber: 4.1 Consensus size: 93
240499 TAGATTGCTT
*
240509 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACAC--TGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
240572 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
240600 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
240665 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
240693 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTC-TTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
240757 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
240785 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
240850 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
240877 AGTAA
1 AGTAA
240882 TGCAATCCAT
Statistics
Matches: 278, Mismatches: 1, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
91 52 0.19
92 98 0.35
93 128 0.46
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:240820 original size:185 final size:183
Alignment explanation
Indices: 240509--240881 Score: 703
Period size: 185 Copynumber: 2.0 Consensus size: 183
240499 TAGATTGCTT
240509 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGAAATAGTATT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGAAATAGTATT
240574 TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGT
66 TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGT
240639 GTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTG-A
*
240693 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTC-TTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACAC--TGAAATAGTA
240757 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
64 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
240822 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
129 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
240877 AGTAA
1 AGTAA
240882 TGCAATCCAT
Statistics
Matches: 186, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
183 7 0.04
184 50 0.27
185 129 0.69
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (183 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGAAATAGTATT
TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGT
GTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:240966 original size:19 final size:19
Alignment explanation
Indices: 240926--241002 Score: 83
Period size: 19 Copynumber: 4.3 Consensus size: 19
240916 TAGTTTACTT
* *
240926 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
240946 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
240965 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
240979 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
240998 TCGCA
1 TCGCA
241003 TTGCGATTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
14 10 0.21
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 19 0.40
20 13 0.27
ACGTcount: A:0.45, C:0.30, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:241036 original size:21 final size:19
Alignment explanation
Indices: 240998--241150 Score: 137
Period size: 19 Copynumber: 8.6 Consensus size: 19
240988 GAAACCAAAA
240998 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
241017 TCGCGTTGCGA--TTC-TT
1 TCGCATTGCGATTTTCATT
241033 T--CATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
241050 TCGCATTGCGA--TTC-TG
1 TCGCATTGCGATTTTCATT
241066 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* **
241083 TCGCGTTGCGATTTTGGTT
1 TCGCATTGCGATTTTCATT
**
241102 TCGCATTGCGATTTTGGTT
1 TCGCATTGCGATTTTCATT
* * *
241121 TCTCGTTGCGATTATCATT
1 TCGCATTGCGATTTTCATT
*
241140 TCGCGTTGCGA
1 TCGCATTGCGA
241151 CTTTAAGTTT
Statistics
Matches: 111, Mismatches: 13, Indels: 20
0.77 0.09 0.14
Matches are distributed among these distances:
14 13 0.12
16 13 0.12
17 13 0.12
19 72 0.65
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:241043 original size:33 final size:33
Alignment explanation
Indices: 241001--241095 Score: 163
Period size: 33 Copynumber: 2.9 Consensus size: 33
240991 ACCAAAATCG
*
241001 CATTGCGATTTTCATTTCGCGTTGCGATTCTTT
1 CATTGCGATTTTCATTTCGCGTTGCGATTCTGT
*
241034 CATTGCGATTTTCATTTCGCATTGCGATTCTGT
1 CATTGCGATTTTCATTTCGCGTTGCGATTCTGT
*
241067 CGTTGCGATTTTCATTTCGCGTTGCGATT
1 CATTGCGATTTTCATTTCGCGTTGCGATT
241096 TTGGTTTCGC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.46
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCGTTGCGATTCTGT
Found at i:243111 original size:14 final size:14
Alignment explanation
Indices: 243092--243127 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
243082 ATTGTTTAAT
243092 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
243106 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
243120 TGATTTGT
1 TGATTTGT
243128 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:243250 original size:19 final size:18
Alignment explanation
Indices: 243234--243349 Score: 122
Period size: 19 Copynumber: 6.7 Consensus size: 18
243224 AAAAATGACT
243234 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
243253 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
*
243271 ATCGCAA--CGAGA-G-A
1 ATCGCAATGCGAAATGAA
243285 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
243304 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATG-AA
*
243324 ATCGCAA--CGAGA-G-A
1 ATCGCAATGCGAAATGAA
243338 ATCGCAATGCGA
1 ATCGCAATGCGA
243350 TTTTAATTTC
Statistics
Matches: 86, Mismatches: 3, Indels: 19
0.80 0.03 0.18
Matches are distributed among these distances:
14 16 0.19
15 1 0.01
16 12 0.14
17 4 0.05
18 10 0.12
19 27 0.31
20 16 0.19
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:243310 original size:51 final size:53
Alignment explanation
Indices: 243234--243349 Score: 218
Period size: 51 Copynumber: 2.2 Consensus size: 53
243224 AAAAATGACT
243234 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATG-AAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
243285 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
243338 ATCGCAATGCGA
1 ATCGCAATGCGA
243350 TTTTAATTTC
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
51 29 0.46
52 6 0.10
53 28 0.44
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:243367 original size:19 final size:19
Alignment explanation
Indices: 243339--243541 Score: 185
Period size: 19 Copynumber: 11.7 Consensus size: 19
243329 AACGAGAGAA
* *
243339 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
243358 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
243374 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
243391 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
243410 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
243426 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
243443 TTGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
243462 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
243478 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
243495 TCCGCATTGCTATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
243513 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
243529 TCGCATTGCGATT
1 TCGCATTGCGATT
243542 CTCTCGTTGC
Statistics
Matches: 149, Mismatches: 14, Indels: 42
0.73 0.07 0.20
Matches are distributed among these distances:
14 28 0.19
16 23 0.15
17 18 0.12
18 3 0.02
19 66 0.44
20 11 0.07
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:243402 original size:52 final size:52
Alignment explanation
Indices: 243339--243513 Score: 305
Period size: 52 Copynumber: 3.3 Consensus size: 52
243329 AACGAGAGAA
* *
243339 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
243391 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
243443 TTGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
243495 TCCGCATTGCTATTTTCAT
1 T-CGCATTGCGATTTTCAT
243514 GTTGGGATTT
Statistics
Matches: 117, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
52 102 0.87
53 15 0.13
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:243563 original size:33 final size:33
Alignment explanation
Indices: 243345--243555 Score: 207
Period size: 33 Copynumber: 6.2 Consensus size: 33
243335 AGAATCGCAA
*
243345 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
243378 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * *
243416 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-T-TGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCT-CGT
243449 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
* *
243482 TGCGATTTTCATTTCCGCATTGCTATTTTCAT-GT
1 TGCGATTTTCATTT-CGCATTGCGATTCTC-TCGT
*
243516 TGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
243549 TGCGATT
1 TGCGATT
243556 GTAATTTCCG
Statistics
Matches: 146, Mismatches: 16, Indels: 32
0.75 0.08 0.16
Matches are distributed among these distances:
31 9 0.06
32 6 0.04
33 69 0.47
34 30 0.21
35 6 0.04
36 4 0.03
37 2 0.01
38 8 0.05
39 3 0.02
40 9 0.06
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:246059 original size:24 final size:24
Alignment explanation
Indices: 246025--246071 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
246015 CTGAAACATC
246025 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
246049 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
246072 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:246782 original size:20 final size:20
Alignment explanation
Indices: 246754--246963 Score: 228
Period size: 20 Copynumber: 10.5 Consensus size: 20
246744 AAATTTCAGT
* * * *
246754 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
246774 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
246794 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
246814 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
246834 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
246854 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
246874 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
246894 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
246914 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
246934 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
246954 GTTGCGATTT
1 GTTGCGATTT
246964 TGGAAAATCG
Statistics
Matches: 165, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.02
20 159 0.96
21 3 0.02
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:246980 original size:21 final size:21
Alignment explanation
Indices: 246956--247011 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
246946 GTGTTCGCGT
246956 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGCAA
* * ** *
246977 TGCGAATTTGTACTATCGCAT
1 TGCGATTTTGGAAAATCGCAA
246998 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
247012 CTGATTTGCG
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (21 bp):
TGCGATTTTGGAAAATCGCAA
Found at i:261287 original size:26 final size:26
Alignment explanation
Indices: 261251--261306 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
261241 AATTGCTTGC
*
261251 CTGATAGCATTAGTTACACCACCTTT
1 CTGATAACATTAGTTACACCACCTTT
261277 CTGATAACATTAGTTACACCACCTTT
1 CTGATAACATTAGTTACACCACCTTT
261303 CTGA
1 CTGA
261307 ATGGGCTTTT
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:0.29, C:0.27, G:0.11, T:0.34
Consensus pattern (26 bp):
CTGATAACATTAGTTACACCACCTTT
Found at i:262985 original size:30 final size:30
Alignment explanation
Indices: 262951--263039 Score: 142
Period size: 30 Copynumber: 3.0 Consensus size: 30
262941 CACAAATCGG
*
262951 TCACTCATGTAATCGTTTGTTACAAAATGA
1 TCACTCACGTAATCGTTTGTTACAAAATGA
