Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009213.1 Hibiscus syriacus cultivar Beakdansim tig00112800_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: 747713
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:286748 original size:60 final size:61
Alignment explanation
Indices: 286651--286783 Score: 180
Period size: 60 Copynumber: 2.2 Consensus size: 61
286641 TAGGGTAAAA
* * **
286651 TACACAAATGGT-TTCTCGATTATAGATTATTGCTTTATTAAGTTCTTTGACTATTAAAAGT
1 TACA-AAATGGTCTTCTCGATTATAGAATATTGCTTTATTAAGTTCCTCAACTATTAAAAGT
* * *
286712 TACAAAATGGTCTTCT-GATTGTAGAATGTTGTTTTATTAAGTTCCTCAACTATTAAAAGT
1 TACAAAATGGTCTTCTCGATTATAGAATATTGCTTTATTAAGTTCCTCAACTATTAAAAGT
286772 TACAAAATGGTC
1 TACAAAATGGTC
286784 ACTCGACTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
60 56 0.88
61 8 0.12
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.41
Consensus pattern (61 bp):
TACAAAATGGTCTTCTCGATTATAGAATATTGCTTTATTAAGTTCCTCAACTATTAAAAGT
Found at i:290614 original size:20 final size:19
Alignment explanation
Indices: 290589--290629 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
290579 ATACTCGAAC
290589 TTAAAATAATTCTTTTA-TTA
1 TTAAAAT-ATT-TTTTACTTA
290609 TTAAAATATTTTTTACTTA
1 TTAAAATATTTTTTACTTA
290628 TT
1 TT
290630 TTTTTTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 8 0.40
20 7 0.35
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
TTAAAATATTTTTTACTTA
Found at i:291578 original size:18 final size:18
Alignment explanation
Indices: 291555--291603 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
291545 CAAATTGTCC
*
291555 ATATTATATATTTGTATA
1 ATATTATATATTTGTAAA
* *
291573 ATATTACA-AATTGTAAA
1 ATATTATATATTTGTAAA
291590 ATATTTATATATTT
1 ATA-TTATATATTT
291604 TTTAAAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
17 10 0.42
18 11 0.46
19 3 0.12
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (18 bp):
ATATTATATATTTGTAAA
Found at i:300736 original size:17 final size:15
Alignment explanation
Indices: 300705--300742 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 15
300695 TAGATTCCAT
300705 TTAAATCAAATCAAA
1 TTAAATCAAATCAAA
300720 TTAAATCAAACATCAAA
1 TTAAATC-AA-ATCAAA
300737 TTAAAT
1 TTAAAT
300743 TAATATCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 7 0.33
16 2 0.10
17 12 0.57
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (15 bp):
TTAAATCAAATCAAA
Found at i:301666 original size:11 final size:11
Alignment explanation
Indices: 301652--301698 Score: 60
Period size: 11 Copynumber: 4.1 Consensus size: 11
301642 AAATTAAATC
301652 AAAATA-ATAA
1 AAAATATATAA
301662 TAAAATATATAA
1 -AAAATATATAA
301674 AAAATATATAA
1 AAAATATATAA
301685 AAAACTTATATAA
1 AAAA--TATATAA
301698 A
1 A
301699 TTATTAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 21 0.64
12 4 0.12
13 8 0.24
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (11 bp):
AAAATATATAA
Found at i:303264 original size:44 final size:44
Alignment explanation
Indices: 303201--303298 Score: 169
Period size: 44 Copynumber: 2.2 Consensus size: 44
303191 GGCTTTTTTG
*
303201 TATGTACATCATCTGCTAAATGGTGGTGATAGAGGAAACGTTCT
1 TATGTATATCATCTGCTAAATGGTGGTGATAGAGGAAACGTTCT
303245 TATGTATATCATCTGCTAAATGGTGGTGATAGAGGAAACGTTCT
1 TATGTATATCATCTGCTAAATGGTGGTGATAGAGGAAACGTTCT
*
303289 TCATGCATAT
1 T-ATGTATAT
303299 GATTTCATGT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 44 0.86
45 7 0.14
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (44 bp):
TATGTATATCATCTGCTAAATGGTGGTGATAGAGGAAACGTTCT
Found at i:306842 original size:21 final size:20
Alignment explanation
Indices: 306818--306881 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
306808 ACTTTGAAAA
306818 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
306839 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
306853 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
306874 AAATGTTT
1 AAATGTTT
306882 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 4 0.12
19 4 0.12
20 7 0.21
21 10 0.29
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:306856 original size:35 final size:36
Alignment explanation
Indices: 306816--306931 Score: 173
Period size: 35 Copynumber: 3.2 Consensus size: 36
306806 CAACTTTGAA
306816 AAAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTG
*
306852 -AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTG
* * *
306887 AAAAATAGTTTTTCAAAGTTTGGTAGATGTTT-GTTG
1 AAAAAT-GATTTTCAAAGTTTGGTAAATGTTTCTTTG
306923 AAAAATGAT
1 AAAAATGAT
306932 AATGGGATAA
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 36 0.49
36 14 0.19
37 23 0.32
ACGTcount: A:0.34, C:0.04, G:0.19, T:0.43
Consensus pattern (36 bp):
AAAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTG
Found at i:311489 original size:37 final size:38
Alignment explanation
Indices: 311434--311517 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 38
311424 TGGTAACCAA
311434 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
* *
311471 CTTTGAAAAATA-GTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
*
311508 -GTTGAAAAAT
1 CTTTGAAAAAT
311518 GATAATGGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 9 0.21
37 33 0.77
38 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (38 bp):
CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:313166 original size:2 final size:2
Alignment explanation
Indices: 313155--313216 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
313145 TACATCTCTT
313155 TA TA TA -A 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
313196 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
313217 TCAATTAGCT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 58 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:321169 original size:32 final size:32
Alignment explanation
Indices: 321140--321201 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
321130 CCGCCTAAGG
*
321140 TAATAATATGACATTTATCACGTCACCTAAAC
1 TAATAATATGACATGTATCACGTCACCTAAAC
* * * *
321172 TAATGATCTGACATGTATCACATTACCTAA
1 TAATAATATGACATGTATCACGTCACCTAA
321202 TATAATGACA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (32 bp):
TAATAATATGACATGTATCACGTCACCTAAAC
Found at i:321208 original size:32 final size:32
Alignment explanation
Indices: 321148--321209 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
321138 GGTAATAATA
* *
321148 TGACATTTATCACGTCACCTAAACTAATGATC
1 TGACATGTATCACATCACCTAAACTAATGATC
*
321180 TGACATGTATCACATTACCTAATA-TAATGA
1 TGACATGTATCACATCACCTAA-ACTAATGA
321210 CATGATATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 25 0.96
33 1 0.04
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.32
Consensus pattern (32 bp):
TGACATGTATCACATCACCTAAACTAATGATC
Found at i:321220 original size:32 final size:32
Alignment explanation
Indices: 321184--321245 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
321174 ATGATCTGAC
* *
321184 ATGTATCACATTACCTAATATAATGACATGAT
1 ATGTATAACATTACCTAAGATAATGACATGAT
* * *
321216 ATGTATAATATTATCTAAGATGATGACATG
1 ATGTATAACATTACCTAAGATAATGACATG
321246 GCATGTGTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.35
Consensus pattern (32 bp):
ATGTATAACATTACCTAAGATAATGACATGAT
Found at i:325197 original size:60 final size:60
Alignment explanation
Indices: 325133--325254 Score: 156
Period size: 60 Copynumber: 2.0 Consensus size: 60
325123 TAATAATCTT
* * *
325133 AAGACTC-AACAAAGTAACATTTCATAGTCGAACGACTATTTTGTAACCTTTAATAGTCGA
1 AAGACTCGAA-AAAATAACATTTCATAGTCAAACGACTATTTTATAACCTTTAATAGTCGA
* * * * *
325193 AAGACTCGAAAAAATAACATTTTATTGTCAAATGACTATTTTATAACTTTTAATAGTTGA
1 AAGACTCGAAAAAATAACATTTCATAGTCAAACGACTATTTTATAACCTTTAATAGTCGA
325253 AA
1 AA
325255 TATTCAATAA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 51 0.96
61 2 0.04
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (60 bp):
AAGACTCGAAAAAATAACATTTCATAGTCAAACGACTATTTTATAACCTTTAATAGTCGA
Found at i:325479 original size:2 final size:2
Alignment explanation
Indices: 325464--325502 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
325454 AGTCCCTCGA
*
325464 AT AT AT ACT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
325503 TAGGGTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 33 0.97
3 1 0.03
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:325556 original size:7 final size:7
Alignment explanation
Indices: 325546--325577 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
325536 ATACTTCTAA
325546 GTATAAT
1 GTATAAT
325553 GTATAAT
1 GTATAAT
325560 -TATAAT
1 GTATAAT
325566 GTATAAT
1 GTATAAT
325573 GTATA
1 GTATA
325578 CTTATATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (7 bp):
GTATAAT
Found at i:325571 original size:20 final size:20
Alignment explanation
Indices: 325546--325583 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
325536 ATACTTCTAA
325546 GTATAATGTATAATTATAAT
1 GTATAATGTATAATTATAAT
*
325566 GTATAATGTATACTTATA
1 GTATAATGTATAATTATA
325584 TAAATATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.45
Consensus pattern (20 bp):
GTATAATGTATAATTATAAT
Found at i:325655 original size:17 final size:17
Alignment explanation
Indices: 325593--325659 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
325583 ATAAATATTA
325593 TATATATAAACTTATAT
1 TATATATAAACTTATAT
*
325610 TATA-AGTATACTTATA-
1 TATATA-TAAACTTATAT
325626 -A-ATATACAA---ATAT
1 TATATATA-AACTTATAT
