Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000418.1 Hibiscus syriacus cultivar Beakdansim tig00000765_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: 909013
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:873799 original size:38 final size:38
Alignment explanation
Indices: 873743--873838 Score: 156
Period size: 38 Copynumber: 2.5 Consensus size: 38
873733 TATAAGACAT
* *
873743 ATGATAGGTCCTACGGGACACAGATTACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
*
873781 ATGACAGGTCCTTCGGGACACAGATGACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
*
873819 ATGATAGGTCTTTCGGGACA
1 ATGATAGGTCCTTCGGGACA
873839 TTTGTACGAG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
Found at i:873815 original size:21 final size:21
Alignment explanation
Indices: 873751--873819 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
873741 ATATGATAGG
* *
873751 TCCTACGGGACACAGATTACA
1 TCCTTCGGGACACAGATGACA
*
873772 TCCTTCGGGATGACAG--G---
1 TCCTTCGGGA-CACAGATGACA
873789 TCCTTCGGGACACAGATGACA
1 TCCTTCGGGACACAGATGACA
873810 TCCTTCGGGA
1 TCCTTCGGGA
873820 TGATAGGTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
16 4 0.11
17 10 0.26
18 1 0.03
21 19 0.50
22 4 0.11
ACGTcount: A:0.25, C:0.28, G:0.26, T:0.22
Consensus pattern (21 bp):
TCCTTCGGGACACAGATGACA
Found at i:880260 original size:16 final size:17
Alignment explanation
Indices: 880219--880260 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
880209 CTTTTTTAAA
880219 AATTTAA-TTTTATTTT
1 AATTTAATTTTTATTTT
* *
880235 ACTTTGATTTTTA-TTT
1 AATTTAATTTTTATTTT
880251 AATTTAATTT
1 AATTTAATTT
880261 CTATAATATT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (17 bp):
AATTTAATTTTTATTTT
Found at i:880341 original size:21 final size:21
Alignment explanation
Indices: 880310--880350 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
880300 TTATTAAACA
880310 TAAAAAAAATTA-TAAAAAAG
1 TAAAAAAAATTATTAAAAAAG
880330 TAAAAAATAATTATTAAAAAA
1 TAAAAAA-AATTATTAAAAAA
880351 ATATTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
21 5 0.26
22 7 0.37
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (21 bp):
TAAAAAAAATTATTAAAAAAG
Found at i:881295 original size:23 final size:24
Alignment explanation
Indices: 881236--881296 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 24
881226 GTACTAAACG
881236 TATAATTATAA-A-TTAATTAAAAA
1 TATAA-TATAATATTTAATTAAAAA
*
881259 TCTAA-AT-ATAATTTAATT-AAAA
1 TATAATATAAT-ATTTAATTAAAAA
881281 TATAATATAATATTTA
1 TATAATATAATATTTA
881297 TAAAACATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
20 1 0.03
21 2 0.06
22 9 0.29
23 17 0.55
24 2 0.06
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
TATAATATAATATTTAATTAAAAA
Found at i:881691 original size:22 final size:22
Alignment explanation
Indices: 881641--881691 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
881631 AATTTTTAAC
*
881641 TAATCTATAATTATACATTTAG
1 TAATTTATAATTATACATTTAG
*
881663 TACTTTATAATT-TAACATTTTA-
1 TAATTTATAATTAT-ACA-TTTAG
881685 TAATTTA
1 TAATTTA
881692 ATTTAATAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 1 0.04
22 19 0.79
23 4 0.17
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (22 bp):
TAATTTATAATTATACATTTAG
Found at i:886162 original size:3 final size:3
Alignment explanation
Indices: 886154--886186 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
886144 AATTATCCAA
886154 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
886187 GCTCGAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:887171 original size:22 final size:22
Alignment explanation
Indices: 887143--887189 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
887133 TTTTATTCCC
887143 GTTAGTTTAATCCAAGCTACAT
1 GTTAGTTTAATCCAAGCTACAT
887165 GTTAGTTTAATCCAAGCTACAT
1 GTTAGTTTAATCCAAGCTACAT
887187 GTT
1 GTT
887190 TTCTTCCCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (22 bp):
GTTAGTTTAATCCAAGCTACAT