262981 TCACTCACGTAATCGTTTGTTACAAAATGA
1 TCACTCACGTAATCGTTTGTTACAAAATGA
* * *
263011 TCACTAACGTTACCGTTTGTTACAAAATG
1 TCACTCACGTAATCGTTTGTTACAAAATG
263040 GTTACTCGAC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (30 bp):
TCACTCACGTAATCGTTTGTTACAAAATGA
Found at i:263128 original size:3 final size:3
Alignment explanation
Indices: 263120--263207 Score: 176
Period size: 3 Copynumber: 29.3 Consensus size: 3
263110 TAACTGACTC
263120 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
263168 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
263208 TCTATCAAAG
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:263290 original size:7 final size:7
Alignment explanation
Indices: 263278--263309 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
263268 CCATTTCAAG
263278 GCCTTTT
1 GCCTTTT
263285 GCCTTTT
1 GCCTTTT
263292 GCCTTTT
1 GCCTTTT
263299 -CC-TTT
1 GCCTTTT
263304 GCCTTT
1 GCCTTT
263310 GCCCATCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
5 3 0.13
6 4 0.17
7 16 0.70
ACGTcount: A:0.00, C:0.31, G:0.12, T:0.56
Consensus pattern (7 bp):
GCCTTTT
Found at i:264426 original size:167 final size:164
Alignment explanation
Indices: 264052--264523 Score: 640
Period size: 167 Copynumber: 2.8 Consensus size: 164
264042 GTTTACCCTT
* * * *
264052 AGCCAAACATTTGTGATCATTGGTGTAATTTACCTGTTATAATTCACATAATAATTTATCATCAT
1 AGCCAAACATTAGTGACCATT-GTGTAATTTACCTTTTATAATTCACATAATAATCTATCAT-AT
* ** *
264117 CGATACTCATTAGCCCGACATTCCCTGACGTGTGTTTAGGCCACGAGCCACTGGTTCAATATTTC
64 CGATACTCATTAGCCCGACATTTCCTGACGTGTGTTTAGGCCACGAGCCACCAGTTCAATGTTTC
* *
264182 ATTTCCATTTCAAACATCAATGGTGAACTAACACTT
129 ATTTCCATTTCAAACATCAATAGTGAACTAACACTA
* *
264218 AGCCAAACATTAGTGACCATTGATGTAGTTTACCCTTTATAATTCACATAATAATCTATCACTAT
1 AGCCAAACATTAGTGACCATTG-TGTAATTTACCTTTTATAATTCACATAATAATCTATCA-TAT
* * * * * *
264283 CAATACTCATTAGCCTGACATTTCCTTAC-TGTGTTTAGGCCATGAGCTACCAGTTCACTGTTTC
64 CGATACTCATTAGCCCGACATTTCCTGACGTGTGTTTAGGCCACGAGCCACCAGTTCAATGTTTC
*
264347 ATTTCCATTTCAAATATCAATAGTGAAAACTAACACTA
129 ATTTCCATTTCAAACATCAATAGTG--AACTAACACTA
* *
264385 AGCCAAATATTAGTGACCATTAGCGTAATTTACCTTTTATAATTCACATAATAATCTATCATTAT
1 AGCCAAACATTAGTGACCATT-GTGTAATTTACCTTTTATAATTCACATAATAATCTATCA-TAT
* * * *
264450 CGATACTCATTAGCCCCACATTTCCAGGCGTGTGTTTAGGCCACGAGCCACCAGTTCATTGTTTC
64 CGATACTCATTAGCCCGACATTTCCTGACGTGTGTTTAGGCCACGAGCCACCAGTTCAATGTTTC
264515 ATTTCCATT
129 ATTTCCATT
264524 CTACGCGCAC
Statistics
Matches: 267, Mismatches: 33, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
165 53 0.20
166 80 0.30
167 92 0.34
168 42 0.16
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (164 bp):
AGCCAAACATTAGTGACCATTGTGTAATTTACCTTTTATAATTCACATAATAATCTATCATATCG
ATACTCATTAGCCCGACATTTCCTGACGTGTGTTTAGGCCACGAGCCACCAGTTCAATGTTTCAT
TTCCATTTCAAACATCAATAGTGAACTAACACTA
Found at i:266410 original size:30 final size:32
Alignment explanation
Indices: 266379--266476 Score: 99
Period size: 37 Copynumber: 2.9 Consensus size: 32
266369 CTTTTTTATA
266379 TTTTTAA-TTTTATAAAAAAATATATAAATAT
1 TTTTTAACTTTTATAAAAAAATATATAAATAT
* *
266410 TATGAATTTAATTTTTTTAAATAAAATATATAAATAT
1 T-T---TTTAACTTTTATAAA-AAAATATATAAATAT
*
266447 TTTTTAACTTGTTAAAAAATAAATATATAA
1 TTTTTAACTT-TTATAAAA-AAATATATAA
266477 TAAAGACAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
31 1 0.02
32 1 0.02
33 8 0.15
34 15 0.27
35 5 0.09
36 9 0.16
37 16 0.29
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (32 bp):
TTTTTAACTTTTATAAAAAAATATATAAATAT
Found at i:266744 original size:21 final size:20
Alignment explanation
Indices: 266713--266754 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
266703 AGTACCAAAC
266713 TCTTCTCTCTCTATTT-CTTT
1 TCTTCTCTCTCT-TTTGCTTT
266733 TCTTCTTCTCTCTTTTGCTTT
1 TCTTC-TCTCTCTTTTGCTTT
266754 T
1 T
266755 GCATGCACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.02, C:0.29, G:0.02, T:0.67
Consensus pattern (20 bp):
TCTTCTCTCTCTTTTGCTTT
Found at i:273587 original size:22 final size:22
Alignment explanation
Indices: 273559--273615 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
273549 TCTTTCTATT
273559 GTTTAGGGTTTT-GAACTTAAGG
1 GTTTAGGGTTTTAG-ACTTAAGG
273581 GTTTAGGGTTTTAGACTTAAGG
1 GTTTAGGGTTTTAGACTTAAGG
273603 GTTTAGGGTTTTA
1 GTTTAGGGTTTTA
273616 AGCTAGGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 33 0.97
23 1 0.03
ACGTcount: A:0.21, C:0.04, G:0.32, T:0.44
Consensus pattern (22 bp):
GTTTAGGGTTTTAGACTTAAGG
Found at i:280825 original size:14 final size:14
Alignment explanation
Indices: 280806--280843 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
280796 TTCTGTCTAT
280806 TGCAGGGATTCT-TA
1 TGCAGGGATT-TATA
*
280820 TGCAGGGATTTATT
1 TGCAGGGATTTATA
280834 TGCAGGGATT
1 TGCAGGGATT
280844 ACTTCCCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 1 0.05
14 21 0.95
ACGTcount: A:0.21, C:0.11, G:0.32, T:0.37
Consensus pattern (14 bp):
TGCAGGGATTTATA
Found at i:298340 original size:115 final size:116
Alignment explanation
Indices: 298149--298386 Score: 295
Period size: 115 Copynumber: 2.1 Consensus size: 116
298139 AATGTTCCTA
* * * *
298149 ATTTTTTATATTTATAATTAGGATCTTTTATTTTATAATTTTATAAAATTTTTAGTTTTTGATCA
1 ATTTTTTATATTTATAATTAGGACCTTATATTTTATAATTTCATAAAATGTTTAGTTTTTGATCA
* *
298214 TCTTTTTCATTTATCTTATTAATTCATTCAGTTTTGAATTAAATATAA-TT
66 TCTTTTTCATTTATCTTATTAACTCATTCAGTTTTAAATTAAATATAACTT
* * * *
298264 ATTTTTTATATTTATTATTAGGCCCCTTAT-TTTTATAATTTCATTATATGTTTAG-TTTTGACT
1 ATTTTTTATATTTATAATTAGG-ACCTTATATTTTATAATTTCATAAAATGTTTAGTTTTTGA-T
* * *
298327 C-TCTTTTTCCATTTCTCTTATTTACTCATTCAGTTTTAAATTAAATTTAATCTT
64 CATCTTTTT-CATTTATCTTATTAACTCATTCAGTTTTAAATTAAATATAA-CTT
298381 ATTTTT
1 ATTTTT
298387 CTCCTTTTTT
Statistics
Matches: 105, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
114 13 0.12
115 80 0.76
116 4 0.04
117 8 0.08
ACGTcount: A:0.27, C:0.10, G:0.05, T:0.58
Consensus pattern (116 bp):
ATTTTTTATATTTATAATTAGGACCTTATATTTTATAATTTCATAAAATGTTTAGTTTTTGATCA
TCTTTTTCATTTATCTTATTAACTCATTCAGTTTTAAATTAAATATAACTT
Found at i:299016 original size:20 final size:20
Alignment explanation
Indices: 298987--299028 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
298977 GCACTTTTTT
*
298987 TTTATTCTTTTCCAATATAA
1 TTTATCCTTTTCCAATATAA
**
299007 TTTATCCTTTTTTAATATAA
1 TTTATCCTTTTCCAATATAA
299027 TT
1 TT
299029 GAGTCCTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTATCCTTTTCCAATATAA
Found at i:311451 original size:15 final size:17
Alignment explanation
Indices: 311423--311456 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
311413 GATGTTAAAT
311423 ATTTATATATTTA-TAA
1 ATTTATATATTTATTAA
311439 ATTTATA-ATTTATTAA
1 ATTTATATATTTATTAA
311455 AT
1 AT
311457 ATGTACGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTATATATTTATTAA
Found at i:311877 original size:6 final size:6
Alignment explanation
Indices: 311868--311896 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
311858 TAAATTTAAA
311868 TATAAT TATAAT TATAAT TAT-AT TATAAT
1 TATAAT TATAAT TATAAT TATAAT TATAAT
311897 CTACTCCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TATAAT
Found at i:316279 original size:36 final size:36
Alignment explanation
Indices: 316232--316371 Score: 246
Period size: 36 Copynumber: 3.9 Consensus size: 36
316222 TCCTGTTTAG
316232 CAATTCTTCACCCTTCATCTCCTCGCCATGGATTAC
1 CAATTCTTCACCCTTCATCTCCTCGCCATGGATTAC
*
316268 CAATTCTTCACCCTTCATCTCCTCGCCATGGACTAC
1 CAATTCTTCACCCTTCATCTCCTCGCCATGGATTAC
*
316304 CAATTCTTCACCCTTCATCTCCTCACCA-GGATTAC
1 CAATTCTTCACCCTTCATCTCCTCGCCATGGATTAC
*
316339 CAATTCTTCACCCTTCATCTCCTCGCCAAGGAT
1 CAATTCTTCACCCTTCATCTCCTCGCCATGGAT
316372 AGAGAGCCCG
Statistics
Matches: 99, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
35 33 0.33
36 66 0.67
ACGTcount: A:0.21, C:0.40, G:0.08, T:0.31
Consensus pattern (36 bp):
CAATTCTTCACCCTTCATCTCCTCGCCATGGATTAC
Found at i:316355 original size:71 final size:72
Alignment explanation
Indices: 316232--316366 Score: 254
Period size: 71 Copynumber: 1.9 Consensus size: 72
316222 TCCTGTTTAG
*
316232 CAATTCTTCACCCTTCATCTCCTCGCCATGGATTACCAATTCTTCACCCTTCATCTCCTCGCCAT
1 CAATTCTTCACCCTTCATCTCCTCACCATGGATTACCAATTCTTCACCCTTCATCTCCTCGCCAT
316297 GGACTAC
66 GGACTAC
316304 CAATTCTTCACCCTTCATCTCCTCACCA-GGATTACCAATTCTTCACCCTTCATCTCCTCGCCA
1 CAATTCTTCACCCTTCATCTCCTCACCATGGATTACCAATTCTTCACCCTTCATCTCCTCGCCA
316367 AGGATAGAGA
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
71 35 0.56
72 27 0.44
ACGTcount: A:0.20, C:0.41, G:0.07, T:0.32
Consensus pattern (72 bp):
CAATTCTTCACCCTTCATCTCCTCACCATGGATTACCAATTCTTCACCCTTCATCTCCTCGCCAT
GGACTAC
Found at i:318162 original size:65 final size:64
Alignment explanation
Indices: 318080--318203 Score: 194
Period size: 65 Copynumber: 1.9 Consensus size: 64
318070 AATTCTTCAC
*
318080 CCTTCATCGGGAAACTGTTGCAAATAGCAAAGGGACGAACTGTCATTTATCGTTGCTAGGTGCCA
1 CCTTCATCGGGAAACTGTTGCAAATAGCAAAGGGACGAACTGTCACTTATCG-TGCTAGGTGCCA
* * * *
318145 CCTTCCTCGGGAAACTGTTGCAAGTTGCAAAGGGACGAGCTGTCACTTATCGTGCTAGG
1 CCTTCATCGGGAAACTGTTGCAAATAGCAAAGGGACGAACTGTCACTTATCGTGCTAGG
318204 CAAGCGTCAA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
64 7 0.13
65 47 0.87
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.26
Consensus pattern (64 bp):
CCTTCATCGGGAAACTGTTGCAAATAGCAAAGGGACGAACTGTCACTTATCGTGCTAGGTGCCA
Found at i:318559 original size:2 final size:2
Alignment explanation
Indices: 318552--318585 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
318542 TACCCCCTAT
318552 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
318586 CTTTATTAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:323427 original size:13 final size:14
Alignment explanation
Indices: 323402--323433 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
323392 TGTTTATCAT
323402 TATTATCTTTAAAA
1 TATTATCTTTAAAA
323416 TATTAT-TTTAAAA
1 TATTATCTTTAAAA
323429 TATTA
1 TATTA
323434 ATTAAGTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTATCTTTAAAA
Found at i:323944 original size:21 final size:19
Alignment explanation
Indices: 323909--323964 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
323899 ATTATTTTTT
323909 AAAA-TTTAA-TAAAAATA
1 AAAATTTTAATTAAAAATA
*
323926 TTAAATTTATAATTAAAAATA
1 -AAAATTT-TAATTAAAAATA
*
323947 AAAATTTTAATAAAAAAT
1 AAAATTTTAATTAAAAAT
323965 TATTTCTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 3 0.09
19 12 0.38
20 9 0.28
21 8 0.25
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATTTTAATTAAAAATA
Found at i:323964 original size:19 final size:19
Alignment explanation
Indices: 323908--323962 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 19
323898 TATTATTTTT
323908 TAAAA-TTTAATAAAAATA
1 TAAAATTTTAATAAAAATA
*
323926 TTAAATTTATAATTAAAAATA
1 TAAAATTT-TAA-TAAAAATA
323947 -AAAATTTTAATAAAAA
1 TAAAATTTTAATAAAAA
323963 ATTATTTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 10 0.31
19 5 0.16
20 9 0.28
21 8 0.25
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAATTTTAATAAAAATA
Found at i:324298 original size:32 final size:32
Alignment explanation
Indices: 324262--324328 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
324252 GATCTAAAGG
* *
324262 TTGACCTAAATCGAAAATC-AACTGATCCGATA
1 TTGACCCAAATC-AAAATCTAACCGATCCGATA
* *
324294 TTGACCCGACTCAAAATCTAACCGATCCGATA
1 TTGACCCAAATCAAAATCTAACCGATCCGATA
324326 TTG
1 TTG
324329 TTTAGACCCG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 6 0.20