325639 TATATATAAACTTATAT
1 TATATATAAACTTATAT
325656 TATA
1 TATA
325660 AGTATAATGT
Statistics
Matches: 39, Mismatches: 2, Indels: 18
0.66 0.03 0.31
Matches are distributed among these distances:
12 3 0.08
14 6 0.15
15 8 0.21
16 1 0.03
17 21 0.54
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.43
Consensus pattern (17 bp):
TATATATAAACTTATAT
Found at i:326053 original size:61 final size:63
Alignment explanation
Indices: 325988--326136 Score: 160
Period size: 71 Copynumber: 2.3 Consensus size: 63
325978 GTTGTGTAAT
325988 TTATTTAAATTTG-TTA-AATTTAGTCCTTAAAATTATATTTGTATATGAAAT-TGACCCATAC
1 TTATTTAAATTTGATTACAATTTAGTCCTTAAAATTATATTTGTATATGAAATCTG-CCCATAC
* *
326049 TTATTTATATTTTTGTAATTTACTTCAATTTTGTCCTTAAAATTATATTTGTATATGAAATCTGC
1 TTATTTA-A-ATTTG--A-TTA---CAATTTAGTCCTTAAAATTATATTTGTATATGAAATCTGC
326114 CCATAC
58 CCATAC
*
326120 TTATTTATATTTCGATT
1 TTATTTAAATTT-GATT
326137 TAGTACCTCA
Statistics
Matches: 72, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
61 7 0.10
62 1 0.01
63 4 0.06
67 5 0.07
68 1 0.01
69 3 0.04
70 1 0.01
71 48 0.67
72 2 0.03
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.50
Consensus pattern (63 bp):
TTATTTAAATTTGATTACAATTTAGTCCTTAAAATTATATTTGTATATGAAATCTGCCCATAC
Found at i:326944 original size:60 final size:60
Alignment explanation
Indices: 326831--326946 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 60
326821 TACCTATATG
* **
326831 TATTAATTTATTAAGTCCATCGACTATTAAAAGTTATAAAATGATAATTCGACTATAGAA
1 TATTAATTTATTAAGTCCATCAACTATTAAAAGTTATAAAATGATAACCCGACTATAGAA
* * *
326891 TATTACTTTGTTAAGTGCCA-CAACTATTAAAAGTTATAAAATAGA-CACCCGACTAT
1 TATTAATTTATTAAGT-CCATCAACTATTAAAAGTTATAAAAT-GATAACCCGACTAT
326947 TCATTATGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
60 43 0.90
61 5 0.10
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.34
Consensus pattern (60 bp):
TATTAATTTATTAAGTCCATCAACTATTAAAAGTTATAAAATGATAACCCGACTATAGAA
Found at i:327718 original size:2 final size:2
Alignment explanation
Indices: 327711--327743 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
327701 TTTACAATTA
327711 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
327744 CCTAATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:330180 original size:31 final size:31
Alignment explanation
Indices: 330145--330210 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
330135 AGTTACATCG
*
330145 GGGACCATATTGCAAACAAACTAAATGTTGA
1 GGGACCATATTACAAACAAACTAAATGTTGA
* *
330176 GGGACCATATTACAAATAGACTAAATGTTGA
1 GGGACCATATTACAAACAAACTAAATGTTGA
330207 GGGA
1 GGGA
330211 TTGTATTACA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.23
Consensus pattern (31 bp):
GGGACCATATTACAAACAAACTAAATGTTGA
Found at i:335002 original size:32 final size:31
Alignment explanation
Indices: 334942--335000 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
334932 TTCACTTTTT
334942 TTAAAATCAATAAAGATGCAATAAAAAAGAA
1 TTAAAATCAATAAAGATGCAATAAAAAAGAA
* *
334973 TTAAAAGTGAATAAA-ATTCAATAAAAAA
1 TTAAAA-TCAATAAAGATGCAATAAAAAA
335001 AGATGTAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.64, C:0.05, G:0.08, T:0.22
Consensus pattern (31 bp):
TTAAAATCAATAAAGATGCAATAAAAAAGAA
Found at i:335755 original size:333 final size:335
Alignment explanation
Indices: 335089--336096 Score: 1605
Period size: 333 Copynumber: 3.0 Consensus size: 335
335079 TATTAAACTC
* * *
335089 TAATTTTATTAAAAAT-AAGTAAACATTATTAACTGTTATTAAAAA-AATAATTAATAAATAATA
1 TAATTTTATTAAAAATGAA-TAAACATTATTAAATGTTGTTAAAAATAATAATTAATGAATAATA
*
335152 ATTCATTTGATCCCTCGAA-TGTAATTAAAAGTTTATTTTAATATTTTTATATTTTTAAACAATT
65 ATTCATTTGATCCCTC-AATTGTAATTAAAAGTTTATTTTAATATTTTT-TATATTTAAACAATT
*
335216 AATTTTAAAAGTCAATAAAATTTTCAAAAATATATAAAATTTATAATTTTTTAAATTATAAAATA
128 AATTTTAAAAGTCAATAAAATTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATA
* * * * *
335281 TTTATTATCATCATCTTCAGCATTTTGCAAAAGAAATACTGGTTATAAAACTTTTATAAAATTAT
193 TTTATTATC-TCATCATCATCATTTTGTAAAAGAAATATTGATTATAAAACTTTTATAAAATTAT
*
335346 TCATATTTTAAAAAACTTATCCTCAAAGTTTTCCTATACTAGATTATATGTATTGTGTAATTTCA
257 TCATATTTTAAAATACTTATCCTCAAAGTTTTCCTATACTAGATTATATGTATTGTGTAATTTCA
335411 TGCAAAAATCAAAA
322 TGCAAAAATCAAAA
* * *
335425 TAATTTTATTAAAATTGAATAAACATTATTAATTGTTGTTAAAAATAATAATTAACGAATAATAA
1 TAATTTTATTAAAAATGAATAAACATTATTAAATGTTGTTAAAAATAATAATTAATGAATAATAA
* * *
335490 TTCATTTGATCGCTCAATTTTAATTAAAATTTTATTTTAATATTTTTTATATTTAAACAATTAAT
66 TTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTAAACAATTAAT
* *
335555 TTTAAAAGTCAATAAAATTTTCAAATATATATGAAATTTATACTTTTTTAAATTATAAAATATTT
131 TTTAAAAGTCAATAAAATTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATTT
*
335620 ATTAT-T-ATCATCATCATTTTGTAAAAGAAATATTGATTATAAAACTTTTATAAAATTACTCAT
196 ATTATCTCATCATCATCATTTTGTAAAAGAAATATTGATTATAAAACTTTTATAAAATTATTCAT
* * * *
335683 ATTTTAAAATACTTATCCTCAAAGTTTTTCTATACTAGATTATACGTATTGTGTAATTTTATACA
261 ATTTTAAAATACTTATCCTCAAAGTTTTCCTATACTAGATTATATGTATTGTGTAATTTCATGCA
335748 AAAATCAAAA
326 AAAATCAAAA
*
335758 TAATTTTATTAAAAAAGAATAAACATTATTAAATGTTGTTAAAAATAATAATTAATGAATAATAA
1 TAATTTTATTAAAAATGAATAAACATTATTAAATGTTGTTAAAAATAATAATTAATGAATAATAA
335823 TTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAATTA
66 TTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATA--TTTAAACAATTA
* * * *
335888 ATTTTAATAGTAAATAAATTTTTCAAAAATATATGAAATTTATAATTTTTAAAATTATAAAATAT
129 ATTTTAAAAGTCAATAAAATTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATAT
* *
335953 TTATCATCGTCATCATCATCATTTTGTAAAATAAATATT-AGTTATAAAACTTTTATAAAATTAT
194 TTATTATC-TCATCATCATCATTTTGTAAAAGAAATATTGA-TTATAAAACTTTTATAAAATTAT
* *
336017 TCATATTTTAAAATACCTACCCTCAAAGTTTTCCTATACTAGATTATATGTATTGTGTAATTTCA
257 TCATATTTTAAAATACTTATCCTCAAAGTTTTCCTATACTAGATTATATGTATTGTGTAATTTCA
336082 TGCAAAAATCAAAA
322 TGCAAAAATCAAAA
336096 T
1 T
336097 TTATCAAGTT
Statistics
Matches: 618, Mismatches: 45, Indels: 16
0.91 0.07 0.02
Matches are distributed among these distances:
333 230 0.37
334 1 0.00
335 77 0.12
336 125 0.20
337 62 0.10
338 123 0.20
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.43
Consensus pattern (335 bp):
TAATTTTATTAAAAATGAATAAACATTATTAAATGTTGTTAAAAATAATAATTAATGAATAATAA
TTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTAAACAATTAAT
TTTAAAAGTCAATAAAATTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATTT
ATTATCTCATCATCATCATTTTGTAAAAGAAATATTGATTATAAAACTTTTATAAAATTATTCAT
ATTTTAAAATACTTATCCTCAAAGTTTTCCTATACTAGATTATATGTATTGTGTAATTTCATGCA
AAAATCAAAA
Found at i:341202 original size:51 final size:52
Alignment explanation
Indices: 341147--341252 Score: 196
Period size: 51 Copynumber: 2.1 Consensus size: 52
341137 CTTTCTATGC
*
341147 AAGTTTACTTTGTAAACAAGAAACTTATCACTA-CAATAGATACTATGGATT
1 AAGTTTACTTTGTAAACAAGAAACTTATCACTATAAATAGATACTATGGATT
341198 AAGTTTACTTTGTAAACAAGAAACTTATCACTATAAATAGATACTATGGATT
1 AAGTTTACTTTGTAAACAAGAAACTTATCACTATAAATAGATACTATGGATT
341250 AAG
1 AAG
341253 GTTCTTGTCA
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 33 0.62
52 20 0.38
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (52 bp):
AAGTTTACTTTGTAAACAAGAAACTTATCACTATAAATAGATACTATGGATT
Found at i:341881 original size:95 final size:94
Alignment explanation
Indices: 341746--341925 Score: 297
Period size: 95 Copynumber: 1.9 Consensus size: 94
341736 CAACACATGT
*
341746 TGTTAATGTGATAATTTTGTATATACTTAATTACTGACGTGATGGGTCATGTTATCTAAAATTAC
1 TGTTAATGTGATAATTTTGTATATACTTAATTACTGACGTGATGGGTCATGTCA-CTAAAATTAC
*
341811 GACGTTACGTGTGTCACATCATCTCTATGA
65 GACGTTACATGTGTCACATCATCTCTATGA
* * *
341841 TGTTGATGTGATAATTTTGTATATACTTAATTACTGACGTGATGTGTCATGTCACTAAAGTTACG
1 TGTTAATGTGATAATTTTGTATATACTTAATTACTGACGTGATGGGTCATGTCACTAAAATTACG
*
341906 ACGTTATATGTGTCACATCA
66 ACGTTACATGTGTCACATCA
341926 CCCATGACGA
Statistics
Matches: 79, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
94 28 0.35
95 51 0.65
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.40
Consensus pattern (94 bp):
TGTTAATGTGATAATTTTGTATATACTTAATTACTGACGTGATGGGTCATGTCACTAAAATTACG
ACGTTACATGTGTCACATCATCTCTATGA
Found at i:363940 original size:24 final size:24
Alignment explanation
Indices: 363913--363968 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
363903 TACCTAGCAA
*
363913 GAGTATTTTCATAATTTCTTTTTC
1 GAGTATTTTCATAATTTCATTTTC
363937 GAGTATTTTCATAATTTCATTTTC
1 GAGTATTTTCATAATTTCATTTTC
*
363961 AAGTATTT
1 GAGTATTT
363969 CCGACATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.11, G:0.09, T:0.55
Consensus pattern (24 bp):
GAGTATTTTCATAATTTCATTTTC
Found at i:366296 original size:81 final size:80
Alignment explanation
Indices: 366032--366541 Score: 345
Period size: 81 Copynumber: 6.3 Consensus size: 80
366022 TAGATGTAAG
* * * * *
366032 TGTCACGTATCAGGATTTATATACA-GATTAATGTATAAGTTTTAGAAAAGTCTAATATTAAGAT
1 TGTCACGTGTCAGGA-TT-TATACATGATCAATGCATAAGATTTAGAAAA-TCTAATATTAAGAC
*
366096 TTTACTTTGTTAAGAGAA
63 TTTACTTTATTAAGAGAA
* * ** * ** * *
366114 TATCACGTGTTAAAATTTATAAATAAGA-CAACACATAAGATTTA-AGAAATACTAATAATCAAT
1 TGTCACGTGTCAGGATTTATACAT--GATCAATGCATAAGATTTAGA-AAAT-CTAAT-ATTAAG
* ** * *
366177 ATTTTGA-TCGACTATGCA-AA
61 ACTTT-ACTTTATTAAG-AGAA
* ** * * * *
366197 TATCACGTGTCAGGATTTATACATGAATCGGTGCATAAGATTTGGAAAATCTAATCTTAAAACCT
1 TGTCACGTGTCAGGATTTATACATG-ATCAATGCATAAGATTTAGAAAATCTAATATTAAGACTT
366262 TACTTTATTAAGAGAA
65 TACTTTATTAAGAGAA