32 24 0.80
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.25
Consensus pattern (32 bp):
TTGACCCAAATCAAAATCTAACCGATCCGATA
Found at i:324535 original size:15 final size:15
Alignment explanation
Indices: 324511--324540 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
324501 ATTTAATCTA
324511 GACCTAAAATGATCC
1 GACCTAAAATGATCC
*
324526 GACCTGAAATGATCC
1 GACCTAAAATGATCC
324541 TACCGGAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.20
Consensus pattern (15 bp):
GACCTAAAATGATCC
Found at i:327687 original size:18 final size:18
Alignment explanation
Indices: 327643--327696 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
327633 AACACGCATA
*
327643 CATACATATGTATACATAAG
1 CATACATATATATACAT--G
327663 CA-A-ATATATATACATG
1 CATACATATATATACATG
*
327679 CATACATATACATACATG
1 CATACATATATATACATG
327697 TATATAACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
16 3 0.10
17 1 0.03
18 23 0.77
19 1 0.03
20 2 0.07
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (18 bp):
CATACATATATATACATG
Found at i:327701 original size:14 final size:14
Alignment explanation
Indices: 327640--327702 Score: 54
Period size: 14 Copynumber: 4.2 Consensus size: 14
327630 GCAAACACGC
*
327640 ATACATACATATGT
1 ATACATACATATAT
327654 ATACATAAGCAAATATAT
1 ATACAT-A-C--ATATAT
* *
327672 ATACATGCATACAT
1 ATACATACATATAT
*
327686 ATACATACATGTAT
1 ATACATACATATAT
327700 ATA
1 ATA
327703 ACTAAAAGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
14 25 0.64
15 1 0.03
16 2 0.05
18 11 0.28
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (14 bp):
ATACATACATATAT
Found at i:329161 original size:21 final size:21
Alignment explanation
Indices: 329132--329194 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
329122 GCATTGACCG
*
329132 TTATAGTGTTGATGTGATAGT
1 TTATAGTGTTGATGTGACAGT
* **
329153 TTATGGTGTCAATGTGACAGT
1 TTATAGTGTTGATGTGACAGT
**
329174 CCATAGTGTTGATGTGACAGT
1 TTATAGTGTTGATGTGACAGT
329195 CTAGTGTGAC
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.24, C:0.08, G:0.29, T:0.40
Consensus pattern (21 bp):
TTATAGTGTTGATGTGACAGT
Found at i:329201 original size:19 final size:19
Alignment explanation
Indices: 329135--329201 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 19
329125 TTGACCGTTA
* *
329135 TAGTGTTGATGTGATAGTT
1 TAGTGTTGATGTGACAGTC
**
329154 TATGGTGTCAATGTGACAGTCC
1 TA--GTGTTGATGTGACAGT-C
329176 ATAGTGTTGATGTGACAGTC
1 -TAGTGTTGATGTGACAGTC
329196 TAGTGT
1 TAGTGT
329202 GACAGATTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
19 8 0.21
20 1 0.03
21 27 0.71
23 2 0.05
ACGTcount: A:0.22, C:0.09, G:0.30, T:0.39
Consensus pattern (19 bp):
TAGTGTTGATGTGACAGTC
Found at i:331145 original size:21 final size:23
Alignment explanation
Indices: 331120--331169 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 23
331110 AATACAAGAT
331120 TTTGAAAAACA-TTTTAAAAT-A
1 TTTGAAAAACATTTTTAAAATAA
* *
331141 TTTGAAAGACATTTTTAATATAA
1 TTTGAAAAACATTTTTAAAATAA
331164 TTTGAA
1 TTTGAA
331170 CTTAAAAGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.40
22 8 0.32
23 7 0.28
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (23 bp):
TTTGAAAAACATTTTTAAAATAA
Found at i:336463 original size:55 final size:55
Alignment explanation
Indices: 336388--336889 Score: 257
Period size: 55 Copynumber: 9.1 Consensus size: 55
336378 GTCAGGATAA
* * *
336388 ATAAGACTTGAAAAATCTTCA-AATGACGAGCCTGCTCCCTATTCCTTCAG-GAAGT
1 ATAAGACTTGAACAATCTTCATAA-AACGAGCCTGCTCCCTATTCATTCAGAG-AGT
* * * *
336443 ATAAGACTCGAACAATCTTCATAAAACGTGTCTGCTCTCTATTCATTCAGAGAGT
1 ATAAGACTTGAACAATCTTCATAAAACGAGCCTGCTCCCTATTCATTCAGAGAGT
* * * * *
336498 ATAATACTTGAACAATCTTAAAAAAAAAAC-AGGTCC-GCTCTCTATTCCTTCAGAGAGT
1 ATAAGACTTGAACAATCTT---CATAAAACGA-G-CCTGCTCCCTATTCATTCAGAGAGT
* *
336556 AT-AGAACTCAGAA-AATCTTCA-ATAAAC-AGGTCC-GCTCCCTATTCTTTCAGAGAGT
1 ATAAG-ACT-TGAACAATCTTCATA-AAACGA-G-CCTGCTCCCTATTCATTCAGAGAGT
* * * * *
336611 ATAGGAC-T---CAATCTTTA-ACAAACGTGTCC-ACTCCCTATTCCTTCAGAGAGT
1 ATAAGACTTGAACAATCTTCATA-AAACGAG-CCTGCTCCCTATTCATTCAGAGAGT
* * * *
336662 AT-AGAACTCGAGCAATCTTCATAAAACGAGTCC-GCTCTCTATTCCTTCAGAGAGT
1 ATAAG-ACTTGAACAATCTTCATAAAACGAG-CCTGCTCCCTATTCATTCAGAGAGT
* * *
336717 AT-AGAACTCGAACAATCTTCA-ACAAACGTGTCC-GCTCTCTATTTC-TTCAGAGAGT
1 ATAAG-ACTTGAACAATCTTCATA-AAACGAG-CCTGCTCCCTA-TTCATTCAGAGAGT
* * * * *
336772 AT-AGAACTCGAACAATCTTCATGAAACGGGTCC-GCTCTCTATTCCTTCAGAGAGT
1 ATAAG-ACTTGAACAATCTTCATAAAACGAG-CCTGCTCCCTATTCATTCAGAGAGT
* ** *
336827 AT-AGAACTAGAACAATCTT--TAACGAACTTGTCC-GCTCCCTATTCCTTCAGAGAGT
1 ATAAG-ACTTGAACAATCTTCATAA--AACGAG-CCTGCTCCCTATTCATTCAGAGAGT
*
336882 ATAGGACT
1 ATAAGACT
336890 CAATCTTCAA
Statistics
Matches: 379, Mismatches: 42, Indels: 52
0.80 0.09 0.11
Matches are distributed among these distances:
50 1 0.00
51 40 0.11
53 2 0.01
54 5 0.01
55 278 0.73
56 9 0.02
57 1 0.00
58 39 0.10
59 4 0.01
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.28
Consensus pattern (55 bp):
ATAAGACTTGAACAATCTTCATAAAACGAGCCTGCTCCCTATTCATTCAGAGAGT
Found at i:336776 original size:110 final size:109
Alignment explanation
Indices: 336421--336890 Score: 582
Period size: 110 Copynumber: 4.3 Consensus size: 109
336411 TGACGAGCCT
* *
336421 GCTCCCTATTCCTTCAG-GAAGTATA-AGACTCGAACAATCTTCATAAAACGTGTCTGCTCTCTA
1 GCTCCCTATTCCTTCAGAG-AGTATAGA-ACTCGAACAATCTTCATAAAACGAGTCCGCTCTCTA
* * *
336484 TTCATTCAGAGAGTATA-ATACTTGAACAATCTTAAAAAAAAAACAG-GTCC
64 TTCCTTCAGAGAGTATAGA-AC-TGAACAATCTT---TAACAAAC-GTGTCC
* *
336534 GCTCTCTATTCCTTCAGAGAGTATAGAACTCAGAA-AATCTTCA-ATAAAC-AGGTCCGCTCCCT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTC-GAACAATCTTCATA-AAACGA-GTCCGCTCTCT
* *
336596 ATTCTTTCAGAGAGTATAGGACT---CAATCTTTAACAAACGTGTCC
63 ATTCCTTCAGAGAGTATAGAACTGAACAATCTTTAACAAACGTGTCC
* *
336640 ACTCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATAAAACGAGTCCGCTCTCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGAGTCCGCTCTCTATT
*
336705 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
66 CCTTCAGAGAGTATAGAACT-GAACAATCTTTAACAAACGTGTCC
* * * *
336750 GCTCTCTATTTCTTCAGAGAGTATAGAACTCGAACAATCTTCATGAAACGGGTCCGCTCTCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGAGTCCGCTCTCTATT
* *
336815 CCTTCAGAGAGTATAGAACTAGAACAATCTTTAACGAACTTGTCC
66 CCTTCAGAGAGTATAGAACT-GAACAATCTTTAACAAACGTGTCC
*
336860 GCTCCCTATTCCTTCAGAGAGTATAGGACTC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTC
336891 AATCTTCAAC
Statistics
Matches: 315, Mismatches: 28, Indels: 31
0.84 0.07 0.08
Matches are distributed among these distances:
105 3 0.01
106 82 0.26
107 2 0.01
109 7 0.02
110 148 0.47
112 2 0.01
113 66 0.21
114 5 0.02
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.29
Consensus pattern (109 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGAGTCCGCTCTCTATT
CCTTCAGAGAGTATAGAACTGAACAATCTTTAACAAACGTGTCC
Found at i:336906 original size:55 final size:52
Alignment explanation
Indices: 336454--336905 Score: 423
Period size: 55 Copynumber: 8.3 Consensus size: 52
336444 TAAGACTCGA
* *
336454 ACAATCTTCATA-AAACGTGTCTGCTCTCTATTCATTCAGAGAGTATA-ATACTT
1 ACAATCTTCA-ACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-AC-T
* *
336507 GAACAATCTTAAAAAAAAAACAG-GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
1 --ACAATCTT---CAACAAAC-GTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
* * * * *
336564 CAGAAAATCTTCAATAAACAG-GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACT
1 ---ACAATCTTCAACAAAC-GTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
* * *
336619 -CAATCTTTAACAAACGTGTCCACTCCCTATTCCTTCAGAGAGTATAGAACT
1 ACAATCTTCAACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
*
336670 CGAGCAATCTTCATA-AAACGAGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
1 --A-CAATCTTCA-ACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
*
336725 CGAACAATCTTCAACAAACGTGTCCGCTCTCTATTTCTTCAGAGAGTATAGAACT
1 ---ACAATCTTCAACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
** *
336780 CGAACAATCTTCATGAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
1 ---ACAATCTTCAACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
* * * * *
336835 AGAACAATCTTTAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT
1 ---ACAATCTTCAACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
336890 -CAATCTTCAACAAACG
1 ACAATCTTCAACAAACG
336906 AGTTTGCTTC
Statistics
Matches: 341, Mismatches: 41, Indels: 34
0.82 0.10 0.08
Matches are distributed among these distances:
50 1 0.00
51 56 0.16
54 1 0.00
55 236 0.69
56 2 0.01
57 2 0.01
58 41 0.12
59 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.28
Consensus pattern (52 bp):
ACAATCTTCAACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
Found at i:338282 original size:17 final size:18
Alignment explanation
Indices: 338260--338329 Score: 60
Period size: 17 Copynumber: 4.1 Consensus size: 18
338250 TCTCCTTTTA
338260 TTTCTCTTTTT-TTCATT
1 TTTCTCTTTTTCTTCATT
* *
338277 TTTCTCTTTTTGTT-TTT
1 TTTCTCTTTTTCTTCATT
338294 CTTTCAT-TTTTTCTTCATT
1 -TTTC-TCTTTTTCTTCATT
*
338313 TTTCT-TTTATC-TCATT
1 TTTCTCTTTTTCTTCATT
338329 T
1 T
338330 CTTCATTTCT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
16 6 0.13
17 19 0.42
18 17 0.38
19 3 0.07
ACGTcount: A:0.07, C:0.17, G:0.01, T:0.74
Consensus pattern (18 bp):
TTTCTCTTTTTCTTCATT
Found at i:338335 original size:35 final size:36
Alignment explanation
Indices: 338266--338343 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 36
338256 TTTATTTCTC
* * *
338266 TTTTT-TTCATTTTTCTCTTTTTGTTTTTCTTTCAT
1 TTTTTCTTCATTTTTCTCTTTATCTATTTCTTTCAT
338301 TTTTTCTTCATTTTTCT-TTTATCTCATTTC-TTCAT
1 TTTTTCTTCATTTTTCTCTTTATCT-ATTTCTTTCAT
*
338336 TTCTTCTT
1 TTTTTCTT
338344 TTTCTTCTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
35 22 0.59
36 15 0.41
ACGTcount: A:0.08, C:0.18, G:0.01, T:0.73
Consensus pattern (36 bp):
TTTTTCTTCATTTTTCTCTTTATCTATTTCTTTCAT
Found at i:338349 original size:17 final size:17
Alignment explanation
Indices: 338259--338352 Score: 51
Period size: 17 Copynumber: 5.6 Consensus size: 17
338249 CTCTCCTTTT
338259 ATTTC-TCTTTTT-TTC
1 ATTTCTTCTTTTTCTTC
* *
338274 ATTTTTCTCTTTTTGTT-
1 ATTTCT-TCTTTTTCTTC
338291 -TTTCTTTCATTTTTTCTTC
1 ATTTC-TTC--TTTTTCTTC
338310 ATTT-TTCTTTTATC-TC
1 ATTTCTTCTTTT-TCTTC
338326 ATTTCTTCATTTCTTCTT-
1 ATTTCTTC-TTT-TTCTTC
338344 -TTTCTTCTT
1 ATTTCTTCTT
338353 CTCATATTTA
Statistics
Matches: 63, Mismatches: 3, Indels: 25
0.69 0.03 0.27
Matches are distributed among these distances:
15 4 0.06
16 17 0.27
17 20 0.32
18 17 0.27
19 2 0.03
20 3 0.05
ACGTcount: A:0.07, C:0.19, G:0.01, T:0.72
Consensus pattern (17 bp):
ATTTCTTCTTTTTCTTC
Found at i:338401 original size:12 final size:12
Alignment explanation
Indices: 338384--338419 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
338374 TCATTTTTCA
338384 TTTTTTTCTTCT
1 TTTTTTTCTTCT
338396 TTTTTTTC-TCT
1 TTTTTTTCTTCT
*
338407 TTTATTTCTTCT
1 TTTTTTTCTTCT
338419 T
1 T
338420 CAAGCAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTTTTCTTCT
Found at i:347827 original size:45 final size:47
Alignment explanation
Indices: 347759--347847 Score: 155
Period size: 45 Copynumber: 1.9 Consensus size: 47
347749 TGCTTTGTTA
347759 TTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCTTG
1 TTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCTTG
*
347806 TTCA-AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGC
1 TTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
347848 ATTTATTCGA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
45 28 0.68
46 9 0.22
47 4 0.10
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.28
Consensus pattern (47 bp):
TTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCTTG
Found at i:354542 original size:15 final size:15
Alignment explanation
Indices: 354522--354561 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
354512 TCCTGGTGGG
354522 CTGATATTAGGCGGA
1 CTGATATTAGGCGGA
* *
354537 CTGATATTAGGTGGG
1 CTGATATTAGGCGGA
*
354552 CTAATATTAG
1 CTGATATTAG
354562 ATGCCGGGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.28, C:0.10, G:0.30, T:0.33
Consensus pattern (15 bp):
CTGATATTAGGCGGA
Found at i:354838 original size:60 final size:60
Alignment explanation
Indices: 354745--354925 Score: 353
Period size: 60 Copynumber: 3.0 Consensus size: 60
354735 TCCCTGCCAC
*
354745 ATAGCCGATAAGAACTTTAGATACACCGTACACGCACATAGGCCATGTACAAATGAAAGA
1 ATAGCTGATAAGAACTTTAGATACACCGTACACGCACATAGGCCATGTACAAATGAAAGA
354805 ATAGCTGATAAGAACTTTAGATACACCGTACACGCACATAGGCCATGTACAAATGAAAGA
1 ATAGCTGATAAGAACTTTAGATACACCGTACACGCACATAGGCCATGTACAAATGAAAGA
354865 ATAGCTGATAAGAACTTTAGATACACCGTACACGCACATAGGCCATGTACAAATGAAAGA
1 ATAGCTGATAAGAACTTTAGATACACCGTACACGCACATAGGCCATGTACAAATGAAAGA
354925 A
1 A
354926 CTTCCGATTT
Statistics
Matches: 120, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 120 1.00
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.19
Consensus pattern (60 bp):
ATAGCTGATAAGAACTTTAGATACACCGTACACGCACATAGGCCATGTACAAATGAAAGA
Found at i:357794 original size:18 final size:18
Alignment explanation
Indices: 357771--357805 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
357761 AATCCGACCT
357771 AAAATAATATATTTATTA
1 AAAATAATATATTTATTA
* *
357789 AAAATATTATTTTTATT
1 AAAATAATATATTTATT
357806 CGATAAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAAATAATATATTTATTA
Found at i:360947 original size:4 final size:4
Alignment explanation
Indices: 360938--360964 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
360928 GTGCTCTTGA
360938 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
360965 CTTCATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:369562 original size:28 final size:28
Alignment explanation
Indices: 369522--369580 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
369512 AAGTGATCGT
*
369522 ATTTTGATGTTTGTTCTCGTGTATAAAC
1 ATTTTGATGTTTGCTCTCGTGTATAAAC
* *
369550 ATTTTGATGTTTGCTCTCGTGTTTATAC
1 ATTTTGATGTTTGCTCTCGTGTATAAAC
369578 ATT
1 ATT
369581 CGATGTTCGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.19, C:0.12, G:0.17, T:0.53
Consensus pattern (28 bp):
ATTTTGATGTTTGCTCTCGTGTATAAAC
Found at i:378525 original size:55 final size:55
Alignment explanation
Indices: 378447--378559 Score: 199
Period size: 55 Copynumber: 2.1 Consensus size: 55
378437 ATATTCAGCT
*
378447 TCTCAACTTACTCTCAACATTCAGAATTTACTCTCCAAGTATTTTCTAAATATTC
1 TCTCAACTTACTCTCAACATTCAGAATTCACTCTCCAAGTATTTTCTAAATATTC
* *
378502 TCTCAACTTATTCTCAACATTCAGAATTCACTCTCCAAGTGTTTTCTAAATATTC
1 TCTCAACTTACTCTCAACATTCAGAATTCACTCTCCAAGTATTTTCTAAATATTC
378557 TCT
1 TCT
378560 TTGTGTTCTT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.29, C:0.26, G:0.04, T:0.41
Consensus pattern (55 bp):
TCTCAACTTACTCTCAACATTCAGAATTCACTCTCCAAGTATTTTCTAAATATTC
Found at i:380482 original size:20 final size:21
Alignment explanation
Indices: 380445--380484 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
380435 AAATTAAGTT
380445 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
380466 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
380485 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:380739 original size:19 final size:19
Alignment explanation
Indices: 380715--380753 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
380705 TCGAATGCAT
380715 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
380734 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
380753 T
1 T
380754 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:380852 original size:64 final size:66
Alignment explanation
Indices: 380701--380861 Score: 204
Period size: 65 Copynumber: 2.5 Consensus size: 66
380691 GAATTAATTG
* * * * *
380701 AACATCGAATGCATTCCATGCACCGATGCAC-TCTCCATGCATCGATGCACTCTGAATATTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACAACTCCATGCATAGATGCACTCAGAATATTTTCA
380765 A
66 A
* * **
380766 AACATCGAATGCATTTGATGCATCGATGCACAAGT-CATGCATAGATGCA-TCAGGCTATTTTTC
1 AACATCGAATGCATTTCATGCATCGATGCACAACTCCATGCATAGATGCACTCAGAATA-TTTTC
380829 -A
65 AA
380830 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
380862 CTTGGTGCAC
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 37 0.44
65 46 0.55
66 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (66 bp):
AACATCGAATGCATTTCATGCATCGATGCACAACTCCATGCATAGATGCACTCAGAATATTTTCA
A
Found at i:380877 original size:64 final size:64
Alignment explanation
Indices: 380701--380881 Score: 211
Period size: 64 Copynumber: 2.8 Consensus size: 64
380691 GAATTAATTG
* * * * *
380701 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTTCATGCATCGATGCA-TCAGAATATTTTCAA
* ** * **
380766 AACATCGAATGCATTTGATGCATCGATGCACAAGTCATGCATAGATGCATCAGGCTATTTTTC-A
1 AACATCGAATGCATTTCATGCATCGATGCACACTTCATGCATCGATGCATCAGAATA-TTTTCAA
** *
380830 AACATCGAATGCATTTCATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 AACATCGAATGCATTTCATGCATCGATGCACACTTCATGCATCGATGCATCA
380882 AGTGTTCCAA
Statistics
Matches: 97, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
64 51 0.53
65 46 0.47
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTTCATGCATCGATGCATCAGAATATTTTCAA
Found at i:382478 original size:47 final size:47
Alignment explanation
Indices: 382409--382505 Score: 185
Period size: 47 Copynumber: 2.1 Consensus size: 47
382399 TCTTCCCACC
*
382409 ATCCCCTACTTTTCCACTTGGCACATGTTGTATCATGACCTAGTACT
1 ATCCCCTACTTTTCCACATGGCACATGTTGTATCATGACCTAGTACT
382456 ATCCCCTACTTTTCCACATGGCACATGTTGTATCATGACCTAGTACT
1 ATCCCCTACTTTTCCACATGGCACATGTTGTATCATGACCTAGTACT
382503 ATC
1 ATC
382506 AGATTATCTG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.23, C:0.30, G:0.12, T:0.35
Consensus pattern (47 bp):
ATCCCCTACTTTTCCACATGGCACATGTTGTATCATGACCTAGTACT
Found at i:382611 original size:29 final size:28
Alignment explanation
Indices: 382569--382623 Score: 92
Period size: 29 Copynumber: 1.9 Consensus size: 28
382559 TCAACGAAAC
*
382569 TAACTCGGGTCATTATCAATATCAAATTT
1 TAACTCGGATCATTATCAATAT-AAATTT
382598 TAACTCGGATCATTATCAATATAAAT
1 TAACTCGGATCATTATCAATATAAAT
382624 ATCAACGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.36
Consensus pattern (28 bp):
TAACTCGGATCATTATCAATATAAATTT
Found at i:388209 original size:21 final size:22
Alignment explanation
Indices: 388170--388215 Score: 85
Period size: 21 Copynumber: 2.1 Consensus size: 22
388160 TTAGAATCAC
388170 CACTATAAGATTAAAAAAACGT
1 CACTATAAGATTAAAAAAACGT
388192 CACTATAAGATT-AAAAAACGT
1 CACTATAAGATTAAAAAAACGT
388213 CAC
1 CAC
388216 CATAGAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.52, C:0.17, G:0.09, T:0.22
Consensus pattern (22 bp):
CACTATAAGATTAAAAAAACGT
Found at i:389674 original size:24 final size:24
Alignment explanation
Indices: 389614--389738 Score: 101
Period size: 24 Copynumber: 5.2 Consensus size: 24
389604 TCACTGAACA
* *
389614 AACATGTTCGTGAACA-CTAAATG
1 AACATGTTCGTGAACATATAAACG
* **
389637 AACACGTTTATGAACATATAAACG
1 AACATGTTCGTGAACATATAAACG
* * *
389661 AATATGTTCGTGAACATATAGATG
1 AACATGTTCGTGAACATATAAACG
* ** *
389685 AGCATGTTCACGAACAT-TAAGCG
1 AACATGTTCGTGAACATATAAACG
389708 AACATGTTCGTGAACAATAAATAAACG
1 AACATGTTCGTGAAC-AT--ATAAACG
389735 AACA
1 AACA
389739 CGATACTAAA
Statistics
Matches: 75, Mismatches: 22, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
23 28 0.37
24 38 0.51
27 9 0.12
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (24 bp):
AACATGTTCGTGAACATATAAACG
Found at i:389715 original size:47 final size:47
Alignment explanation
Indices: 389614--389729 Score: 137
Period size: 47 Copynumber: 2.5 Consensus size: 47
389604 TCACTGAACA
* *
389614 AACATGTTCGTGAACACTAAATGAACACGTTTATGAACATATAAACG
1 AACATGTTCGTGAACACTAAATGAACACGTTCACGAACATATAAACG
* * * *
389661 AATATGTTCGTGAACA-TATAGATGAGCATGTTCACGAACAT-TAAGCG
1 AACATGTTCGTGAACACTA-A-ATGAACACGTTCACGAACATATAAACG
*
389708 AACATGTTCGTGAACAATAAAT
1 AACATGTTCGTGAACACTAAAT
389730 AAACGAACAC
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
46 4 0.07
47 37 0.63
48 18 0.31
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.27
Consensus pattern (47 bp):
AACATGTTCGTGAACACTAAATGAACACGTTCACGAACATATAAACG
Found at i:393053 original size:12 final size:12
Alignment explanation
Indices: 393036--393060 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
393026 CTAAATCATA
393036 AAACTTTTGTTC
1 AAACTTTTGTTC
393048 AAACTTTTGTTC
1 AAACTTTTGTTC
393060 A
1 A
393061 TATTCATTTT
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:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (12 bp):
AAACTTTTGTTC
Found at i:394364 original size:214 final size:216
Alignment explanation
Indices: 393995--396085 Score: 2930
Period size: 215 Copynumber: 9.7 Consensus size: 216
393985 CAACACATGT
* * * * * * * * *
393995 CCATATCCAACACAATCAAGTCTGAGTAGCATA-ATCACCAGCATGACAAATA-GCGTAAAACCA
1 CCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCATGAGAAA-AGGTGTAAAGCCA
* * *
394058 TGATGTTTATAGGAAAGT--AACTAGTACTCGTTTCCATTTCAGAGAGTTTGAGCTAAGCTCTAC
65 TGATGTTTATACGAAGGTAAAAC-AGTACTCGTTTCCCTTTCAGAGAGTTTGAGCTAAGCTCTAC
* *
394121 ACATGCTTGAAAGACAGAACTTCATGACCAAAACTCGTGTAGGGGATATGGCTGTTCGAAGATCT
129 ACATGCTTGAAAGACAGAACTTCATGACCAAAACTCGTGCAGGGGATATGACTGTTCGAAGATCT
394186 CCCAAACCCACATTGG-ACACAC
194 CCCAAACCCACATTGGAACACAC
* * *
394208 CCATATCCAAGACACTCAAGTCGGAGTAACATACACCATCGGCGTGAGAAAAGGTGTAAAGCCAT
1 CCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGCCAT
* * * * *
394273 GATGTTTGTAGGAAGGTAAAACGGTACTCGTTTCCCTTTTAGAGAGTTTGAGCTAAGCTTTACAC
66 GATGTTTATACGAAGGTAAAACAGTACTCGTTTCCCTTTCAGAGAGTTTGAGCTAAGCTCTACAC
* *
394338 -TGCTTGAAAGACAGAACTTTATGACCAAAACTCGTGCAGGGGATATGACCGTTCGAAGATCTCC
131 ATGCTTGAAAGACAGAACTTCATGACCAAAACTCGTGCAGGGGATATGACTGTTCGAAGATCTCC
394402 CAAACCCACATTGGACACACAC
196 CAAACCCACATTGGA-ACACAC
* * *
394424 CCATATCCGACACACTCAAGTCAGAGTAACATAGACGATCGGCATGAGAAAAGGTGTAAAGCCAT
1 CCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGCCAT
* * * * *
394489 GATGTTTATACGAAGGTAAAAC-GTTACTCGTTTCCATCTCCGAGAGCTTGAGCTAAGCTATACA
66 GATGTTTATACGAAGGTAAAACAG-TACTCGTTTCCCTTTCAGAGAGTTTGAGCTAAGCTCTACA
** *
394553 CATGCAAG-AAG--AGAACTTCATGACCAAAACTCCTGCAGGGGATATGACTGTTCGAAGATCTC
130 CATGCTTGAAAGACAGAACTTCATGACCAAAACTCGTGCAGGGGATATGACTGTTCGAAGATCTC
*
394615 CCAAACCCACATTGGACACGCAC
195 CCAAACCCACATTGGA-ACACAC
** * * **
394638 CCATATCTGACACACTCAAGTCGGAGTAACATAGACCATTGGCGTGAGAAAAGGTGTAAAGATAT
1 CCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGCCAT
* * * * *
394703 GATGTTTGTAGGAAGGTAAAACGGTACTCGTTTCCCTTTCAAAGTGTTTGAGCTAAGCTCTACAC
66 GATGTTTATACGAAGGTAAAACAGTACTCGTTTCCCTTTCAGAGAGTTTGAGCTAAGCTCTACAC
394768 ATGCTTGAAAGAC--AACTTCATGACCAAAACTCGTGCAGGGGATATGACTGTTCGAAGATCTCC
131 ATGCTTGAAAGACAGAACTTCATGACCAAAACTCGTGCAGGGGATATGACTGTTCGAAGATCTCC
*
394831 CAAACCCAAATTGGACACACAC
196 CAAACCCACATTGGA-ACACAC
* * *