* * * *
366278 TGTCACGTGTCAGGATTTATATACAT-ATTAATGCTTATGATTT-GAGAAATATAATATTAAGAC
1 TGTCACGTGTCAGGA-TT-TATACATGATCAATGCATAAGATTTAGA-AAATCTAATATTAAGAC
* *
366341 TTTATTTTGTTAAGAGAA
63 TTTACTTTATTAAGAGAA
* * * * * * * * *
366359 TGTCACGTGTCCGGACTTATCCATAAATCGATGCATAAGATTTAGACAATCAAATCTTAAGATTT
1 TGTCACGTGTCAGGATTTATACAT-GATCAATGCATAAGATTTAGAAAATCTAATATTAAGACTT
*
366424 TACCTTATTAAGAGAA
65 TACTTTATTAAGAGAA
* * * *
366440 TGTTACGTGTC-GAGATTTATATACA-GGTCAATGCATAAGATTTAGAAAATCTAGTATTAAGAT
1 TGTCACGTGTCAG-GA-TT-TATACATGATCAATGCATAAGATTTAGAAAATCTAATATTAAGAC
*
366503 TTTACTTTGTTAAGAGAA
63 TTTACTTTATTAAGAGAA
**
366521 TGTCACGTGTCAAAATTTATA
1 TGTCACGTGTCAGGATTTATA
366542 AATAAGACAC
Statistics
Matches: 327, Mismatches: 78, Indels: 49
0.72 0.17 0.11
Matches are distributed among these distances:
79 10 0.03
80 13 0.04
81 197 0.60
82 40 0.12
83 64 0.20
84 3 0.01
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (80 bp):
TGTCACGTGTCAGGATTTATACATGATCAATGCATAAGATTTAGAAAATCTAATATTAAGACTTT
ACTTTATTAAGAGAA
Found at i:366434 original size:162 final size:162
Alignment explanation
Indices: 366199--366532 Score: 438
Period size: 162 Copynumber: 2.1 Consensus size: 162
366189 TATGCAAATA
* * * * *
366199 TCACGTGTCAGGATTTATACATGAATCGGTGCATAAGATTTGGAAAATCTAATCTTAAAACCTTA
1 TCACGTGTCAGGACTTATACATAAATCGATGCATAAGATTTAGAAAATCAAATCTTAAAACCTTA
* * * * *
366264 CTTTATTAAGAGAATGTCACGTGTC-AGGATTTATATACATATTAATGCTTATGATTT-GAGAAA
66 CCTTATTAAGAGAATGTCACGTGTCGA-GATTTATATACAGATCAATGCATAAGATTTAGA-AAA
*
366327 TATAATATTAAGACTTTATTTTGTTAAGAGAATG
129 TATAATATTAAGACTTTACTTTGTTAAGAGAATG
* * * * **
366361 TCACGTGTCCGGACTTATCCATAAATCGATGCATAAGATTTAGACAATCAAATCTTAAGATTTTA
1 TCACGTGTCAGGACTTATACATAAATCGATGCATAAGATTTAGAAAATCAAATCTTAAAACCTTA
* * *
366426 CCTTATTAAGAGAATGTTACGTGTCGAGATTTATATACAGGTCAATGCATAAGATTTAGAAAATC
66 CCTTATTAAGAGAATGTCACGTGTCGAGATTTATATACAGATCAATGCATAAGATTTAGAAAATA
* *
366491 TAGTATTAAGATTTTACTTTGTTAAGAGAATG
131 TAATATTAAGACTTTACTTTGTTAAGAGAATG
366523 TCACGTGTCA
1 TCACGTGTCA
366533 AAATTTATAA
Statistics
Matches: 147, Mismatches: 23, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
162 144 0.98
163 3 0.02
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (162 bp):
TCACGTGTCAGGACTTATACATAAATCGATGCATAAGATTTAGAAAATCAAATCTTAAAACCTTA
CCTTATTAAGAGAATGTCACGTGTCGAGATTTATATACAGATCAATGCATAAGATTTAGAAAATA
TAATATTAAGACTTTACTTTGTTAAGAGAATG
Found at i:371374 original size:2 final size:2
Alignment explanation
Indices: 371367--371393 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
371357 CGTAGCACAT
371367 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 T
371394 TAGGGAGGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:371515 original size:2 final size:2
Alignment explanation
Indices: 371508--371543 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
371498 GGTCCATCCC
371508 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
371544 GAGAGAGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:371548 original size:2 final size:2
Alignment explanation
Indices: 371543--371574 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
371533 ATATATATAT
*
371543 AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
371575 GGAGGGAGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:371579 original size:10 final size:10
Alignment explanation
Indices: 371543--371582 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
371533 ATATATATAT
*
371543 AGAGAGAGAG
1 AGAGAGGGAG
*
371553 AGAGAGAGAG
1 AGAGAGGGAG
371563 AGAGAGGGAG
1 AGAGAGGGAG
*
371573 AGGGAGGGAG
1 AGAGAGGGAG
371583 CAATTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.57, T:0.00
Consensus pattern (10 bp):
AGAGAGGGAG
Found at i:385198 original size:21 final size:19
Alignment explanation
Indices: 385156--385209 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
385146 TGTTTGTTTT
* *
385156 ATATAATTGATTTTTCAGA
1 ATATAATTTATTTTCCAGA
385175 ATATAATTTATTTTCCTAGTA
1 ATATAATTTATTTTCC-AG-A
* *
385196 ATAGAATTTCTTTT
1 ATATAATTTATTTT
385210 ATATTTTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 14 0.48
20 2 0.07
21 13 0.45
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.52
Consensus pattern (19 bp):
ATATAATTTATTTTCCAGA
Found at i:385394 original size:34 final size:33
Alignment explanation
Indices: 385310--385394 Score: 79
Period size: 31 Copynumber: 2.6 Consensus size: 33
385300 ATTTTATAAA
* *
385310 TTTAATATTA-ATAAAATATTTTAATATTATTT
1 TTTAATATTACATAAAATAATATAATATTATTT
* **
385342 ATT--TATT-CATATTTATAATATAATATTATATT
1 TTTAATATTACATA-AAATAATATAATATTAT-TT
385374 TTTAATATTACATAAAATAAT
1 TTTAATATTACATAAAATAAT
385395 CAATTATATT
Statistics
Matches: 39, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
30 7 0.18
31 13 0.33
32 6 0.15
34 9 0.23
35 4 0.10
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (33 bp):
TTTAATATTACATAAAATAATATAATATTATTT
Found at i:385465 original size:29 final size:29
Alignment explanation
Indices: 385425--385510 Score: 88
Period size: 28 Copynumber: 3.0 Consensus size: 29
385415 AAGATATTTT
*
385425 ATTTTTAT-TTTAATAATATATAATAAAA
1 ATTTATATATTTAATAATATATAATAAAA
**
385453 ATTTATATATTTAATAATGA-ATAAT-ATT
1 ATTTATATATTTAATAAT-ATATAATAAAA
*
385481 ATTTATATATTTAAATAATATTTTAATAAA
1 ATTTATATATTT-AATAATA-TATAATAAA
385511 TATATTTAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
28 21 0.45
29 20 0.43
30 5 0.11
31 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (29 bp):
ATTTATATATTTAATAATATATAATAAAA
Found at i:385479 original size:19 final size:19
Alignment explanation
Indices: 385436--385509 Score: 57
Period size: 19 Copynumber: 3.9 Consensus size: 19
385426 TTTTTATTTT
385436 AATAATATA--TAATAA-A
1 AATAATATATTTAATAATA
* *
385452 AATTTATATATTTAATAATG
1 AA-TAATATATTTAATAATA
*
385472 AATAATATTATTTATATATTTA
1 AATAATA-TATTTA-ATA-ATA
385494 AATAATAT-TTTAATAA
1 AATAATATATTTAATAA
385510 ATATATTTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
16 2 0.04
17 6 0.13
19 13 0.29
20 12 0.27
21 4 0.09
22 8 0.18
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (19 bp):
AATAATATATTTAATAATA
Found at i:385493 original size:28 final size:29
Alignment explanation
Indices: 385399--385501 Score: 97
Period size: 29 Copynumber: 3.5 Consensus size: 29
385389 AATAATCAAT
* *
385399 TATATTATAATAATATA-AGATATTTTATTTT
1 TATATT-TAATAATATATA-ATA-ATTATTTA
**
385430 TAT-TTTAATAATATATAATAAAAATTTA
1 TATATTTAATAATATATAATAATTATTTA
385458 TATATTTAATAATGA-ATAAT-ATTATTTA
1 TATATTTAATAAT-ATATAATAATTATTTA
385486 TATATTTAAATAATAT
1 TATATTT-AATAATAT
385502 TTTAATAAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
28 21 0.34
29 33 0.54
30 4 0.07
31 3 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (29 bp):
TATATTTAATAATATATAATAATTATTTA
Found at i:385523 original size:15 final size:14
Alignment explanation
Indices: 385485--385525 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
385475 AATATTATTT
385485 ATATATTTAAAT-A
1 ATATATTTAAATAA
385498 ATAT-TTT-AATAA
1 ATATATTTAAATAA
385510 ATATATTTAAAATAA
1 ATATATTT-AAATAA
385525 A
1 A
385526 CTTAATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 3 0.12
12 8 0.33
13 7 0.29
15 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATATTTAAATAA
Found at i:385536 original size:24 final size:26
Alignment explanation
Indices: 385485--385547 Score: 78
Period size: 24 Copynumber: 2.5 Consensus size: 26
385475 AATATTATTT
*
385485 ATATATTT-AAATAATATTTTAATAA
1 ATATATTTAAAATAATATCTTAATAA
*
385510 ATATATTTAAAATAA-A-CTTAATTA
1 ATATATTTAAAATAATATCTTAATAA
*
385534 ATATTTTTAAAATA
1 ATATATTTAAAATA
385548 TAATATAACA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 19 0.56
25 9 0.26
26 6 0.18
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (26 bp):
ATATATTTAAAATAATATCTTAATAA
Found at i:385859 original size:15 final size:15
Alignment explanation
Indices: 385820--385884 Score: 78
Period size: 15 Copynumber: 4.4 Consensus size: 15
385810 TTTCATAAAT
**
385820 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
*
385835 G-AATTTAAATTCCA
1 GTAATTCAAATTCCA
385849 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
* *
385864 ATAATTTAAATTCCA
1 GTAATTCAAATTCCA
385879 GTAATT
1 GTAATT
385885 TATTTTCCGA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
14 11 0.26
15 31 0.74
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.40
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:385862 original size:29 final size:30
Alignment explanation
Indices: 385820--385884 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
385810 TTTCATAAAT
**
385820 GTAATTCATTTTCC-AGAATTTAAATTCCA
1 GTAATTCAAATTCCAAGAATTTAAATTCCA
*
385849 GTAATTCAAATTCCAATAATTTAAATTCCA
1 GTAATTCAAATTCCAAGAATTTAAATTCCA
385879 GTAATT
1 GTAATT
385885 TATTTTCCGA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 12 0.38
30 20 0.62
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.40
Consensus pattern (30 bp):
GTAATTCAAATTCCAAGAATTTAAATTCCA
Found at i:385892 original size:15 final size:15
Alignment explanation
Indices: 385830--385886 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
385820 GTAATTCATT
385830 TTCCAG-AATTTAAA
1 TTCCAGTAATTTAAA
*
385844 TTCCAGTAATTCAAA
1 TTCCAGTAATTTAAA
*
385859 TTCCAATAATTTAAA
1 TTCCAGTAATTTAAA
385874 TTCCAGTAATTTA
1 TTCCAGTAATTTA
385887 TTTTCCGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.39
Consensus pattern (15 bp):
TTCCAGTAATTTAAA
Found at i:389202 original size:7 final size:7
Alignment explanation
Indices: 389190--389301 Score: 224
Period size: 7 Copynumber: 16.0 Consensus size: 7
389180 TTCCTAGGCA
389190 GAAGCAT
1 GAAGCAT
389197 GAAGCAT
1 GAAGCAT
389204 GAAGCAT
1 GAAGCAT
389211 GAAGCAT
1 GAAGCAT
389218 GAAGCAT
1 GAAGCAT
389225 GAAGCAT
1 GAAGCAT
389232 GAAGCAT
1 GAAGCAT
389239 GAAGCAT
1 GAAGCAT
389246 GAAGCAT
1 GAAGCAT
389253 GAAGCAT
1 GAAGCAT
389260 GAAGCAT
1 GAAGCAT
389267 GAAGCAT
1 GAAGCAT
389274 GAAGCAT
1 GAAGCAT
389281 GAAGCAT
1 GAAGCAT
389288 GAAGCAT
1 GAAGCAT
389295 GAAGCAT
1 GAAGCAT
389302 CCAAGGACAA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 105 1.00
ACGTcount: A:0.43, C:0.14, G:0.29, T:0.14
Consensus pattern (7 bp):
GAAGCAT
Found at i:395561 original size:13 final size:14
Alignment explanation
Indices: 395543--395571 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
395533 AAATTAAAAA
395543 TTATTATTTTA-TT
1 TTATTATTTTACTT
395556 TTATTATTTTACTT
1 TTATTATTTTACTT
395570 TT
1 TT
395572 GATAAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (14 bp):
TTATTATTTTACTT
Found at i:396792 original size:2 final size:2
Alignment explanation
Indices: 396773--396834 Score: 106
Period size: 2 Copynumber: 30.5 Consensus size: 2
396763 TAACATTGCG
*
396773 TA TA TCA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
396816 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
396835 TGTTTGTTGC
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 55 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:398735 original size:60 final size:60
Alignment explanation
Indices: 398604--398723 Score: 177
Period size: 60 Copynumber: 2.0 Consensus size: 60
398594 TTATGTATTT
* * * * *
398604 AAAAAATAAAAATTATACTTTATCAGCTAATTATTCTTGAGCATTGATTTATTATTTTAT
1 AAAAAATAAAAATTATACTTTATCAGCTAATTATTCTTGAGCATTGATTGAGTATGTAAC
* *
398664 AAAAAATAAAAATTATACTTTATCAGCTAATTATTCTTGAGCATTGATTGGGTGTGTAAC
1 AAAAAATAAAAATTATACTTTATCAGCTAATTATTCTTGAGCATTGATTGAGTATGTAAC
398724 GTAAGATAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (60 bp):
AAAAAATAAAAATTATACTTTATCAGCTAATTATTCTTGAGCATTGATTGAGTATGTAAC
Found at i:400611 original size:45 final size:45
Alignment explanation
Indices: 400560--400649 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
400550 CCTTGCGTAG
400560 TCTCCACTCATGCATCACCAAGAAAATGCTATCACTAAGAGAACA
1 TCTCCACTCATGCATCACCAAGAAAATGCTATCACTAAGAGAACA
400605 TCTCCACTCATGCATCACCAAGAAAATGCTATCACTAAGAGAACA
1 TCTCCACTCATGCATCACCAAGAAAATGCTATCACTAAGAGAACA
400650 CTATATACAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.40, C:0.29, G:0.11, T:0.20
Consensus pattern (45 bp):
TCTCCACTCATGCATCACCAAGAAAATGCTATCACTAAGAGAACA
Found at i:400667 original size:2 final size:2
Alignment explanation
Indices: 400651--400691 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
400641 AAGAGAACAC
* *
400651 TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
400692 TAAACATAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:405722 original size:4 final size:4
Alignment explanation
Indices: 405713--405741 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
405703 TGTGTTAATA
405713 TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG T
405742 TTGCATGTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:416067 original size:26 final size:26
Alignment explanation
Indices: 416038--416091 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
416028 GCTCATGTTC
416038 CCCGAAAATACTATAATACCCCGAAT
1 CCCGAAAATACTATAATACCCCGAAT
416064 CCCGAAAATACTATAATACCCCGAAT
1 CCCGAAAATACTATAATACCCCGAAT
416090 CC
1 CC
416092 AGGGTCAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.41, C:0.33, G:0.07, T:0.19
Consensus pattern (26 bp):
CCCGAAAATACTATAATACCCCGAAT
Found at i:420856 original size:12 final size:12
Alignment explanation
Indices: 420839--420864 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
420829 TTGATTGAGT
420839 CAGCTGAAGAAA
1 CAGCTGAAGAAA
420851 CAGCTGAAGAAA
1 CAGCTGAAGAAA
420863 CA
1 CA
420865 ACGGCTCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.19, G:0.23, T:0.08
Consensus pattern (12 bp):
CAGCTGAAGAAA
Found at i:429388 original size:7 final size:7
Alignment explanation
Indices: 429376--429410 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
429366 CCTGGAAAGC
429376 ACTCGGT
1 ACTCGGT
429383 ACTCGGT
1 ACTCGGT
429390 ACTCGGT
1 ACTCGGT
429397 ACTCGGT
1 ACTCGGT
429404 ACTCGGT
1 ACTCGGT
429411 CTTGAGTCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.29
Consensus pattern (7 bp):
ACTCGGT
Found at i:435948 original size:26 final size:26
Alignment explanation
Indices: 435919--436003 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
435909 ATGAGTTACC
435919 ATTTTGTAACTTTTAATAGTCGAAGG
1 ATTTTGTAACTTTTAATAGTCGAAGG
* *
435945 ATTTAGTAA-TATTCT-ATAGT-TAGAGG
1 ATTTTGTAACT-TT-TAATAGTCGA-AGG
*
435971 ACCATTTTGTAACTTTTAATAGTCGAGGG
1 ---ATTTTGTAACTTTTAATAGTCGAAGG
436000 ATTT
1 ATTT
436004 AATAAAATAG
Statistics
Matches: 45, Mismatches: 5, Indels: 18
0.66 0.07 0.26
Matches are distributed among these distances:
25 2 0.04
26 22 0.49
27 1 0.02
28 1 0.02
29 17 0.38
30 2 0.04
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (26 bp):
ATTTTGTAACTTTTAATAGTCGAAGG
Found at i:435992 original size:29 final size:30
Alignment explanation
Indices: 435916--435993 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 30
435906 AGGATGAGTT
*
435916 ACCATTTTGTAACTTTTAATAG-TCGAAGG
1 ACCATTTTGTAACTTTTAATAGTTAGAAGG
*
435945 ---ATTTAGTAA-TATTCT-ATAGTTAG-AGG
1 ACCATTTTGTAACT-TT-TAATAGTTAGAAGG
435971 ACCATTTTGTAACTTTTAATAGT
1 ACCATTTTGTAACTTTTAATAGT
435994 CGAGGGATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 16
0.67 0.05 0.28
Matches are distributed among these distances:
25 1 0.03
26 17 0.45
27 3 0.08
28 1 0.03
29 15 0.39
30 1 0.03
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.42
Consensus pattern (30 bp):
ACCATTTTGTAACTTTTAATAGTTAGAAGG
Found at i:437055 original size:6 final size:6
Alignment explanation
Indices: 437044--437068 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
437034 GGAGAAGATC
437044 TGCCTT TGCCTT TGCCTT TGCCTT T
1 TGCCTT TGCCTT TGCCTT TGCCTT T
437069 ACCCTCACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.16, T:0.52
Consensus pattern (6 bp):
TGCCTT
Found at i:437827 original size:58 final size:59
Alignment explanation
Indices: 437753--437874 Score: 151
Period size: 59 Copynumber: 2.1 Consensus size: 59
437743 AATCGGTGAC
* * * *
437753 CATTTTGTAACTTTTAATAGTC-GATGA-CCAACAAAGTAGTGTTCTATAGTCGGA-GAT
1 CATTTTATAACTTTTAATAGTCGGA-GATCCAACAAAGCAGTGCTCTATAGTCGAAGGAT
**
437810 CATTTTATAAACTTTTAATAGTCGGAGATTTAACAAAGCAGTGCTCTATAGTCGAAGGAT
1 CATTTTAT-AACTTTTAATAGTCGGAGATCCAACAAAGCAGTGCTCTATAGTCGAAGGAT
437870 CATTT
1 CATTT
437875 GTATTCTTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
57 7 0.13
58 16 0.29
59 24 0.44
60 8 0.15
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (59 bp):
CATTTTATAACTTTTAATAGTCGGAGATCCAACAAAGCAGTGCTCTATAGTCGAAGGAT
Found at i:452294 original size:2 final size:2
Alignment explanation
Indices: 452287--452335 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
452277 TTTAATACAT
* *
452287 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA -A TA CA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
452327 TA TA TA TA T
1 TA TA TA TA T
452336 TATTTAGCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:452336 original size:18 final size:19
Alignment explanation
Indices: 452274--452336 Score: 83
Period size: 20 Copynumber: 3.3 Consensus size: 19
452264 AAATTATTAA
452274 ATATTTAATACATTATATAT
1 ATATTTAATACA-TATATAT
* *
452294 ATATATATATATATATATAT
1 ATATTTA-ATACATATATAT
452314 ATATTTAATACA-ATATAT
1 ATATTTAATACATATATAT
452332 ATATT
1 ATATT
452337 ATTTAGCTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
18 11 0.29
19 4 0.11
20 19 0.50
21 4 0.11
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTAATACATATATAT
Found at i:456434 original size:31 final size:31
Alignment explanation
Indices: 456356--456442 Score: 90
Period size: 32 Copynumber: 2.8 Consensus size: 31
456346 ATATATTTAG
* *
456356 TAAATTAAGATAAAATATATACTTTGAAATTT
1 TAAATTAAGTTAAAATATA-ATTTTGAAATTT
*
456388 TAAAATAA-TAATAAAATATAATTTTGAGAA-TT
1 TAAATTAAGT--TAAAATATAATTTTGA-AATTT
456420 TAAATTAAGTTAAAATAT-ATTTT
1 TAAATTAAGTTAAAATATAATTTT
456443 ATTCGATTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
30 5 0.11
31 8 0.17
32 22 0.47
33 12 0.26
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41
Consensus pattern (31 bp):
TAAATTAAGTTAAAATATAATTTTGAAATTT
Found at i:467676 original size:13 final size:13
Alignment explanation
Indices: 467658--467683 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
467648 CATAGTTGAA
467658 CAGTCTTCTTATG
1 CAGTCTTCTTATG
467671 CAGTCTTCTTATG
1 CAGTCTTCTTATG
467684 TGAGAGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.46
Consensus pattern (13 bp):
CAGTCTTCTTATG
Found at i:474378 original size:3 final size:3
Alignment explanation
Indices: 474370--474408 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
474360 CACCCGCCAT
* * *
474370 TTC TTC TTC TTA TTC TTC TTC ATC TTC TTC ATC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