394853 CCATATCCGACACACTCAAGTCAGAGTAGCATAGACCATCGGCATGAGAAAAGGTGTAAAGCCAT
1 CCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGCCAT
* * * * *
394918 GATGTTTATACGAAGGTAAAACATTACTCGTTTCCCTCTCCGAGAGCTTGAGCTAAGCTATACAC
66 GATGTTTATACGAAGGTAAAACAGTACTCGTTTCCCTTTCAGAGAGTTTGAGCTAAGCTCTACAC
** * * *
394983 ATGCAGGAAAGAGAGAACTTCATGACCAAAACTCTTGCAGGGGATATGA-TCGTTCAAAGATCT-
131 ATGCTTGAAAGACAGAACTTCATGACCAAAACTCGTGCAGGGGATATGACT-GTTCGAAGATCTC
395046 CCAAACCCACATTGGACACACAC
195 CCAAACCCACATTGGA-ACACAC
*
395069 CCATATCCAACACACTCAAGTCGGAGTAACATAGACTATCGGCATGAG-AAAGGTGTAAAGCCAT
1 CCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGCCAT
* * * * *
395133 GATGTTTATACGAAGGTAAAACCGTACTTGTTTCCCTTTCAGAGTGTATGAGGTAAGCTCTACAC
66 GATGTTTATACGAAGGTAAAACAGTACTCGTTTCCCTTTCAGAGAGTTTGAGCTAAGCTCTACAC
* * * *
395198 ATGCTTGAAAGACAGAACTTCATGACCAAAACTCGGGCAGGAGATATGACCGTTCGAAGATCTTC
131 ATGCTTGAAAGACAGAACTTCATGACCAAAACTCGTGCAGGGGATATGACTGTTCGAAGATCTCC
395263 CAAACCCACATTGG-ACAAGCAC
196 CAAACCCACATTGGAAC-A-CAC
* **
395285 CCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCGTGAGAAAAGGTGTAAAGATAT
1 CCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGCCAT
* * * * *
395350 GATGTTTGTAGGAAGGTAAAACGGTACTTGTTTCCCTTTCAAAGAGTTTGAGCTAAGCTCTACAC
66 GATGTTTATACGAAGGTAAAACAGTACTCGTTTCCCTTTCAGAGAGTTTGAGCTAAGCTCTACAC
*
395415 ATGCTTGAAAGAC--AACTTCATGACCAAAACTCGTGCAGGGGATATGACCGTTCGAAGATCTCC
131 ATGCTTGAAAGACAGAACTTCATGACCAAAACTCGTGCAGGGGATATGACTGTTCGAAGATCTCC
395478 CAAACCCACATTGGACACACAC
196 CAAACCCACATTGGA-ACACAC
* *
395500 CCATATCAAACACACTCAAGTCAGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGCCAT
1 CCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGCCAT
* * * * *
395565 GATGTTTATACGAAGGTAAAACATTACTCGTTTCCCTCTCTGAGAGCTTGAGCTAAGCTATACAC
66 GATGTTTATACGAAGGTAAAACAGTACTCGTTTCCCTTTCAGAGAGTTTGAGCTAAGCTCTACAC
* * * *
395630 ATGCTGGAAAG--AGAACTTCATGGCCAAAACTCCTGCAGGGGATATGA-TCGTTCAAAGATCT-
131 ATGCTTGAAAGACAGAACTTCATGACCAAAACTCGTGCAGGGGATATGACT-GTTCGAAGATCTC
395691 CCAAACCCACATTGGACACACAC
195 CCAAACCCACATTGGA-ACACAC
395714 CCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGCCAT
1 CCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGCCAT
* * * *
395779 GATGTTTATACGAAGGTTAAACCGTACTCGTTTCCCTTTCAGAGAGTATGAGGTAAGCTCTACAC
66 GATGTTTATACGAAGGTAAAACAGTACTCGTTTCCCTTTCAGAGAGTTTGAGCTAAGCTCTACAC
* * *
395844 ATGCTTGAAAGACAGAACTTCATGACCAAAACTCGGGCAGGAGATATGACAGTTCGAAGATCTCC
131 ATGCTTGAAAGACAGAACTTCATGACCAAAACTCGTGCAGGGGATATGACTGTTCGAAGATCTCC
395909 CAAACCCACATTGGACACACAC
196 CAAACCCACATTGGA-ACACAC
* ** *
395931 CCATATCCGACACACTCAAGTTAGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGTCAT
1 CCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGCCAT
* * *
395996 GATGTTTATACAAAGGTAAAACAGTACTCGTTTCCCTTTCCGAGAGCTTGAGCTAAGCTCTACAC
66 GATGTTTATACGAAGGTAAAACAGTACTCGTTTCCCTTTCAGAGAGTTTGAGCTAAGCTCTACAC
* * *
396061 ATGCATGAAAGAGAGAACTTAATGA
131 ATGCTTGAAAGACAGAACTTCATGA
396086 AATAAACAAA
Statistics
Matches: 1676, Mismatches: 173, Indels: 54
0.88 0.09 0.03
Matches are distributed among these distances:
213 30 0.02
214 452 0.27
215 594 0.35
216 301 0.18
217 299 0.18
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (216 bp):
CCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGCCAT
GATGTTTATACGAAGGTAAAACAGTACTCGTTTCCCTTTCAGAGAGTTTGAGCTAAGCTCTACAC
ATGCTTGAAAGACAGAACTTCATGACCAAAACTCGTGCAGGGGATATGACTGTTCGAAGATCTCC
CAAACCCACATTGGAACACAC
Found at i:395434 original size:647 final size:648
Alignment explanation
Indices: 394081--396072 Score: 3209
Period size: 647 Copynumber: 3.1 Consensus size: 648
394071 AAAGTAACTA
* *
394081 GTACTCGTTTCCATTTCAGAGAGTTTGAGCTAAGCTCTACACATGCTTGAAAGACAGAACTTCAT
1 GTACTCGTTTCCCTTTCAAAGAGTTTGAGCTAAGCTCTACACATGCTTGAAAGAC--AACTTCAT
* *
394146 GACCAAAACTCGTGTAGGGGATATGGCTGTTCGAAGATCTCCCAAACCCACATTGG--ACACACC
64 GACCAAAACTCGTGCAGGGGATATGACTGTTCGAAGATCTCCCAAACCCACATTGGACACACACC
* * * *
394209 CATATCCAAGACACTCAAGTCGGAGTAACATACACCATCGGCGTGAGAAAAGGTGTAAAGCCATG
129 CATATCCAACACACTCAAGTCAGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGCCATG
* * ** * * * *
394274 ATGTTTGTAGGAAGGTAAAACGGTACTCGTTTCCCTTTTAGAGAGTTTGAGCTAAGCTTTACAC-
194 ATGTTTATACGAAGGTAAAACATTACTCGTTTCCCTCTCAGAGAGCTTGAGCTAAGCTATACACA
* * * * * *
394338 TGCTTGAAAGACAGAACTTTATGACCAAAACTCGTGCAGGGGATATGACCGTTCGAAGATCTCCC
259 TGCTGGAAAGAGAGAACTTCATGACCAAAACTCCTGCAGGGGATATGATCGTTCAAAGATCT-CC
* * *
394403 AAACCCACATTGGACACACACCCATATCCGACACACTCAAGTCAGAGTAACATAGACGATCGGCA
323 AAACCCACATTGGACACACACCCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCA
* * *
394468 TGAGAAAAGGTGTAAAGCCATGATGTTTATACGAAGGTAAAA-CGTTACTCGTTTCCATCTCCGA
388 TGAGAAAAGGTGTAAAGCCATGATGTTTATACGAAGGTAAAACCG-TACTCGTTTCCCTTTCAGA
* * ** ** *
394532 GAGCT-TGAGCTAAGCTATACACATGCAAG-AAG--AGAACTTCATGACCAAAACTCCTGCAGGG
452 GAG-TATGAGGTAAGCTCTACACATGCTTGAAAGACAGAACTTCATGACCAAAACTCGGGCAGGA
* * *
394593 GATATGACTGTTCGAAGATCTCCCAAACCCACATTGGACACGCACCCATATCTGACACACTCAAG
516 GATATGACAGTTCGAAGATCTCCCAAACCCACATTGGACAAGCACCCATATCCGACACACTCAAG
*
394658 TCGGAGTAACATAGACCATTGGCGTGAGAAAAGGTGTAAAGATATGATGTTTGTAGGAAGGTAAA
581 TCGGAGTAACATAGACCATCGGCGTGAGAAAAGGTGTAAAGATATGATGTTTGTAGGAAGGTAAA
394723 ACG
646 ACG
*
394726 GTACTCGTTTCCCTTTCAAAGTGTTTGAGCTAAGCTCTACACATGCTTGAAAGACAACTTCATGA
1 GTACTCGTTTCCCTTTCAAAGAGTTTGAGCTAAGCTCTACACATGCTTGAAAGACAACTTCATGA
*
394791 CCAAAACTCGTGCAGGGGATATGACTGTTCGAAGATCTCCCAAACCCAAATTGGACACACACCCA
66 CCAAAACTCGTGCAGGGGATATGACTGTTCGAAGATCTCCCAAACCCACATTGGACACACACCCA
* *
394856 TATCCGACACACTCAAGTCAGAGTAGCATAGACCATCGGCATGAGAAAAGGTGTAAAGCCATGAT
131 TATCCAACACACTCAAGTCAGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGCCATGAT
*
394921 GTTTATACGAAGGTAAAACATTACTCGTTTCCCTCTCCGAGAGCTTGAGCTAAGCTATACACATG
196 GTTTATACGAAGGTAAAACATTACTCGTTTCCCTCTCAGAGAGCTTGAGCTAAGCTATACACATG
* *
394986 CAGGAAAGAGAGAACTTCATGACCAAAACTCTTGCAGGGGATATGATCGTTCAAAGATCTCCAAA
261 CTGGAAAGAGAGAACTTCATGACCAAAACTCCTGCAGGGGATATGATCGTTCAAAGATCTCCAAA
*
395051 CCCACATTGGACACACACCCATATCCAACACACTCAAGTCGGAGTAACATAGACTATCGGCATGA
326 CCCACATTGGACACACACCCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCATGA
* *
395116 G-AAAGGTGTAAAGCCATGATGTTTATACGAAGGTAAAACCGTACTTGTTTCCCTTTCAGAGTGT
391 GAAAAGGTGTAAAGCCATGATGTTTATACGAAGGTAAAACCGTACTCGTTTCCCTTTCAGAGAGT
395180 ATGAGGTAAGCTCTACACATGCTTGAAAGACAGAACTTCATGACCAAAACTCGGGCAGGAGATAT
456 ATGAGGTAAGCTCTACACATGCTTGAAAGACAGAACTTCATGACCAAAACTCGGGCAGGAGATAT
* * *
395245 GACCGTTCGAAGATCTTCCAAACCCACATTGGACAAGCACCCATATCCAACACACTCAAGTCGGA
521 GACAGTTCGAAGATCTCCCAAACCCACATTGGACAAGCACCCATATCCGACACACTCAAGTCGGA
395310 GTAACATAGACCATCGGCGTGAGAAAAGGTGTAAAGATATGATGTTTGTAGGAAGGTAAAACG
586 GTAACATAGACCATCGGCGTGAGAAAAGGTGTAAAGATATGATGTTTGTAGGAAGGTAAAACG
*
395373 GTACTTGTTTCCCTTTCAAAGAGTTTGAGCTAAGCTCTACACATGCTTGAAAGACAACTTCATGA
1 GTACTCGTTTCCCTTTCAAAGAGTTTGAGCTAAGCTCTACACATGCTTGAAAGACAACTTCATGA
*
395438 CCAAAACTCGTGCAGGGGATATGACCGTTCGAAGATCTCCCAAACCCACATTGGACACACACCCA
66 CCAAAACTCGTGCAGGGGATATGACTGTTCGAAGATCTCCCAAACCCACATTGGACACACACCCA
*
395503 TATCAAACACACTCAAGTCAGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGCCATGAT
131 TATCCAACACACTCAAGTCAGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGCCATGAT
*
395568 GTTTATACGAAGGTAAAACATTACTCGTTTCCCTCTCTGAGAGCTTGAGCTAAGCTATACACATG
196 GTTTATACGAAGGTAAAACATTACTCGTTTCCCTCTCAGAGAGCTTGAGCTAAGCTATACACATG
*
395633 CTGG-AA-AGAGAACTTCATGGCCAAAACTCCTGCAGGGGATATGATCGTTCAAAGATCTCCAAA
261 CTGGAAAGAGAGAACTTCATGACCAAAACTCCTGCAGGGGATATGATCGTTCAAAGATCTCCAAA
395696 CCCACATTGGACACACACCCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCATGA
326 CCCACATTGGACACACACCCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCATGA
*
395761 GAAAAGGTGTAAAGCCATGATGTTTATACGAAGGTTAAACCGTACTCGTTTCCCTTTCAGAGAGT
391 GAAAAGGTGTAAAGCCATGATGTTTATACGAAGGTAAAACCGTACTCGTTTCCCTTTCAGAGAGT
395826 ATGAGGTAAGCTCTACACATGCTTGAAAGACAGAACTTCATGACCAAAACTCGGGCAGGAGATAT
456 ATGAGGTAAGCTCTACACATGCTTGAAAGACAGAACTTCATGACCAAAACTCGGGCAGGAGATAT
**
395891 GACAGTTCGAAGATCTCCCAAACCCACATTGGACACA-CACCCATATCCGACACACTCAAGTTAG
521 GACAGTTCGAAGATCTCCCAAACCCACATTGGACA-AGCACCCATATCCGACACACTCAAGTCGG
* * ** *
395955 AGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAG-TCATGATGTTTATACAAAGGTAAAACA
585 AGTAACATAGACCATCGGCGTGAGAAAAGGTGTAAAGAT-ATGATGTTTGTAGGAAGGTAAAACG
** * *
396019 GTACTCGTTTCCCTTTCCGAGAGCTTGAGCTAAGCTCTACACATGCATGAAAGA
1 GTACTCGTTTCCCTTTCAAAGAGTTTGAGCTAAGCTCTACACATGCTTGAAAGA
396073 GAGAACTTAA
Statistics
Matches: 1257, Mismatches: 79, Indels: 21
0.93 0.06 0.02
Matches are distributed among these distances:
643 62 0.05
644 74 0.06
645 367 0.29
646 345 0.27
647 409 0.33
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.23
Consensus pattern (648 bp):
GTACTCGTTTCCCTTTCAAAGAGTTTGAGCTAAGCTCTACACATGCTTGAAAGACAACTTCATGA
CCAAAACTCGTGCAGGGGATATGACTGTTCGAAGATCTCCCAAACCCACATTGGACACACACCCA
TATCCAACACACTCAAGTCAGAGTAACATAGACCATCGGCATGAGAAAAGGTGTAAAGCCATGAT
GTTTATACGAAGGTAAAACATTACTCGTTTCCCTCTCAGAGAGCTTGAGCTAAGCTATACACATG
CTGGAAAGAGAGAACTTCATGACCAAAACTCCTGCAGGGGATATGATCGTTCAAAGATCTCCAAA
CCCACATTGGACACACACCCATATCCAACACACTCAAGTCGGAGTAACATAGACCATCGGCATGA
GAAAAGGTGTAAAGCCATGATGTTTATACGAAGGTAAAACCGTACTCGTTTCCCTTTCAGAGAGT
ATGAGGTAAGCTCTACACATGCTTGAAAGACAGAACTTCATGACCAAAACTCGGGCAGGAGATAT
GACAGTTCGAAGATCTCCCAAACCCACATTGGACAAGCACCCATATCCGACACACTCAAGTCGGA
GTAACATAGACCATCGGCGTGAGAAAAGGTGTAAAGATATGATGTTTGTAGGAAGGTAAAACG
Found at i:402236 original size:19 final size:19
Alignment explanation
Indices: 402214--402272 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
402204 ATATATATAT
*
402214 ATTAATAAATTTAATTTAA
1 ATTAATATATTTAATTTAA
* *
402233 ATTAATATATAT-ATATAA
1 ATTAATATATTTAATTTAA
*
402251 TATTTATATATTTAATTTAA
1 -ATTAATATATTTAATTTAA
402271 AT
1 AT
402273 ATATATATAC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
18 5 0.16
19 22 0.69
20 5 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTAATATATTTAATTTAA
Found at i:402260 original size:15 final size:15
Alignment explanation
Indices: 402238--402279 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
402228 TTTAAATTAA
402238 TATATATATATAATAT
1 TATATATATATAAT-T
*
402254 T-TATATATTTAATT
1 TATATATATATAATT
*
402268 TAAATATATATA
1 TATATATATATA
402280 TACCCGACCT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 2 0.09
15 19 0.86
16 1 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATATATATATAATT
Found at i:402260 original size:17 final size:17
Alignment explanation
Indices: 402196--402281 Score: 56
Period size: 17 Copynumber: 5.2 Consensus size: 17
402186 ATTAAAAATA
402196 ATAA-TTATATATATAT
1 ATAATTTATATATATAT
* * *
402212 AT-ATTAATAAATTTAAT
1 ATAATTTATATATAT-AT
* *
402229 TTAAATTAATATATATAT
1 AT-AATTTATATATATAT
402247 ATAATATT-TATATAT-T
1 ATAAT-TTATATATATAT
*
402263 -TAATTTAAATATATAT
1 ATAATTTATATATATAT
402279 ATA
1 ATA
402282 CCCGACCTGA
Statistics
Matches: 53, Mismatches: 9, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
14 2 0.04
15 11 0.21
16 11 0.21
17 15 0.28
18 4 0.08
19 10 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATAATTTATATATATAT
Found at i:409535 original size:12 final size:12
Alignment explanation
Indices: 409508--409550 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
409498 CGCCGTCTCG
409508 GGTCG-GGTCA-
1 GGTCGTGGTCAT
*
409518 GGTCGTGGTCGT
1 GGTCGTGGTCAT
409530 GGTCGTGGTCAT
1 GGTCGTGGTCAT
*
409542 GGTTGTGGT
1 GGTCGTGGT
409551 AATACGTGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 5 0.18
11 4 0.14
12 19 0.68
ACGTcount: A:0.05, C:0.14, G:0.49, T:0.33
Consensus pattern (12 bp):
GGTCGTGGTCAT
Found at i:409718 original size:20 final size:20
Alignment explanation
Indices: 409649--409755 Score: 92
Period size: 20 Copynumber: 5.2 Consensus size: 20
409639 CAGTTTTGCG
**
409649 ATCGCGTTGCGATTCTTGGAA
1 ATCGCGTTGCGATT-TTCTAA
409670 TATCGCGTTGCGATTTTCT--
1 -ATCGCGTTGCGATTTTCTAA
* *
409689 TTTGACCGTTGCGATTTTCTAA
1 ATCG--CGTTGCGATTTTCTAA
* *
409711 ATCGCGTTGCGATTCTCTTA
1 ATCGCGTTGCGATTTTCTAA
* *
409731 ATCGCGTTGCGATTCTCTTA
1 ATCGCGTTGCGATTTTCTAA
409751 ATCGC
1 ATCGC
409756 CTTTGAAACA
Statistics
Matches: 73, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
18 2 0.03
20 53 0.73
21 2 0.03
22 16 0.22
ACGTcount: A:0.16, C:0.22, G:0.21, T:0.40
Consensus pattern (20 bp):
ATCGCGTTGCGATTTTCTAA
Found at i:409739 original size:40 final size:39
Alignment explanation
Indices: 409649--409755 Score: 108
Period size: 40 Copynumber: 2.6 Consensus size: 39
409639 CAGTTTTGCG
** *
409649 ATCGCGTTGCGATTCTTGGAATATCGCGTTGCGATTTTCTT
1 ATCGCGTTGCGATT-TTCTAA-ATCGCGTTGCGATTCTCTT
*
409690 -TTGACCGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTT
1 ATCG--CGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTT
* *
409730 AATCGCGTTGCGATTCTCTTAATCGC
1 -ATCGCGTTGCGATTTTCTAAATCGC
409756 CTTTGAAACA
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
40 39 0.71
41 4 0.07
42 12 0.22
ACGTcount: A:0.16, C:0.22, G:0.21, T:0.40
Consensus pattern (39 bp):
ATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTT
Found at i:412988 original size:20 final size:20
Alignment explanation
Indices: 412963--413004 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
412953 ACTTGTTTTA
*
412963 AAATTCAAATTCAATAGATC
1 AAATTCAAATTCAAAAGATC
* *
412983 AAATTCGAATTTAAAAGATC
1 AAATTCAAATTCAAAAGATC
413003 AA
1 AA
413005 CTTGGGATGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.52, C:0.12, G:0.07, T:0.29
Consensus pattern (20 bp):
AAATTCAAATTCAAAAGATC
Found at i:415083 original size:3 final size:3
Alignment explanation
Indices: 415075--415099 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
415065 TTAATCAGTG
415075 ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC A
415100 GTGTGTTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:416044 original size:2 final size:2
Alignment explanation
Indices: 416037--416065 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
416027 TCTGCTTTCC
416037 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
416066 GATAATAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:418868 original size:38 final size:37
Alignment explanation
Indices: 418821--418907 Score: 140
Period size: 38 Copynumber: 2.4 Consensus size: 37
418811 TAAAAATAAT
418821 AATTATATATATATATAATATTAATAAATTTAATTTA
1 AATTATATATATATATAATATTAATAAATTTAATTTA
* *
418858 AATTAATATATATATATAATATTTATATATTTAATTTA
1 AATT-ATATATATATATAATATTAATAAATTTAATTTA
418896 AA-TATATATATA
1 AATTATATATATA
418908 CCCGACCTGA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
36 9 0.19
37 5 0.11
38 33 0.70
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (37 bp):
AATTATATATATATATAATATTAATAAATTTAATTTA
Found at i:418878 original size:32 final size:33
Alignment explanation
Indices: 418829--418907 Score: 92
Period size: 32 Copynumber: 2.4 Consensus size: 33
418819 ATAATTATAT
418829 ATATATATAATATTAATAAATT-TA-ATTTAAATTA
1 ATATATAT-ATA-TAAT-AATTATATATTTAAATTA
* *
418863 ATATATATATATAATATTTATATATTTAATTTA
1 ATATATATATATAATAATTATATATTTAAATTA
418896 A-ATATATATATA
1 ATATATATATATA
418908 CCCGACCTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
31 3 0.07
32 17 0.41
33 13 0.32
34 8 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (33 bp):
ATATATATATATAATAATTATATATTTAAATTA
Found at i:418886 original size:15 final size:15
Alignment explanation
Indices: 418819--418905 Score: 55
Period size: 13 Copynumber: 6.2 Consensus size: 15
418809 ATTAAAAATA
418819 ATAATTATATATATAT
1 ATAATT-TATATATAT
*
418835 ATAATATTA-ATAAAT
1 ATAAT-TTATATATAT
* *
418850 TTAATTTAAAT-TA-
1 ATAATTTATATATAT
*
418863 AT-ATATATATATA-
1 ATAATTTATATATAT
418876 AT-ATTTATATAT-T
1 ATAATTTATATATAT
*
418889 -TAATTTAAATATAT
1 ATAATTTATATATAT
418903 ATA
1 ATA
418906 TACCCGACCT
Statistics
Matches: 56, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
12 7 0.12
13 23 0.41
14 5 0.09
15 13 0.23
16 7 0.12
17 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATAATTTATATATAT
Found at i:418886 original size:17 final size:17
Alignment explanation
Indices: 418819--418907 Score: 60
Period size: 17 Copynumber: 5.2 Consensus size: 17
418809 ATTAAAAATA
418819 ATAA-TTATATATATAT
1 ATAATTTATATATATAT
* *
418835 ATAATATTAATAAATTTAAT
1 ATAAT-TT-ATATATAT-AT
* *
418855 TTAAATTAATATATATAT
1 AT-AATTTATATATATAT
418873 ATAATATT-TATATAT-T
1 ATAAT-TTATATATATAT
*
418889 -TAATTTAAATATATAT
1 ATAATTTATATATATAT
418905 ATA
1 ATA
418908 CCCGACCTGA
Statistics
Matches: 55, Mismatches: 9, Indels: 17
0.68 0.11 0.21
Matches are distributed among these distances:
14 2 0.04
15 10 0.18
16 6 0.11
17 12 0.22
18 6 0.11
19 12 0.22
20 4 0.07
21 3 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATAATTTATATATATAT
Found at i:426152 original size:12 final size:12
Alignment explanation
Indices: 426125--426167 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
426115 CGCCGTCTCG
426125 GGTCG-GGTCA-
1 GGTCGTGGTCAT
*
426135 GGTCGTGGTCGT
1 GGTCGTGGTCAT
426147 GGTCGTGGTCAT
1 GGTCGTGGTCAT
*
426159 GGTTGTGGT
1 GGTCGTGGT
426168 AATACGTGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 5 0.18
11 4 0.14
12 19 0.68
ACGTcount: A:0.05, C:0.14, G:0.49, T:0.33
Consensus pattern (12 bp):
GGTCGTGGTCAT
Found at i:426335 original size:20 final size:20
Alignment explanation
Indices: 426266--426372 Score: 92
Period size: 20 Copynumber: 5.2 Consensus size: 20
426256 CAGTTTTGCG
**
426266 ATCGCGTTGCGATTCTTGGAA
1 ATCGCGTTGCGATT-TTCTAA
426287 TATCGCGTTGCGATTTTCT--
1 -ATCGCGTTGCGATTTTCTAA
* *
426306 TTTGACCGTTGCGATTTTCTAA
1 ATCG--CGTTGCGATTTTCTAA
* *
426328 ATCGCGTTGCGATTCTCTTA
1 ATCGCGTTGCGATTTTCTAA
* *
426348 ATCGCGTTGCGATTCTCTTA
1 ATCGCGTTGCGATTTTCTAA
426368 ATCGC
1 ATCGC
426373 CTTTGAAACA
Statistics
Matches: 73, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
18 2 0.03
20 53 0.73
21 2 0.03
22 16 0.22
ACGTcount: A:0.16, C:0.22, G:0.21, T:0.40
Consensus pattern (20 bp):
ATCGCGTTGCGATTTTCTAA
Found at i:426356 original size:40 final size:39
Alignment explanation
Indices: 426266--426372 Score: 108
Period size: 40 Copynumber: 2.6 Consensus size: 39
426256 CAGTTTTGCG
** *
426266 ATCGCGTTGCGATTCTTGGAATATCGCGTTGCGATTTTCTT
1 ATCGCGTTGCGATT-TTCTAA-ATCGCGTTGCGATTCTCTT
*
426307 -TTGACCGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTT
1 ATCG--CGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTT
* *
426347 AATCGCGTTGCGATTCTCTTAATCGC
1 -ATCGCGTTGCGATTTTCTAAATCGC
426373 CTTTGAAACA
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
40 39 0.71
41 4 0.07
42 12 0.22
ACGTcount: A:0.16, C:0.22, G:0.21, T:0.40
Consensus pattern (39 bp):
ATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTT
Found at i:429599 original size:20 final size:20
Alignment explanation
Indices: 429574--429615 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
429564 ACTTGTTTTA
*
429574 AAATTCAAATTCAATAGATC
1 AAATTCAAATTCAAAAGATC
* *
429594 AAATTCGAATTTAAAAGATC
1 AAATTCAAATTCAAAAGATC
429614 AA
1 AA
429616 CTTGGGATGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.52, C:0.12, G:0.07, T:0.29
Consensus pattern (20 bp):
AAATTCAAATTCAAAAGATC
Found at i:431695 original size:3 final size:3
Alignment explanation
Indices: 431687--431711 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
431677 TTAATCAGTG
431687 ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC A
431712 GTGTGTTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:432657 original size:2 final size:2
Alignment explanation
Indices: 432650--432674 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
432640 TCTGCTTTCC
432650 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
432675 GATAATAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:437360 original size:37 final size:39
Alignment explanation
Indices: 437315--437387 Score: 114
Period size: 37 Copynumber: 1.9 Consensus size: 39
437305 ATCATCGTTA
* *
437315 TTACATCGGAAATCAAATG-GAAAAAA-TTGTATATCGT
1 TTACATCGGAAACCAAATGCAAAAAAATTTGTATATCGT
437352 TTACATCGGAAACCAAATGCAAAAAAATTTGTATAT
1 TTACATCGGAAACCAAATGCAAAAAAATTTGTATAT
437388 GAATAATTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 18 0.56
38 6 0.19
39 8 0.25
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (39 bp):
TTACATCGGAAACCAAATGCAAAAAAATTTGTATATCGT
Found at i:451969 original size:31 final size:31
Alignment explanation
Indices: 451931--451997 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
451921 ACCGGTCATA
* *
451931 ACCCGACCCGACCCGTTTAC-CTGACCAGTTG
1 ACCCGACCCGACCCATTGACTC-GACCAGTTG
*
451962 ACCCGACCCGACCCATTGACTCGACCCGTTG
1 ACCCGACCCGACCCATTGACTCGACCAGTTG
451993 ACCCG
1 ACCCG
451998 TTGACCGTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.19, C:0.45, G:0.19, T:0.16
Consensus pattern (31 bp):
ACCCGACCCGACCCATTGACTCGACCAGTTG
Found at i:452007 original size:15 final size:16
Alignment explanation
Indices: 451987--452020 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
451977 TTGACTCGAC
451987 CCGTTGACC-CGTTGA
1 CCGTTGACCGCGTTGA
452002 CCGTTGACCGGCGTTGA
1 CCGTTGACC-GCGTTGA
452019 CC
1 CC
452021 ACTGTTAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.12, C:0.35, G:0.29, T:0.24
Consensus pattern (16 bp):
CCGTTGACCGCGTTGA
Found at i:452963 original size:18 final size:18
Alignment explanation
Indices: 452937--452972 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
452927 TCGAAAGGAC
*
452937 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
452955 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
452973 CGGATGGCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:454152 original size:12 final size:12
Alignment explanation
Indices: 454137--454206 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
454127 GATACATTAC
454137 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
454149 CTGATTTCTGAT
1 CTGAATTCTGTT
*
454161 CTGGATTCTGTT
1 CTGAATTCTGTT
*
454173 CTG-ATATCTGAT
1 CTGAAT-TCTGTT
454185 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
454197 TTGATTTCTG
1 CTGAATTCTG
454207 ATATCTCCAT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 2 0.04
12 43 0.91
13 2 0.04
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.50
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:454156 original size:48 final size:48
Alignment explanation
Indices: 454100--454208 Score: 141
Period size: 48 Copynumber: 2.3 Consensus size: 48
454090 AAATATTTTA
* *
454100 TCTGATTTCTGA-CTTTAATTCTGTTCTGATA-CATTACCTGAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGTTCTGATATC-TGACCTGAATTCTGT
* *
454148 TCTGATTTCTGATCTGGATTCTGTTCTGATATCTGATCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGTTCTGATATCTGACCTGAATTCTGT
*
454196 TTTGATTTCTGAT
1 TCTGATTTCTGAT
454209 ATCTCCATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
48 52 0.96
49 2 0.04