474409 ATCATCCTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.08, C:0.31, G:0.00, T:0.62
Consensus pattern (3 bp):
TTC
Found at i:474387 original size:9 final size:9
Alignment explanation
Indices: 474374--474411 Score: 60
Period size: 9 Copynumber: 4.2 Consensus size: 9
474364 CGCCATTTCT
474374 TCTTCTT-A
1 TCTTCTTCA
474382 TTCTTCTTCA
1 -TCTTCTTCA
474392 TCTTCTTCA
1 TCTTCTTCA
474401 TCTTCTTCA
1 TCTTCTTCA
474410 TC
1 TC
474412 ATCCTCATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 27 0.96
10 1 0.04
ACGTcount: A:0.11, C:0.32, G:0.00, T:0.58
Consensus pattern (9 bp):
TCTTCTTCA
Found at i:474419 original size:18 final size:18
Alignment explanation
Indices: 474383--474420 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
474373 TTCTTCTTAT
* *
474383 TCTTCTTCATCTTCTTCA
1 TCTTCTTCATCATCCTCA
474401 TCTTCTTCATCATCCTCA
1 TCTTCTTCATCATCCTCA
474419 TC
1 TC
474421 AACTAGCTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.37, G:0.00, T:0.50
Consensus pattern (18 bp):
TCTTCTTCATCATCCTCA
Found at i:476018 original size:24 final size:25
Alignment explanation
Indices: 475975--476021 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
475965 AACTCAAAAA
475975 AAAATTAGAAGCTCGATTGAAGTCT
1 AAAATTAGAAGCTCGATTGAAGTCT
* *
476000 AAAATTCGAA-CTTGATTGAAGT
1 AAAATTAGAAGCTCGATTGAAGT
476022 GAAAGAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (25 bp):
AAAATTAGAAGCTCGATTGAAGTCT
Found at i:476317 original size:14 final size:14
Alignment explanation
Indices: 476281--476307 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
476271 ATTTAATTTT
476281 TAATTATATTTATA
1 TAATTATATTTATA
476295 TAATTATATTTAT
1 TAATTATATTTAT
476308 TATTTAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATTATATTTATA
Found at i:480561 original size:60 final size:60
Alignment explanation
Indices: 480450--480562 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
480440 TATAGGATGA
* * *
480450 TGCTTAGTTGAGTCTCCTTACTATTAAAAGTTATAAAATAATCCTTCAACTATATAGTGT
1 TGCTTAGTTGAGTCTCCTTACTATTAAAACTTACAAAATAATCATTCAACTATATAGTGT
* * *
480510 TGCTTTGTTGAGTC-CGTTGACTATTAAAACTTACAAAATTATCA-TCTAACTAT
1 TGCTTAGTTGAGTCTCCTT-ACTATTAAAACTTACAAAATAATCATTC-AACTAT
480563 TCATATATTC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 5 0.11
60 40 0.89
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.40
Consensus pattern (60 bp):
TGCTTAGTTGAGTCTCCTTACTATTAAAACTTACAAAATAATCATTCAACTATATAGTGT
Found at i:491317 original size:6 final size:6
Alignment explanation
Indices: 491303--491756 Score: 675
Period size: 6 Copynumber: 76.5 Consensus size: 6
491293 TGCAGGTGGG
* * * * * *
491303 TGTATA TGTACA TGTACA TGTACA TGTATA TGTACA TGTACA TGTACA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
* *
491351 TG--TA TGTATA TGTATA TGTATA TGTATA TGTATA TGTACA TGTACA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
*
491397 TGTACA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
491445 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
* *
491493 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA AGTATA TGTACA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
* * * * * * * *
491541 TGTACA TGTACA TGTACA TGTACA TGTACA TG-ACA TGTACA TGTACA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
* * *
491588 TGTACA --TACA TGTACA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
491634 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
491682 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
491730 TGTATA TGTATA TGTATA TGTATA TGT
1 TGTATA TGTATA TGTATA TGTATA TGT
491757 GGTGCTTGCT
Statistics
Matches: 433, Mismatches: 10, Indels: 10
0.96 0.02 0.02
Matches are distributed among these distances:
4 7 0.02
5 5 0.01
6 421 0.97
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (6 bp):
TGTATA
Found at i:495172 original size:38 final size:39
Alignment explanation
Indices: 495103--495181 Score: 124
Period size: 38 Copynumber: 2.1 Consensus size: 39
495093 TTTGTTCGAG
*
495103 TTTTTTAAGTGTGATATTCGGGTCAATTCGGGTT-GGGT
1 TTTTTTAAGTGTGATATTCGGGTCAAGTCGGGTTCGGGT
**
495141 TTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGT
1 TTTTTTAAGTGTGATATTCGGGTCAAGTCGGGTTCGGGT
495180 TT
1 TT
495182 AGGGTAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
38 31 0.84
39 6 0.16
ACGTcount: A:0.13, C:0.09, G:0.34, T:0.44
Consensus pattern (39 bp):
TTTTTTAAGTGTGATATTCGGGTCAAGTCGGGTTCGGGT
Found at i:495608 original size:26 final size:26
Alignment explanation
Indices: 495572--495622 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
495562 CGGGTTGGGT
495572 TTTTTAAGTGTGATATTCGGGTCATG
1 TTTTTAAGTGTGATATTCGGGTCATG
495598 TTTTTAAGTGTGATATTCGGGTCAT
1 TTTTTAAGTGTGATATTCGGGTCAT
495623 ATCGGGTCGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.20, C:0.08, G:0.25, T:0.47
Consensus pattern (26 bp):
TTTTTAAGTGTGATATTCGGGTCATG
Found at i:496227 original size:16 final size:18
Alignment explanation
Indices: 496203--496246 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
496193 TATGAAATTG
496203 GATTTCAATTCC-T-ACA
1 GATTTCAATTCCTTCACA
*
496219 GATTACAATTCCTTCACA
1 GATTTCAATTCCTTCACA
496237 GATTTCAATT
1 GATTTCAATT
496247 ATCTCGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 11 0.46
17 1 0.04
18 12 0.50
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.39
Consensus pattern (18 bp):
GATTTCAATTCCTTCACA
Found at i:497329 original size:33 final size:34
Alignment explanation
Indices: 497281--497347 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 34
497271 TCGTTCATTT
*
497281 AAATGATAAACGAACACAAATAAACGAATATAAA
1 AAATGATAAACGAACACAAATAAACGAACATAAA
* * **
497315 AAAT-ATAAATGAACAGATGTAAACGAACATAAA
1 AAATGATAAACGAACACAAATAAACGAACATAAA
497348 CAAACACAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 24 0.86
34 4 0.14
ACGTcount: A:0.63, C:0.10, G:0.10, T:0.16
Consensus pattern (34 bp):
AAATGATAAACGAACACAAATAAACGAACATAAA
Found at i:497353 original size:10 final size:10
Alignment explanation
Indices: 497334--497408 Score: 51
Period size: 10 Copynumber: 7.2 Consensus size: 10
497324 TGAACAGATG
*
497334 TAAACGAACA
1 TAAACAAACA
497344 TAAACAAACA
1 TAAACAAACA
* * *
497354 CAAACGAACG
1 TAAACAAACA
497364 TAAACAAACA
1 TAAACAAACA
*
497374 CAAACGAACACAA
1 TAAAC-AA-AC-A
* **
497387 TAAACGAATG
1 TAAACAAACA
497397 TAAACAAACA
1 TAAACAAACA
497407 TA
1 TA
497409 TTATCGAACA
Statistics
Matches: 47, Mismatches: 15, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
10 36 0.77
11 3 0.06
12 3 0.06
13 5 0.11
ACGTcount: A:0.61, C:0.21, G:0.08, T:0.09
Consensus pattern (10 bp):
TAAACAAACA
Found at i:497358 original size:20 final size:20
Alignment explanation
Indices: 497335--497383 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
497325 GAACAGATGT
497335 AAACGAACATAAACAAACAC
1 AAACGAACATAAACAAACAC
*
497355 AAACGAACGTAAACAAACAC
1 AAACGAACATAAACAAACAC
497375 AAACGAACA
1 AAACGAACA
497384 CAATAAACGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.63, C:0.24, G:0.08, T:0.04
Consensus pattern (20 bp):
AAACGAACATAAACAAACAC
Found at i:500369 original size:26 final size:26
Alignment explanation
Indices: 500333--500387 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
500323 GGCCCTAGAG
500333 GAAACCAATCATTGAAAAGTTTGTAA
1 GAAACCAATCATTGAAAAGTTTGTAA
500359 GAAACCAATCATTGAAAAGTTTGTAA
1 GAAACCAATCATTGAAAAGTTTGTAA
500385 GAA
1 GAA
500388 GCAAAGGAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.25
Consensus pattern (26 bp):
GAAACCAATCATTGAAAAGTTTGTAA
Found at i:504896 original size:20 final size:20
Alignment explanation
Indices: 504860--504897 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
504850 ATCCTATTCT
**
504860 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
504880 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
504898 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:505364 original size:2 final size:2
Alignment explanation
Indices: 505357--505392 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
505347 TATAATTTAA
505357 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
505393 CTTCTAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:506055 original size:33 final size:31
Alignment explanation
Indices: 506013--506090 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 31
506003 TTTTATTTTG
* *
506013 TGAAACAAAAAGTTAACAGATGATGTATTAAAA
1 TGAAACAAAAAGTTAA-AGATG-GGTACTAAAA
**
506046 TGAAACAAAAAAGTTAATTATGGGTACTAAAA
1 TGAAAC-AAAAAGTTAAAGATGGGTACTAAAA
506078 TGAAACAAAAAGT
1 TGAAACAAAAAGT
506091 AAATGTCAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
31 7 0.17
32 14 0.35
33 9 0.22
34 10 0.25
ACGTcount: A:0.55, C:0.06, G:0.15, T:0.23
Consensus pattern (31 bp):
TGAAACAAAAAGTTAAAGATGGGTACTAAAA
Found at i:511309 original size:14 final size:15
Alignment explanation
Indices: 511279--511311 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
511269 TTAATCATTA
511279 TATTGTTCATGACAT
1 TATTGTTCATGACAT
*
511294 TATTGTT-ATGATAT
1 TATTGTTCATGACAT
511308 TATT
1 TATT
511312 AACATATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.55
Consensus pattern (15 bp):
TATTGTTCATGACAT
Found at i:511910 original size:58 final size:58
Alignment explanation
Indices: 511763--512147 Score: 338
Period size: 58 Copynumber: 6.7 Consensus size: 58
511753 AATCTTACTT
* * *
511763 TGATTCTAACTTTGTAAGGGATATAAATTGTTAAATTTATTTCCTTGAGAATCTTAAA
1 TGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATTTCCTTGAGAATCTTAAA
* * * *
511821 TGA-T-T--CTTTGTAAGAAAAATAAATTGTTGAATTTCTTTCCTCGAGAATCTTGAA
1 TGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATTTCCTTGAGAATCTTAAA
** * *
511875 TGATTCTAACTTTGTAAGGAAAATAAACCGTTGAATTTATTTCCTTTAGAATATTAAA
1 TGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATTTCCTTGAGAATCTTAAA
* ** * *
511933 TGATTCTAACTTTGTAA-GAGAAATATATTGTTGAATTTATTTTATTG-GAAATTTTGAA
1 TGATTCTAACTTTGTAAGGA-AAATAAATTGTTGAATTTATTTCCTTGAG-AATCTTAAA
* * * * * * * **
511991 TGATTTTAACTTTGTAAGAAAAATAAATTATCGAATTTATTTTCTTGAGAGTCGTGGA
1 TGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATTTCCTTGAGAATCTTAAA
* * * ** * *
512049 CGATTCTATCCTT-TAAAAAGAAATAAATTGTTAAATTTATTTCCTTAAGAATCTTAAA
1 TGATTCTAACTTTGTAAGGA-AAATAAATTGTTGAATTTATTTCCTTGAGAATCTTAAA
* * **
512107 TGATTAT-ATTTTGTTAAAGG-AAATAAATTGTCAAATTTATT
1 TGATTCTAACTTTG-T-AAGGAAAATAAATTGTTGAATTTATT
512148 ATCTCAAGAA
Statistics
Matches: 260, Mismatches: 55, Indels: 24
0.77 0.16 0.07
Matches are distributed among these distances:
54 45 0.17
55 1 0.00
56 2 0.01
57 11 0.04
58 196 0.75
59 3 0.01
60 2 0.01
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.42
Consensus pattern (58 bp):
TGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATTTCCTTGAGAATCTTAAA
Found at i:512075 original size:174 final size:170
Alignment explanation
Indices: 511763--512147 Score: 409
Period size: 174 Copynumber: 2.2 Consensus size: 170
511753 AATCTTACTT
* * *
511763 TGATTCTAACTTTGTAAGGGATATAAATTGTTAAATTTATTTCCTTGAGAATCTTAAATGATTCT
1 TGATTCTAACTTTGTAAGAGAAATAAATTGTTAAATTTATTTCATTGAGAATCTTAAATGATTCT
* * * * * ** *
511828 TTGTAAGAAAAATAAATTGTTGAATTTCTTTCCTCGAGAATCTTGAATGATTCTAACTTTGTAAG
66 TTGTAAGAAAAATAAATTATCGAATTTATTTCCTCGAGAATCGTGAACGATTCTAACTTTAAAAA
* *
511893 GAAAATAAACCGTTGAATTTATTTCCTTTAGAATATTAAA
131 GAAAATAAACCGTTAAATTTATTTCCTTAAGAATATTAAA
* * * * *
511933 TGATTCTAACTTTGTAAGAGAAATATATTGTTGAATTTATTTTATTG-GAAATTTTGAATGATTT
1 TGATTCTAACTTTGTAAGAGAAATAAATTGTTAAATTTATTTCATTGAG-AATCTTAAATGA--T
* * * * *
511997 TAACTTTGTAAGAAAAATAAATTATCGAATTTATTTTCTTGAGAGTCGTGGACGATTCTATCCTT
63 T--CTTTGTAAGAAAAATAAATTATCGAATTTATTTCCTCGAGAATCGTGAACGATTCTA-ACTT
** *
512062 TAAAAAG-AAATAAATTGTTAAATTTATTTCCTTAAGAATCTTAAA
125 TAAAAAGAAAATAAACCGTTAAATTTATTTCCTTAAGAATATTAAA
* * *
512107 TGATTAT-ATTTTGTTAA-AGGAAATAAATTGTCAAATTTATT
1 TGATTCTAACTTTG-TAAGA-GAAATAAATTGTTAAATTTATT
512148 ATCTCAAGAA
Statistics
Matches: 176, Mismatches: 31, Indels: 12
0.80 0.14 0.05
Matches are distributed among these distances:
169 1 0.01
170 51 0.29
172 2 0.01
173 6 0.03
174 109 0.62
175 7 0.04
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.42
Consensus pattern (170 bp):
TGATTCTAACTTTGTAAGAGAAATAAATTGTTAAATTTATTTCATTGAGAATCTTAAATGATTCT
TTGTAAGAAAAATAAATTATCGAATTTATTTCCTCGAGAATCGTGAACGATTCTAACTTTAAAAA
GAAAATAAACCGTTAAATTTATTTCCTTAAGAATATTAAA
Found at i:512362 original size:39 final size:39
Alignment explanation
Indices: 512219--512394 Score: 143
Period size: 39 Copynumber: 4.6 Consensus size: 39
512209 TTTTAATAGA
* * *
512219 AAATAAATCGTCAT-ATTTATTTTCTTATTTTG-GAAAAT
1 AAATAAATCGT-ATAATTTATTTTCCTGTTTTGTAAAAAT
* ** * *
512257 AAAAAAAGGGT-TAAACTTAGTTTCCTGTTTTGTATAAAA-
1 AAATAAATCGTAT-AATTTATTTTCCTGTTTTGTA-AAAAT
* * *
512296 AAAT--ATCGTTTGATTTATTTTTCTGTTTTGTAAAAAT
1 AAATAAATCGTATAATTTATTTTCCTGTTTTGTAAAAAT
*
512333 AAATAAATCATATAATTTATTTTCCTGTTTTG-AAAAAGT
1 AAATAAATCGTATAATTTATTTTCCTGTTTTGTAAAAA-T
512372 AAATAAATCGGTA-AATTTATTTT
1 AAATAAATC-GTATAATTTATTTT
512395 TCTAAGAATC
Statistics
Matches: 108, Mismatches: 20, Indels: 19
0.73 0.14 0.13
Matches are distributed among these distances:
36 5 0.05
37 24 0.22
38 28 0.26
39 45 0.42
40 6 0.06
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (39 bp):
AAATAAATCGTATAATTTATTTTCCTGTTTTGTAAAAAT
Found at i:512563 original size:97 final size:96
Alignment explanation
Indices: 512324--512573 Score: 261
Period size: 97 Copynumber: 2.6 Consensus size: 96
512314 TTTTCTGTTT
* * * * *
512324 TGTAAAAATAAATAAATCATATAATTTATTTTCCTGTTTTGAAAAAGTAAATAAATCGGTAAATT
1 TGTAAAAAGAAATAAATCATAT-ATTTATTTTACTGTTTTGAAAAAGGAAATAAATAGATAAATT
*
512389 TATTTTTCTAAGAATCTTGTATGATTATAAAA
65 TATTTCTCTAAGAATCTTGTATGATTATAAAA
* * * * * * *
512421 TGTAAAAGGAAATATACCGTATACTTTATTTTAATGTTTTAAAAAAGGAAATATATAGATAAATT
1 TGTAAAAAGAAATAAATCATATA-TTTATTTTACTGTTTTGAAAAAGGAAATAAATAGATAAATT
* * *
512486 TAATTTCT-TAAGAATCTTGTATGATTCTGATA
65 T-ATTTCTCTAAGAATCTTGTATGATTATAAAA
* * **
512518 TGTAAAAAGAAATAAATCAT-TGGATTTATTTTTCTATTTTGAAAAATAAAATAAAT
1 TGTAAAAAGAAATAAATCATAT--ATTTATTTTACTGTTTTGAAAAAGGAAATAAAT
512574 CATAGAATTT
Statistics
Matches: 122, Mismatches: 27, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
96 2 0.02
97 114 0.93
98 6 0.05
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (96 bp):
TGTAAAAAGAAATAAATCATATATTTATTTTACTGTTTTGAAAAAGGAAATAAATAGATAAATTT
ATTTCTCTAAGAATCTTGTATGATTATAAAA
Found at i:512574 original size:39 final size:40
Alignment explanation
Indices: 512518--512946 Score: 243
Period size: 39 Copynumber: 10.5 Consensus size: 40
512508 GATTCTGATA
512518 TGTAAAAAG-AAATAAATCATTGGATTTATTTTTCTATTT
1 TGTAAAAAGAAAATAAATCATTGGATTTATTTTTCTATTT
* * * * *
512557 TG-AAAAATAAAATAAATCATAGAATTT-TGTTTCTTAGTT
1 TGTAAAAAGAAAATAAATCATTGGATTTATTTTTC-TATTT
* * * * * ** *
512596 TAT-GAAAGGAAATAAATCGTTGAATTT-GGTTTCTTATAT
1 TGTAAAAAGAAAATAAATCATTGGATTTATTTTTC-TATTT
* * *
512635 TGTAAAAAGGAAATAAATCGTTGGATTTA-GTTTCTTATTT
1 TGTAAAAAGAAAATAAATCATTGGATTTATTTTTC-TATTT
* * **
512675 TGTAAAAATAAGTAAATCGAAACAAATCAATT-GATTTATTTTTATGGTT
1 TGT--AAA-AAG---A---AAATAAATC-ATTGGATTTATTTTTCTATTT
* * * *
512724 TGT-AAAAGAAAATAAATTATTGAATTTATTTTACTATAT
1 TGTAAAAAGAAAATAAATCATTGGATTTATTTTTCTATTT
* *
512763 TGTAAAAAGGAAATAAGTCATTGGATTTAGTTTTT-TATTT
1 TGTAAAAAGAAAATAAATCATTGGATTTA-TTTTTCTATTT
* * * *
512803 TGTAAGGAAA-TAAATCGAAATAAATTGTTTGATTTATTTTCCTGTTT
1 TGTAA--AAAGAAAAT--AAAT-CATTG---GATTTATTTTTCTATTT
* * *
512850 TGTAAAAAG-AAATAAATCGTTGGATTTATTTTCCTATAT
1 TGTAAAAAGAAAATAAATCATTGGATTTATTTTTCTATTT
* * * *
512889 TGTAAAAAGAAAATAAATCGTTGGATCTAGTTTCCTATTT
1 TGTAAAAAGAAAATAAATCATTGGATTTATTTTTCTATTT
512929 TGT-AAAAGAAAATAAATC
1 TGTAAAAAGAAAATAAATC
512947 GAAACAAATC
Statistics
Matches: 309, Mismatches: 51, Indels: 60
0.74 0.12 0.14
Matches are distributed among these distances:
38 13 0.04
39 113 0.37
40 95 0.31
41 8 0.03
42 10 0.03
43 10 0.03
44 4 0.01
45 10 0.03
46 6 0.02
47 15 0.05
49 20 0.06
50 5 0.02
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.41
Consensus pattern (40 bp):
TGTAAAAAGAAAATAAATCATTGGATTTATTTTTCTATTT
Found at i:512653 original size:40 final size:39
Alignment explanation
Indices: 512510--512682 Score: 140
Period size: 40 Copynumber: 4.4 Consensus size: 39
512500 TCTTGTATGA
* * *
512510 TTCTGATA-TGTAAAAA-GAAATAAATCATTGGATTTAT
1 TTCTTATATTGTAAAAAGGAAATAAATCATTGAATTTGT
* * ** *
512547 TT-TTCTATTTTGAAAAATAAAATAAATCATAGAATTTTGT
1 TTCTTATATTGT-AAAAAGGAAATAAATCATTGAA-TTTGT
* * *
512587 TTCTTA-GTT-TATGAAAGGAAATAAATCGTTGAATTTGGT
1 TTCTTATATTGTA-AAAAGGAAATAAATCATTGAATTT-GT
* *
512626 TTCTTATATTGTAAAAAGGAAATAAATCGTTGGATTTAGT
1 TTCTTATATTGTAAAAAGGAAATAAATCATTGAATTT-GT
*
512666 TTCTTATTTTGTAAAAA
1 TTCTTATATTGTAAAAA
512683 TAAGTAAATC
Statistics
Matches: 108, Mismatches: 19, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
36 3 0.03
37 4 0.04
38 9 0.08
39 38 0.35
40 50 0.46
41 4 0.04
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.42
Consensus pattern (39 bp):
TTCTTATATTGTAAAAAGGAAATAAATCATTGAATTTGT
Found at i:512777 original size:40 final size:40
Alignment explanation
Indices: 512723--512946 Score: 170
Period size: 40 Copynumber: 5.5 Consensus size: 40
512713 TTTTTATGGT
* * * *
512723 TTGT-AAAAGAAAATAAATTATTGAATTTATTTTACTATA
1 TTGTAAAAAGGAAATAAATCATTGGATTTATTTTCCTATA
* * *
512762 TTGTAAAAAGGAAATAAGTCATTGGATTTAGTTTT-TTATT
1 TTGTAAAAAGGAAATAAATCATTGGATTTA-TTTTCCTATA
* * * *
512802 TTGTAAGGAAA-TAAATCGAAATAAATTGTTTGATTTATTTTCCTGTT
1 TTGTAA--AAAGGAAAT--AAAT-CATTG---GATTTATTTTCCTATA
*
512849 TTGTAAAAA-GAAATAAATCGTTGGATTTATTTTCCTATA
1 TTGTAAAAAGGAAATAAATCATTGGATTTATTTTCCTATA
* * * * *
512888 TTGTAAAAAGAAAATAAATCGTTGGATCTAGTTTCCTATT
1 TTGTAAAAAGGAAATAAATCATTGGATTTATTTTCCTATA
*
512928 TTGT-AAAAGAAAATAAATC
1 TTGTAAAAAGGAAATAAATC
512947 GAAACAAATC
Statistics
Matches: 153, Mismatches: 20, Indels: 24
0.78 0.10 0.12
Matches are distributed among these distances:
39 42 0.27
40 60 0.39
41 8 0.05
42 6 0.04
43 7 0.05
44 4 0.03
45 7 0.05
46 4 0.03
47 15 0.10
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.41
Consensus pattern (40 bp):
TTGTAAAAAGGAAATAAATCATTGGATTTATTTTCCTATA
Found at i:513817 original size:39 final size:39
Alignment explanation
Indices: 513761--513848 Score: 167
Period size: 39 Copynumber: 2.3 Consensus size: 39
513751 CTTGTGCATG
513761 AATCAAAGAATCCTGAGATTCACAAGAACACAATAACGA
1 AATCAAAGAATCCTGAGATTCACAAGAACACAATAACGA
*
513800 AATCAAAGAATCTTGAGATTCACAAGAACACAATAACGA
1 AATCAAAGAATCCTGAGATTCACAAGAACACAATAACGA
513839 AATCAAAGAA
1 AATCAAAGAA
513849 CATCTCATTC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.53, C:0.18, G:0.12, T:0.16
Consensus pattern (39 bp):