ACGTcount: A:0.18, C:0.17, G:0.16, T:0.50
Consensus pattern (48 bp):
TCTGATTTCTGATCTGAATTCTGTTCTGATATCTGACCTGAATTCTGT
Found at i:454206 original size:24 final size:24
Alignment explanation
Indices: 454100--454208 Score: 123
Period size: 24 Copynumber: 4.5 Consensus size: 24
454090 AAATATTTTA
*
454100 TCTGATTTCTGA-CTTTAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGT
* * *
454124 TCTGA-TACATTACCTGAATTCTGT
1 TCTGATTTC-TGATCTGAATTCTGT
*
454148 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
454172 TCTGATATCTGATCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
454196 TTTGATTTCTGAT
1 TCTGATTTCTGAT
454209 ATCTCCATTT
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
23 2 0.03
24 66 0.93
25 3 0.04
ACGTcount: A:0.18, C:0.17, G:0.16, T:0.50
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:459442 original size:20 final size:21
Alignment explanation
Indices: 459329--459443 Score: 87
Period size: 20 Copynumber: 5.7 Consensus size: 21
459319 AAATAACCAA
***
459329 CAAATTCGCAACGCGA-ACAC
1 CAAATTCGCAACGCGATTTTC
* * *
459349 CAATTTCGCAACAC-AGTTTC
1 CAAATTCGCAACGCGATTTTC
* *
459369 CAAATTCGCAACTC-AGTTTC
1 CAAATTCGCAACGCGATTTTC
* * *
459389 GGAAA-TCGTAACACGATTTTC
1 -CAAATTCGCAACGCGATTTTC
459410 CAAATTCGCAACGCGATTTT-
1 CAAATTCGCAACGCGATTTTC
459430 CAAATTCGCAACGC
1 CAAATTCGCAACGC
459444 TAATTACCGA
Statistics
Matches: 77, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
19 1 0.01
20 55 0.71
21 21 0.27
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (21 bp):
CAAATTCGCAACGCGATTTTC
Found at i:459579 original size:58 final size:57
Alignment explanation
Indices: 459415--459581 Score: 255
Period size: 57 Copynumber: 2.9 Consensus size: 57
459405 TTTTCCAAAT
*
459415 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACATAACTA
1 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACACAACTA
* *
459472 TCGCAACGCGATTTTCAAATTAGCAACGCTAATTACCGATATAGATAAACACAACTA
1 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACACAACTA
* * *
459529 TCGCAACGCGAATTCGTCAATTTCGCAAC-TTAATTACCGATATAGGTAAACAC
1 TCGCAACGCG-ATT-TTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAC
459582 GGTAGAAAAA
Statistics
Matches: 100, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
57 64 0.64
58 25 0.25
59 11 0.11
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (57 bp):
TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACACAACTA
Found at i:459948 original size:20 final size:20
Alignment explanation
Indices: 459922--459976 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
459912 AATTAAGTTG
*
459922 CGAAATTCGCATTGCAAAAAT
1 CGAAATTCGTATTGC-AAAAT
459943 -GAAATTCGTATTGCAAAAT
1 CGAAATTCGTATTGCAAAAT
459962 CGAAATTCGTATTGC
1 CGAAATTCGTATTGC
459977 GAATTTGGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 5 0.16
20 27 0.84
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.29
Consensus pattern (20 bp):
CGAAATTCGTATTGCAAAAT
Found at i:460053 original size:20 final size:21
Alignment explanation
Indices: 460023--460159 Score: 122
Period size: 20 Copynumber: 6.7 Consensus size: 21
460013 CTATATCGGT
*
460023 AATTAGCGTTGCGAA-TTGGA
1 AATTCGCGTTGCGAATTTGGA
* ***
460043 AAATCGCGTTGCGAA-AAAGA
1 AATTCGCGTTGCGAATTTGGA
* *
460063 AATTCGCGTTGCGATTTTCGA
1 AATTCGCGTTGCGAATTTGGA
* *
460084 AACT-GAGTTGCGAATTTGTGA
1 AATTCGCGTTGCGAATTTG-GA
460105 AATTCGCGTTGCGAATTTGGA
1 AATTCGCGTTGCGAATTTGGA
* *
460126 AACT-GTGTTGCGAATTTGG-
1 AATTCGCGTTGCGAATTTGGA
*
460145 AGTTCGCGTTGCGAA
1 AATTCGCGTTGCGAA
460160 GTTGTTGGTT
Statistics
Matches: 92, Mismatches: 21, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
19 2 0.02
20 62 0.67
21 15 0.16
22 13 0.14
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (21 bp):
AATTCGCGTTGCGAATTTGGA
Found at i:460116 original size:42 final size:41
Alignment explanation
Indices: 460061--460159 Score: 146
Period size: 42 Copynumber: 2.4 Consensus size: 41
460051 TTGCGAAAAA
*
460061 GAAATTCGCGTTGCGATTTTCGAAACTGAGTTGCGAATTTG
1 GAAATTCGCGTTGCGAATTTCGAAACTGAGTTGCGAATTTG
* *
460102 TGAAATTCGCGTTGCGAATTTGGAAACTGTGTTGCGAATTTG
1 -GAAATTCGCGTTGCGAATTTCGAAACTGAGTTGCGAATTTG
*
460144 G-AGTTCGCGTTGCGAA
1 GAAATTCGCGTTGCGAA
460160 GTTGTTGGTT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
40 14 0.26
41 1 0.02
42 38 0.72
ACGTcount: A:0.23, C:0.14, G:0.29, T:0.33
Consensus pattern (41 bp):
GAAATTCGCGTTGCGAATTTCGAAACTGAGTTGCGAATTTG
Found at i:462088 original size:125 final size:125
Alignment explanation
Indices: 461864--462115 Score: 441
Period size: 125 Copynumber: 2.0 Consensus size: 125
461854 TTAAATTTCG
* *
461864 TCTTGATTAATCTAAATTGATCCGAATCACATACTTAACTTTGGTGAATGAGTCTTCTAACGAGG
1 TCTTGATTAATCTAAATTGATCCAAATCACATACTTAACTTTGGTGAATGAATCTTCTAACGAGG
* *
461929 ATTTTCTACATATATAAAAACTCGAATTCTAAAATTGTTTAAGCAATATTAAACTACTTA
66 ATTTTCTACATATACAAAAACTCGAATTCGAAAATTGTTTAAGCAATATTAAACTACTTA
* *
461989 TCTTGATTAATCTAAATTGATCCAAATCACATACTTAATTTTGGTGAATGAATCTTCTAATGAGG
1 TCTTGATTAATCTAAATTGATCCAAATCACATACTTAACTTTGGTGAATGAATCTTCTAACGAGG
*
462054 ATTTTCTATATATACAAAAACTCGAATTCGAAAATTGTTTAAGCAATATTAAACTACTTA
66 ATTTTCTACATATACAAAAACTCGAATTCGAAAATTGTTTAAGCAATATTAAACTACTTA
462114 TC
1 TC
462116 ACTTGAACTA
Statistics
Matches: 120, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
125 120 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (125 bp):
TCTTGATTAATCTAAATTGATCCAAATCACATACTTAACTTTGGTGAATGAATCTTCTAACGAGG
ATTTTCTACATATACAAAAACTCGAATTCGAAAATTGTTTAAGCAATATTAAACTACTTA
Found at i:464780 original size:2 final size:2
Alignment explanation
Indices: 464775--464817 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
464765 TTATTAGTGT
464775 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
464817 T
1 T
464818 TTCCTATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:464933 original size:2 final size:2
Alignment explanation
Indices: 464886--464914 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
464876 TTATTTTACT
464886 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
464915 GTTTTTACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:468180 original size:10 final size:10
Alignment explanation
Indices: 468167--468217 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
468157 CAAAAAGGGC
468167 AAAAAGAAAA
1 AAAAAGAAAA
468177 AAAAAGAAGCAA
1 AAAAAGAA--AA
*
468189 AAAAGGAAAA
1 AAAAAGAAAA
* *
468199 AACAAGAACA
1 AAAAAGAAAA
468209 AAAAAGAAA
1 AAAAAGAAA
468218 GAACAAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 24 0.73
12 9 0.27
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:468188 original size:20 final size:21
Alignment explanation
Indices: 468167--468217 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
468157 CAAAAAGGGC
468167 AAAAAGAAAAAAAAAGAAGCA
1 AAAAAGAAAAAAAAAGAAGCA
*
468188 AAAAAGGAAAAAACAAGAA-CA
1 AAAAA-GAAAAAAAAAGAAGCA
468209 AAAAAGAAA
1 AAAAAGAAA
468218 GAACAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 4 0.14
21 12 0.43
22 12 0.43
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (21 bp):
AAAAAGAAAAAAAAAGAAGCA
Found at i:468197 original size:22 final size:21
Alignment explanation
Indices: 468167--468245 Score: 74
Period size: 21 Copynumber: 3.8 Consensus size: 21
468157 CAAAAAGGGC
468167 AAAAA-GAAAAAAAAAGAAGCA
1 AAAAAGGAAAAAAAAAGAA-CA
*
468188 AAAAAGGAAAAAACAAGAACA
1 AAAAAGGAAAAAAAAAGAACA
* *
468209 AAAAA-GAAAGAACAAA-AATA
1 AAAAAGGAAA-AAAAAAGAACA
* *
468229 AAAAAGGGAACAAAAAG
1 AAAAAGGAAAAAAAAAG
468246 TACATGCAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
20 16 0.34
21 19 0.40
22 12 0.26
ACGTcount: A:0.77, C:0.06, G:0.15, T:0.01
Consensus pattern (21 bp):
AAAAAGGAAAAAAAAAGAACA
Found at i:468222 original size:20 final size:20
Alignment explanation
Indices: 468167--468234 Score: 82
Period size: 20 Copynumber: 3.3 Consensus size: 20
468157 CAAAAAGGGC
*
468167 AAAAAGAAAAAAAAAGAAGCA
1 AAAAAGAAAAAACAAGAA-CA
468188 AAAAAGGAAAAAACAAGAACA
1 AAAAA-GAAAAAACAAGAACA
* * *
468209 AAAAAGAAAGAACAAAAATA
1 AAAAAGAAAAAACAAGAACA
468229 AAAAAG
1 AAAAAG
468235 GGAACAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
20 18 0.43
21 12 0.29
22 12 0.29
ACGTcount: A:0.79, C:0.06, G:0.13, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAAAACAAGAACA
Found at i:468870 original size:22 final size:22
Alignment explanation
Indices: 468842--468892 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
468832 CCCCATCAAT
468842 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
468864 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
468886 CCTTTGA
1 CCTTTGA
468893 CCAAACACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:469798 original size:36 final size:36
Alignment explanation
Indices: 469751--469855 Score: 156
Period size: 36 Copynumber: 2.9 Consensus size: 36
469741 GTGCTCATCA
469751 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
* *
469787 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
* * *
469824 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
469856 TAAACATTGA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
36 31 0.50
37 31 0.50
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.39
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
Found at i:469845 original size:37 final size:37
Alignment explanation
Indices: 469751--469860 Score: 159
Period size: 37 Copynumber: 3.0 Consensus size: 37
469741 GTGCTCATCA
469751 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
* *
469787 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
* * *
469824 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAAC
469861 ATTGAAAACA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
36 30 0.46
37 32 0.49
38 3 0.05
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
Found at i:470004 original size:36 final size:36
Alignment explanation
Indices: 469962--470053 Score: 109
Period size: 36 Copynumber: 2.6 Consensus size: 36
469952 TACCATTTCC
* *
469962 CTTGAGACAGTTTCTTTTG-GAACTAAG-TTT-GTCTCT
1 CTTGAGACAGTTTCTCTTGAG-AC--AGTTTTCGTCTAT
469998 CTTGAGACAGTTTCTCTTGAGACAGTTTTCGTCTAT
1 CTTGAGACAGTTTCTCTTGAGACAGTTTTCGTCTAT
*
470034 CTTGAGACAGTTTCCCTTGA
1 CTTGAGACAGTTTCTCTTGA
470054 AACAAAATCT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
34 2 0.04
35 3 0.06
36 44 0.88
37 1 0.02
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (36 bp):
CTTGAGACAGTTTCTCTTGAGACAGTTTTCGTCTAT
Found at i:470015 original size:15 final size:15
Alignment explanation
Indices: 469995--470025 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
469985 TAAGTTTGTC
469995 TCTCTTGAGACAGTT
1 TCTCTTGAGACAGTT
470010 TCTCTTGAGACAGTT
1 TCTCTTGAGACAGTT
470025 T
1 T
470026 TCGTCTATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (15 bp):
TCTCTTGAGACAGTT
Found at i:470144 original size:67 final size:68
Alignment explanation
Indices: 470034--470190 Score: 214
Period size: 68 Copynumber: 2.4 Consensus size: 68
470024 TTTCGTCTAT
* **
470034 CTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTT-CCTCTAAAACA-AATTTTGT
1 CTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCT-TAAAACATAATTTTGT
470095 CTCC
65 CTCC
* *
470099 CTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACATAATTTTGTT
1 CTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACATAATTTTGTC
470164 TCC
66 TCC
* *
470167 CTTGAGACCGTTTCTCATGAAACA
1 CTTGAGACAGTTTCTCTTGAAACA
470191 ACAGATATCT
Statistics
Matches: 80, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
65 17 0.21
66 2 0.03
67 26 0.32
68 35 0.44
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.37
Consensus pattern (68 bp):
CTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACATAATTTTGTC
TCC
Found at i:471150 original size:105 final size:104
Alignment explanation
Indices: 470795--471967 Score: 1694
Period size: 105 Copynumber: 11.3 Consensus size: 104
470785 GCCATCCGCG
* * * * * *
470795 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * *
470860 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCGCTGCTTGTCAAC-AACAACTTCCCAA-TTCAGAGCCA
470904 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
470969 ACCGCTGGTTGTCAATAAACAATTTTCCCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAA-CAACAA-CTTCCCAA-TTCAGAGCCA
* *
471011 ATTTCAACTTCACAGCGAAGGATATTGGATTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
471076 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAAT-TCAGAGCCA
*
471116 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
471181 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAAT-TCAGAGCCA
471221 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
471286 AGCGCTGCTTGTCAACAA-AA-TT-TC-ATTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTCAGAGCCA
** *
471321 ATTTCAACTTCACAGTGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
471386 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAAT-TCAGAGCCA
*
471426 ATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
471491 ACCGCTGCTTGTCAACAA-AA-TT-TC-ATTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTCAGAGCCA
*
471526 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
471591 ACCGCTGCTTGTCAGCAA-AA-TT-TC-ATTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTCAGAGCCA
* *
471626 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
471691 ACCGCTGTTTGTCAACAACAACTTCCCAATCCCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAAT-TCAGAGCCA
*
471731 ATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
471796 ACCGCTGCTTGTCAACAA-AA-TT-TC-ATTCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTCAGAGCCA
* * *
471831 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * **
471896 ACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
66 ACCGCTGCTTGTCAAC-AACAACTTCCCAATT-CAGAGCCA
* *
471937 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
471968 TGGAACAATG
Statistics
Matches: 987, Mismatches: 58, Indels: 41
0.91 0.05 0.04
Matches are distributed among these distances:
100 355 0.36
101 12 0.01
102 9 0.01
103 10 0.01
104 12 0.01
105 376 0.38
106 93 0.09
107 98 0.10
109 22 0.02
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (104 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCCCAATTCAGAGCCA
Found at i:471396 original size:205 final size:207
Alignment explanation
Indices: 470795--471967 Score: 1735
Period size: 205 Copynumber: 5.7 Consensus size: 207
470785 GCCATCCGCG
* * * * * *
470795 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
470860 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
63 GGGACCGCTGGTTGTCAAC-AACAACTTCTCAA-TTCAGAGCCAATTTCAACTTCACAACGAAGG
* *
470925 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
126 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-CAACA
470990 ATTTTCCCAATTTCAGAGCCA
190 A-TTT-CCAA-TTCAGAGCCA
* *
471011 ATTTCAACTTCACAGCGAAGGATATTGGATTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
471076 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
66 ACCGCTGGTTGTCAACAACAACTTCTCAAT-TCAGAGCCAATTTCAACTTCACAACGAAGGATAT
*
471141 TGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTT
130 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAA-TTT
471206 CCAATCTCAGAGCCA
194 CCAAT-TCAGAGCCA
471221 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * **
471286 AGCGCTGCTTGTCAACAA-AA-TT-TC-ATTCAGAGCCAATTTCAACTTCACAGTGAAGGATATT
66 ACCGCTGGTTGTCAACAACAACTTCTCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
*
471347 GGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTC
131 GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAA-TTTC
471412 CAATCTCAGAGCCA
195 CAAT-TCAGAGCCA
*
471426 ATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
471491 ACCGCTGCTTGTCAACAA-AA-TT-TC-ATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATT
66 ACCGCTGGTTGTCAACAACAACTTCTCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
*
471552 GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAGCAA-AATTT-C
131 GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAATTTCC
471615 -ATTCAGAGCCA
196 AATTCAGAGCCA
* *
471626 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * *
471691 ACCGCTGTTTGTCAACAACAACTTCCCAATCCCAGAGCCAATTTCAACTTCACAACGAAAGATAT
66 ACCGCTGGTTGTCAACAACAACTTCTCAAT-TCAGAGCCAATTTCAACTTCACAACGAAGGATAT
471756 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AATTT-
130 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAATTTC
**
471819 C-ATTCAGATTCA
195 CAATTCAGAGCCA
* * *
471831 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * ** * *
471896 ACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATA
66 ACCGCTGGTTGTCAAC-AACAACTTCTCAATT-CAGAGCCAATTTCAACTTCACAACGAAGGATA
471961 TTGGACT
129 TTGGACT
471968 TGGAACAATG
Statistics
Matches: 897, Mismatches: 51, Indels: 28
0.92 0.05 0.03
Matches are distributed among these distances:
200 88 0.10
201 4 0.00
202 3 0.00
203 4 0.00
204 4 0.00
205 467 0.52
206 49 0.05
207 1 0.00
208 2 0.00
209 3 0.00
210 92 0.10
211 9 0.01
212 99 0.11
213 48 0.05
214 3 0.00
216 21 0.02
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (207 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGGTTGTCAACAACAACTTCTCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAATTTCC
AATTCAGAGCCA
Found at i:471669 original size:305 final size:311
Alignment explanation
Indices: 470795--471967 Score: 1814
Period size: 305 Copynumber: 3.8 Consensus size: 311
470785 GCCATCCGCG
* * * * * *
470795 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
470860 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
63 GGGACCGCTGCTTGTCAAC-AACAACTT-TCAA-TTCAGAGCCAATTTCAACTTCACAACGAAGG
* *
470925 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
125 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-CAACA
* *
470990 ATTTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGATTCCAGACAACGCAA
189 A-TTT-CCAA-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAA
*
471055 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
251 GTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
*
471116 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
471181 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
66 ACCGCTGCTTGTCAACAACAACTTT-CAAT-TCAGAGCCAATTTCAACTTCACAACGAAGGATAT
*
471246 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAGCGCTGCTTGTCAACAA-AATTT-
129 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAATTTC
*
471309 C-ATTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCCAGACAATGCAAGTTCAACT
194 CAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACT
*
471373 TCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
259 TCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
*
471426 ATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
471491 ACCGCTGCTTGTCAACAA-AA-TTTC-ATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTG
66 ACCGCTGCTTGTCAACAACAACTTTCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTG
*
471553 GACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAGCAA-AATTT-C-
131 GACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAATTTCCA
471615 ATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTC
196 ATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTC
* *
471680 ACGACGAAGGGACCGCTGTTTGTCAACAACAACTTCCCAATCCCAGAGCCA
261 ACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
*
471731 ATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
**
471796 ACCGCTGCTTGTCAACAA-AA-TTTC-ATTCAGATTCAATTTCAACTTCACAACGAAGGATATTG
66 ACCGCTGCTTGTCAACAACAACTTTCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTG
* * * * *
471858 GACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCC
131 GACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAATTT-C
** *
471923 CGGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGGACT
194 CAATT-CAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACT
471968 TGGAACAATG
Statistics
Matches: 804, Mismatches: 39, Indels: 28
0.92 0.04 0.03
Matches are distributed among these distances:
305 377 0.47
306 4 0.00
307 6 0.01
308 3 0.00
309 3 0.00
310 194 0.24
311 37 0.05
312 1 0.00
314 3 0.00
315 2 0.00
316 4 0.00
317 98 0.12
318 47 0.06
319 3 0.00
321 22 0.03
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (311 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTTCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTG
GACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAATTTCCA
ATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTC
ACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
Found at i:473184 original size:17 final size:16
Alignment explanation
Indices: 473152--473185 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
473142 TTTACTCATT
*
473152 TATTTATCTATTTTTA
1 TATTTATCTATATTTA
473168 TATTTATCCTATATTTA
1 TATTTAT-CTATATTTA
473185 T
1 T
473186 GTTTTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTATCTATATTTA
Found at i:476208 original size:21 final size:21
Alignment explanation
Indices: 476091--476228 Score: 68
Period size: 21 Copynumber: 6.7 Consensus size: 21
476081 ACGCGAAATA
**
476091 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
476111 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
* *
476131 AAAATCGCAACACGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* ** *
476152 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* **
476173 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
* * * *
476194 AGAATCGCAACGCGAATAT-G
1 AAAATCGCAACGCGATTTTCC
476214 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
476229 ACACATAAAT
Statistics
Matches: 86, Mismatches: 28, Indels: 8
0.70 0.23 0.07
Matches are distributed among these distances:
19 1 0.01
20 38 0.44
21 45 0.52
22 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.20
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:476221 original size:20 final size:20
Alignment explanation
Indices: 476196--476389 Score: 87
Period size: 20 Copynumber: 9.7 Consensus size: 20
476186 GATTTTCCAG
* *
476196 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
476216 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
476236 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
476256 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
476276 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
476296 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
476316 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
476336 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
476357 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
476377 AATCGCAACGCGA
1 AATCGCAACGCGA
476390 TATTTAAAGC
Statistics
Matches: 149, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
19 3 0.02
20 130 0.87
21 15 0.10
22 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Done.