AATCAAAGAATCCTGAGATTCACAAGAACACAATAACGA
Found at i:513849 original size:21 final size:21
Alignment explanation
Indices: 513784--513850 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
513774 TGAGATTCAC
513784 AAGAACACAATAACGAAATCA
1 AAGAACACAATAACGAAATCA
* * * *
513805 AAGAA-TC-TTGA-G-ATTCA
1 AAGAACACAATAACGAAATCA
513822 CAAGAACACAATAACGAAATCA
1 -AAGAACACAATAACGAAATCA
513844 AAGAACA
1 AAGAACA
513851 TCTCATTCTT
Statistics
Matches: 33, Mismatches: 8, Indels: 10
0.65 0.16 0.20
Matches are distributed among these distances:
17 4 0.12
18 6 0.18
19 3 0.09
20 3 0.09
21 13 0.39
22 4 0.12
ACGTcount: A:0.57, C:0.18, G:0.12, T:0.13
Consensus pattern (21 bp):
AAGAACACAATAACGAAATCA
Found at i:514137 original size:30 final size:30
Alignment explanation
Indices: 514101--514158 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
514091 AATTTAAGGA
514101 AAAATGTTTTTGGACTTGAATTGAATTTGC
1 AAAATGTTTTTGGACTTGAATTGAATTTGC
*
514131 AAAATGTTTTTGGATTTGAATTGAATTT
1 AAAATGTTTTTGGACTTGAATTGAATTT
514159 AATCAAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTGC
Found at i:514255 original size:8 final size:8
Alignment explanation
Indices: 514242--514341 Score: 55
Period size: 8 Copynumber: 14.0 Consensus size: 8
514232 GGTGTCAAAG
514242 TGCATCCA
1 TGCATCCA
*
514250 TGCATCCC
1 TGCATCCA
*
514258 TGCA---G
1 TGCATCCA
514263 TGCATCCA
1 TGCATCCA
*
514271 TGCATCCC
1 TGCATCCA
514279 TGCA---A
1 TGCATCCA
514284 TGCATCCA
1 TGCATCCA
514292 TGCAT-C-
1 TGCATCCA
*
514298 TGCA-CTAA
1 TGCATC-CA
*
514306 TGCATCGA
1 TGCATCCA
514314 TGCAT-CA
1 TGCATCCA
514321 TGCA---A
1 TGCATCCA
514326 TGCATCCA
1 TGCATCCA
514334 TGCATCCA
1 TGCATCCA
514342 AACATCGAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 26
0.68 0.08 0.25
Matches are distributed among these distances:
5 13 0.18
6 4 0.06
7 6 0.08
8 47 0.66
9 1 0.01
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (8 bp):
TGCATCCA
Found at i:514266 original size:21 final size:21
Alignment explanation
Indices: 514242--514340 Score: 123
Period size: 21 Copynumber: 4.7 Consensus size: 21
514232 GGTGTCAAAG
*
514242 TGCATCCATGCATCCCTGCAG
1 TGCATCCATGCATCCCTGCAA
514263 TGCATCCATGCATCCCTGCAA
1 TGCATCCATGCATCCCTGCAA
514284 TGCATCCATGCAT--CTGCACTAA
1 TGCATCCATGCATCCCTG--C-AA
* *
514306 TGCATCGATGCAT-CATGCAA
1 TGCATCCATGCATCCCTGCAA
514326 TGCATCCATGCATCC
1 TGCATCCATGCATCC
514341 AAACATCGAA
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
19 3 0.04
20 14 0.20
21 36 0.52
22 14 0.20
23 2 0.03
ACGTcount: A:0.24, C:0.34, G:0.16, T:0.25
Consensus pattern (21 bp):
TGCATCCATGCATCCCTGCAA
Found at i:514286 original size:13 final size:13
Alignment explanation
Indices: 514270--514337 Score: 50
Period size: 13 Copynumber: 5.0 Consensus size: 13
514260 CAGTGCATCC
*
514270 ATGCATCCCTGCA
1 ATGCATCCATGCA
514283 ATGCATCCATGCA
1 ATGCATCCATGCA
* *
514296 TCTGCA-CTAATGCA
1 -ATGCATC-CATGCA
514310 TCGATGCAT-CATGCA
1 ---ATGCATCCATGCA
514325 ATGCATCCATGCA
1 ATGCATCCATGCA
514338 TCCAAACATC
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
12 6 0.14
13 19 0.44
14 9 0.21
15 5 0.12
16 4 0.09
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.25
Consensus pattern (13 bp):
ATGCATCCATGCA
Found at i:515803 original size:14 final size:15
Alignment explanation
Indices: 515775--515808 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
515765 AGATGATGGT
515775 AAAG-GAAGATGAAG
1 AAAGAGAAGATGAAG
515789 AAAGAGAAGAT-AAG
1 AAAGAGAAGATGAAG
515803 AAAGAG
1 AAAGAG
515809 GTAGGCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.62, C:0.00, G:0.32, T:0.06
Consensus pattern (15 bp):
AAAGAGAAGATGAAG
Found at i:517665 original size:30 final size:30
Alignment explanation
Indices: 517594--517653 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
517584 ACAATTTAAG
517594 GCAAAATGTTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
517624 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
517654 ATTCAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:517750 original size:8 final size:8
Alignment explanation
Indices: 517737--517844 Score: 71
Period size: 8 Copynumber: 15.0 Consensus size: 8
517727 GGTGTCAAAG
517737 TGCATCCA
1 TGCATCCA
517745 TGCATCCA
1 TGCATCCA
*
517753 TGCATCCC
1 TGCATCCA
*
517761 TGCA---G
1 TGCATCCA
517766 TGCATCCA
1 TGCATCCA
*
517774 TGCATCCC
1 TGCATCCA
517782 TGCA---A
1 TGCATCCA
517787 TGCATCCA
1 TGCATCCA
517795 TGCAT-C-
1 TGCATCCA
*
517801 TGCA-CTAA
1 TGCATC-CA
*
517809 TGCATCGA
1 TGCATCCA
517817 TGCAT-CA
1 TGCATCCA
517824 TGCA---A
1 TGCATCCA
517829 TGCATCCA
1 TGCATCCA
517837 TGCATCCA
1 TGCATCCA
517845 AACATCGAAT
Statistics
Matches: 79, Mismatches: 8, Indels: 26
0.70 0.07 0.23
Matches are distributed among these distances:
5 13 0.16
6 4 0.05
7 6 0.08
8 55 0.70
9 1 0.01
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (8 bp):
TGCATCCA
Found at i:517769 original size:21 final size:21
Alignment explanation
Indices: 517744--517843 Score: 125
Period size: 21 Copynumber: 4.8 Consensus size: 21
517734 AAGTGCATCC
517744 ATGCATCCATGCATCCCTGCA
1 ATGCATCCATGCATCCCTGCA
*
517765 GTGCATCCATGCATCCCTGCA
1 ATGCATCCATGCATCCCTGCA
517786 ATGCATCCATGCAT--CTGCACTA
1 ATGCATCCATGCATCCCTG--C-A
* *
517808 ATGCATCGATGCAT-CATGCA
1 ATGCATCCATGCATCCCTGCA
517828 ATGCATCCATGCATCC
1 ATGCATCCATGCATCC
517844 AAACATCGAA
Statistics
Matches: 69, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
19 3 0.04
20 14 0.20
21 36 0.52
22 14 0.20
23 2 0.03
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (21 bp):
ATGCATCCATGCATCCCTGCA
Found at i:517789 original size:13 final size:13
Alignment explanation
Indices: 517737--517840 Score: 51
Period size: 13 Copynumber: 7.9 Consensus size: 13
517727 GGTGTCAAAG
517737 TGCATCCATGCATCCA
1 TGCATCCATGCA---A
* *
517753 TGCATCCCTGCAG
1 TGCATCCATGCAA
517766 TGCATCCATGC-A
1 TGCATCCATGCAA
517778 T-C--CC-TGCAA
1 TGCATCCATGCAA
*
517787 TGCATCCATGCATC
1 TGCATCCATGCA-A
*
517801 TGCA-CTAATGCATCGA
1 TGCATC-CATGCA---A
517817 TGCAT-CATGCAA
1 TGCATCCATGCAA
517829 TGCATCCATGCA
1 TGCATCCATGCA
517841 TCCAAACATC
Statistics
Matches: 68, Mismatches: 9, Indels: 25
0.67 0.09 0.25
Matches are distributed among these distances:
8 3 0.04
9 4 0.06
10 1 0.01
11 1 0.01
12 9 0.13
13 21 0.31
14 9 0.13
15 5 0.07
16 15 0.22
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (13 bp):
TGCATCCATGCAA
Found at i:522370 original size:2 final size:2
Alignment explanation
Indices: 522363--522423 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
522353 ATAACATGGA
522363 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
522405 AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
522424 AACTAAAATG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:530486 original size:13 final size:13
Alignment explanation
Indices: 530468--530498 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
530458 AAACTAATAA
530468 TTTATGATCAAAT
1 TTTATGATCAAAT
530481 TTTATGATCAAAT
1 TTTATGATCAAAT
530494 TTTAT
1 TTTAT
530499 CATATCACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.52
Consensus pattern (13 bp):
TTTATGATCAAAT
Found at i:543872 original size:23 final size:23
Alignment explanation
Indices: 543823--543866 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
543813 ACCATATATC
543823 TGAAAGAATATTCTTTTTTTTAA
1 TGAAAGAATATTCTTTTTTTTAA
543846 TGAAAGAATATTCTTTTTTTT
1 TGAAAGAATATTCTTTTTTTT
543867 TTTGAATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.55
Consensus pattern (23 bp):
TGAAAGAATATTCTTTTTTTTAA
Found at i:543880 original size:25 final size:26
Alignment explanation
Indices: 543823--543885 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 26
543813 ACCATATATC
543823 TGAAAGAATATTC---TTTTTTTTAA
1 TGAAAGAATATTCTTTTTTTTTTTAA
543846 TGAAAGAATATTCTTTTTTTTTTTGAA
1 TGAAAGAATATTCTTTTTTTTTTT-AA
543873 TG-AA-AATATTCTT
1 TGAAAGAATATTCTT
543886 ACATCTTGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
23 13 0.36
25 9 0.25
26 10 0.28
27 4 0.11
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.52
Consensus pattern (26 bp):
TGAAAGAATATTCTTTTTTTTTTTAA
Found at i:549887 original size:72 final size:72
Alignment explanation
Indices: 549796--549936 Score: 203
Period size: 72 Copynumber: 2.0 Consensus size: 72
549786 TAACATTCCA
* * * *
549796 ATTTCTTCCGGTATGGACCCTGAAATGTTATTGTTAAAAAGG-CTAAGATAAGATAAGTTGGCTA
1 ATTTCTTCCGGTATCGACCCCGAAATGTTATTGCTAAAAAGGTC-AAGATAAGATAAGTAGGCTA
549860 AGTTTTCG
65 AGTTTTCG
* * *
549868 ATTTCTTTCGGTATCGACCCCGAAATTTTATTGCTAGAAAGGTCAAGATAAGATAAGTAGGCTAA
1 ATTTCTTCCGGTATCGACCCCGAAATGTTATTGCTAAAAAGGTCAAGATAAGATAAGTAGGCTAA
549933 GTTT
66 GTTT
549937 CCAATAGAGG
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
72 60 0.98
73 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.34
Consensus pattern (72 bp):
ATTTCTTCCGGTATCGACCCCGAAATGTTATTGCTAAAAAGGTCAAGATAAGATAAGTAGGCTAA
GTTTTCG
Found at i:563829 original size:20 final size:19
Alignment explanation
Indices: 563804--563844 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
563794 ATAATAATAA
*
563804 TATATTTAACTTTTAATTTT
1 TATATTTAA-TTTTAATCTT
*
563824 TATATTTTATTTTAATCTT
1 TATATTTAATTTTAATCTT
563843 TA
1 TA
563845 GACTTTTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (19 bp):
TATATTTAATTTTAATCTT
Found at i:569395 original size:2 final size:2
Alignment explanation
Indices: 569388--569415 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
569378 GATCTAACAA
569388 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
569416 TGTAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:571707 original size:22 final size:22
Alignment explanation
Indices: 571679--571793 Score: 130
Period size: 22 Copynumber: 5.4 Consensus size: 22
571669 AATTTGAAAA
571679 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
** *
571701 ATCGCAACGA-ATTTGTAAACT
1 ATCGCAACGACAACTGTAGACT
*
571722 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
571744 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
571763 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
571785 ATCGCAACG
1 ATCGCAACG
571794 CGAATTTGCG
Statistics
Matches: 73, Mismatches: 16, Indels: 8
0.75 0.16 0.08
Matches are distributed among these distances:
19 13 0.18
20 2 0.03
21 19 0.26
22 39 0.53
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.20
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:571800 original size:43 final size:41
Alignment explanation
Indices: 571661--571793 Score: 221
Period size: 41 Copynumber: 3.2 Consensus size: 41
571651 CAACGAATTT
571661 TCGCAACGAATTTGAAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGAAAAATCGCAACGACAACTGTAGACTA
* *
571702 TCGCAACGAATTTGTAAACTATCGCAACAACAACTGTAGACTA
1 TCGCAACGAATTTG-AAA-AATCGCAACGACAACTGTAGACTA
*
571745 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGAAAAATCGCAACGACAACTGTAGACTA
571786 TCGCAACG
1 TCGCAACG
571794 CGAATTTGCG
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
41 44 0.52
42 5 0.06
43 36 0.42
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.20
Consensus pattern (41 bp):
TCGCAACGAATTTGAAAAATCGCAACGACAACTGTAGACTA
Found at i:572029 original size:6 final size:6
Alignment explanation
Indices: 572007--572038 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
571997 TATGCCTTAA
572007 TATATT TAT-TT TA-ATT TATATT TATATT TATA
1 TATATT TATATT TATATT TATATT TATATT TATA
572039 ATTTTTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 8 0.33
6 16 0.67
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TATATT
Found at i:573421 original size:2 final size:2
Alignment explanation
Indices: 573411--573441 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
573401 TTTTTTAACC
573411 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
573442 TATTTTCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:576663 original size:2 final size:2
Alignment explanation
Indices: 576609--576647 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
576599 TTAAAAAAAT
576609 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
576648 GACGAACCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:584503 original size:33 final size:33
Alignment explanation
Indices: 584465--584548 Score: 159
Period size: 33 Copynumber: 2.5 Consensus size: 33
584455 TTCAGAACTA
584465 TTGGAAAGTATCGAAACTTTTCGAGAAACTATC
1 TTGGAAAGTATCGAAACTTTTCGAGAAACTATC
584498 TTGGAAAGTATCGAAACTTTTCGAGAAACTATC
1 TTGGAAAGTATCGAAACTTTTCGAGAAACTATC
*
584531 TTGGAAAGTTTCGAAACT
1 TTGGAAAGTATCGAAACT
584549 ATTGTAGAAG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (33 bp):
TTGGAAAGTATCGAAACTTTTCGAGAAACTATC
Found at i:584546 original size:21 final size:20
Alignment explanation
Indices: 584531--584573 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
584521 AGAAACTATC
584531 TTGGA-AAGTTTCGAAACTA
1 TTGGAGAAGTTTCGAAACTA
* *
584550 TTGTAGAAGTTTCGAAAATA
1 TTGGAGAAGTTTCGAAACTA
584570 TTGG
1 TTGG
584574 TCAAAATACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (20 bp):
TTGGAGAAGTTTCGAAACTA
Found at i:592089 original size:37 final size:37
Alignment explanation
Indices: 592048--592126 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
592038 TTTTACATCA
* * *
592048 TTCACTCGATCTAACCCGACCCAAAAAATATATACTC
1 TTCACTCGACCCAACCCGACCAAAAAAATATATACTC
*
592085 TTCACTCGACCCGACCCGACCAAAAAAATATATACTC
1 TTCACTCGACCCAACCCGACCAAAAAAATATATACTC
592122 TTCAC
1 TTCAC
592127 ACAACCCGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.37, C:0.34, G:0.06, T:0.23
Consensus pattern (37 bp):
TTCACTCGACCCAACCCGACCAAAAAAATATATACTC
Found at i:592134 original size:37 final size:37
Alignment explanation
Indices: 592061--592135 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
592051 ACTCGATCTA
* * *
592061 ACCCGACCCAAAAAATATATACTCTTCACTCGACCCG
1 ACCCGACCAAAAAAATATATACTCTTCACACAACCCG
592098 ACCCGACCAAAAAAATATATACTCTTCACACAACCCG
1 ACCCGACCAAAAAAATATATACTCTTCACACAACCCG
592135 A
1 A
592136 ACTTGAACCG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.40, C:0.36, G:0.07, T:0.17
Consensus pattern (37 bp):
ACCCGACCAAAAAAATATATACTCTTCACACAACCCG
Found at i:596361 original size:22 final size:20
Alignment explanation
Indices: 596335--596383 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
596325 CCGCTGCTAA
*
596335 AAACTTAACGTGTTTAGTATCT
1 AAACTTAA-GT-TTTAGTACCT
*
596357 AAACTATTAGTTTTAGTACCT
1 AAACT-TAAGTTTTAGTACCT
596378 AAACTT
1 AAACTT
596384 TCAAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 1 0.04
21 14 0.58
22 7 0.29
23 2 0.08
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (20 bp):
AAACTTAAGTTTTAGTACCT
Found at i:600517 original size:37 final size:37
Alignment explanation
Indices: 600420--600734 Score: 267
Period size: 36 Copynumber: 8.5 Consensus size: 37
600410 TGTAAATTGT
* *
600420 TTTTA-AAAATATTTATATAATATATAATTTTTAAGACA
1 TTTTAGAAAATA--TATATAATATATAGTTTTTAAAACA
** *
600458 TTTTTTAAAA-CTATATAATATATAGTTTTTAAAACA
1 TTTTAGAAAATATATATAATATATAGTTTTTAAAACA
* *
600494 TTCTAGAAAATATATATAATATATAATTTTTAAAATCA
1 TTTTAGAAAATATATATAATATATAGTTTTTAAAA-CA
600532 TTTT-GAAAACT-TATATAATATATAG-TTTTAAAATCA
1 TTTTAGAAAA-TATATATAATATATAGTTTTTAAAA-CA
* * * *
600568 TTTT-GAAAACT-CATATAATATAAAGTTTTGAAACCA
1 TTTTAGAAAA-TATATATAATATATAGTTTTTAAAACA
* * *
600604 TTTTGAAAAAATTATATATAACTTTCAAAACGTTTTTAAAACA
1 TTTT-AGAAAA-TATATATAA-TAT--ATA-GTTTTTAAAACA
600647 TTTTTA-AAAATATATATAATATATAG--TTTAAAACA
1 -TTTTAGAAAATATATATAATATATAGTTTTTAAAACA
* * *
600682 TTTTTGAAAATATATATATTATATAG-TTTAAAAACA
1 TTTTAGAAAATATATATAATATATAGTTTTTAAAACA
600718 TTTTTA-AAAATATATAT
1 -TTTTAGAAAATATATAT
600735 TATAGTTTTT
Statistics
Matches: 234, Mismatches: 27, Indels: 34
0.79 0.09 0.12
Matches are distributed among these distances:
34 4 0.02
35 28 0.12
36 89 0.38
37 51 0.22
38 17 0.07
39 10 0.04
40 4 0.02
41 9 0.04
42 7 0.03
43 11 0.05
44 4 0.02
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.43
Consensus pattern (37 bp):
TTTTAGAAAATATATATAATATATAGTTTTTAAAACA
Found at i:600643 original size:80 final size:82
Alignment explanation
Indices: 600557--600726 Score: 197
Period size: 79 Copynumber: 2.1 Consensus size: 82
600547 TAATATATAG
* *
600557 TTTTAAAATCATTTTGAAAACT-CATATAATATAAAGTTTTGAAACCA-TTTTGAAAAAAT-TAT
1 TTTTAAAA-CATTTTGAAAAATACATATAATATAAAG-TTT-AAAACATTTTTGAAAAAATATAT
* *
600619 A-TATA-ACTTTCAAAACGT
63 ATTATATACTTTAAAAACAT
* * * *
600637 TTTTAAAACATTTTTAAAAATATATATAATATATAGTTTAAAACATTTTTGAAAATATATATATT
1 TTTTAAAACATTTTGAAAAATACATATAATATAAAGTTTAAAACATTTTTGAAAAAATATATATT
*
600702 ATATAGTTTAAAAACAT
66 ATATACTTTAAAAACAT
600719 TTTTAAAA
1 TTTTAAAA
600727 ATATATATTA
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
78 5 0.07
79 25 0.33
80 24 0.32
81 4 0.05
82 18 0.24
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (82 bp):
TTTTAAAACATTTTGAAAAATACATATAATATAAAGTTTAAAACATTTTTGAAAAAATATATATT
ATATACTTTAAAAACAT
Found at i:601963 original size:9 final size:8
Alignment explanation
Indices: 601944--602003 Score: 52
Period size: 9 Copynumber: 7.2 Consensus size: 8
601934 TCCTCACTTC
601944 TTTTA-TA
1 TTTTATTA
601951 TTTTATCTA
1 TTTTAT-TA
601960 TTTTATTA
1 TTTTATTA
* *
601968 GTATTATCA
1 -TTTTATTA
601977 TTTCTATTA
1 TTT-TATTA
601986 TTTTATT-
1 TTTTATTA
601993 TATTTATTA
1 T-TTTATTA
602002 TT
1 TT
602004 ATTTTCTCAG
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
7 6 0.14
8 15 0.35
9 22 0.51
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (8 bp):
TTTTATTA
Found at i:609719 original size:2 final size:2
Alignment explanation
Indices: 609714--609754 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
609704 TTGTTTTTTA
609714 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
609755 ACTGTATCGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:613764 original size:8 final size:8
Alignment explanation
Indices: 613751--613787 Score: 56
Period size: 8 Copynumber: 4.4 Consensus size: 8
613741 TTTAAATTGA
613751 AATATTAT
1 AATATTAT
613759 AATATTAT
1 AATATTAT
613767 AATATTAT
1 AATATTAT
613775 AAATATTGAT
1 -AATATT-AT
613785 AAT
1 AAT
613788 TAAATTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 16 0.59
9 9 0.33
10 2 0.07
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (8 bp):
AATATTAT
Found at i:613772 original size:16 final size:18
Alignment explanation
Indices: 613746--613787 Score: 63
Period size: 16 Copynumber: 2.5 Consensus size: 18
613736 AATTATTTAA
613746 ATTGA-AATATTAT-AAT
1 ATTGATAATATTATAAAT
613762 ATT-ATAATATTATAAAT
1 ATTGATAATATTATAAAT
613779 ATTGATAAT
1 ATTGATAAT
613788 TAAATTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 1 0.04
16 11 0.48
17 6 0.26
18 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (18 bp):
ATTGATAATATTATAAAT
Done.