Found at i:889424 original size:38 final size:40
Alignment explanation
Indices: 889373--889469 Score: 108
Period size: 38 Copynumber: 2.4 Consensus size: 40
889363 TGGTAACAAA
*
889373 AAACGCCGTAATAGGTAACGATATATAGCGGCG-TTT-AC
1 AAACGCCGCAATAGGTAACGATATATAGCGGCGTTTTAAC
*** *
889411 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTGACAC
1 AAACGCCGCAATAGGTAACGATATATAGCGGCG-TTTT-A-AC
889454 AAACGCCGCAATAGGT
1 AAACGCCGCAATAGGT
889470 CTTGAGATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
38 28 0.57
40 3 0.06
43 18 0.37
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.25
Consensus pattern (40 bp):
AAACGCCGCAATAGGTAACGATATATAGCGGCGTTTTAAC
Found at i:889480 original size:43 final size:43
Alignment explanation
Indices: 889409--889550 Score: 146
Period size: 43 Copynumber: 3.3 Consensus size: 43
889399 AGCGGCGTTT
* *
889409 ACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTGAC
1 ACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTGAC
** **
889452 ACAAACGCCGCAATAGGTCTTGAGATTTAGCGATGTTTTTCCC
1 ACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTGAC
* * *
889495 ACAAACGCCGCAAAAGATC-TG-GTATATAGCGGCGTTTTTTAGA-
1 ACAAACGCCGCAATAGGTCTTGAG-ATTTAGCGGCG-TTTTT-GAC
*
889538 ACAAACACCGCAA
1 ACAAACGCCGCAA
889551 AATGTCATAT
Statistics
Matches: 82, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
41 1 0.01
42 10 0.12
43 71 0.87
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (43 bp):
ACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTGAC
Found at i:889734 original size:22 final size:22
Alignment explanation
Indices: 889700--889759 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 22
889690 ATTTTCCAAT
*
889700 AAACTTGACATCCATAAACAAC
1 AAACTTGAAATCCATAAACAAC
* *
889722 AAACTTAAAATCCAT-AACAAG
1 AAACTTGAAATCCATAAACAAC
*
889743 AAAATTGAAATCCATAA
1 AAACTTGAAATCCATAA
889760 TAATAAATCA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.55, C:0.20, G:0.05, T:0.20
Consensus pattern (22 bp):
AAACTTGAAATCCATAAACAAC
Found at i:892683 original size:41 final size:40
Alignment explanation
Indices: 892620--893106 Score: 378
Period size: 41 Copynumber: 11.8 Consensus size: 40
892610 ACATACCAAA
* * *
892620 CTATTGCGGCTTTTATATAAAAACGCCGCTAAAGTACTACT
1 CTATTGCGGCGTTTGT-TAAAAACGCCACTAAAGTACTACT
* * * * *
892661 TTATTACGGCGTTTGTTGAAAAAATGCCACTACAG-A-TGAACC
1 CTATTGCGGCGTTTGTT--AAAAACGCCACTAAAGTACT--ACT
* *
892703 CTATTGCGGCATTTGTATAAAAATGCCACTAAAGTACTACT
1 CTATTGCGGCGTTTGT-TAAAAACGCCACTAAAGTACTACT
* * *
892744 CTATTACGGCGTTTCTTGAAAAACGCCACTAAAG-A-TGAACC
1 CTATTGCGGCGTTTGTT-AAAAACGCCACTAAAGTACT--ACT
** * *
892785 CTATTATGGCATTTTTATAAAAACGCCACTAAAGTACTACT
1 CTATTGCGGCGTTTGT-TAAAAACGCCACTAAAGTACTACT
* * *
892826 CTATTGCGGCGTTTGTTGAAAAAATGCCACTACAG-A-TGAACC
1 CTATTGCGGCGTTTGTT--AAAAACGCCACTAAAGTACT--ACT
* * * * *
892868 CTATTGCGGCATTTATATAAAAACGTCGCTAAAGTAATACT
1 CTATTGCGGCGTTTGT-TAAAAACGCCACTAAAGTACTACT
*
892909 CTATTGCGGCGTTTGTATAAAAACGCCGCTAAAGTACTACT
1 CTATTGCGGCGTTTGT-TAAAAACGCCACTAAAGTACTACT
* * * *
892950 CTGTTGCAGCGTTAGTATAAAAACGCCCCTAAAGTACTACT
1 CTATTGCGGCGTTTGT-TAAAAACGCCACTAAAGTACTACT
* *
892991 CTATTGTGGCGTTTGTATAAAAACGCCGCT-AAGTACTACT
1 CTATTGCGGCGTTTGT-TAAAAACGCCACTAAAGTACTACT
* * * *
893031 CTTTTGCGGCGTTTGTTAAAAAAACGCCACTATAG-ATTACC
1 CTATTGCGGCGTTTGTT--AAAAACGCCACTAAAGTACTACT
* * *
893072 CTATTGCGGCGTTTTTGTAAAAACACCGCTAAAGT
1 CTATTGCGGCGTTTGT-TAAAAACGCCACTAAAGT
893107 TACCATTTTG
Statistics
Matches: 361, Mismatches: 60, Indels: 50
0.77 0.13 0.11
Matches are distributed among these distances:
39 2 0.01
40 43 0.12
41 246 0.68
42 65 0.18
43 5 0.01
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (40 bp):
CTATTGCGGCGTTTGTTAAAAACGCCACTAAAGTACTACT
Found at i:892854 original size:165 final size:164
Alignment explanation
Indices: 892630--893006 Score: 506
Period size: 165 Copynumber: 2.3 Consensus size: 164
892620 CTATTGCGGC
* * *
892630 TTTTATATAAAAACGCCGCTAAAGTACTACTTTATTACGGCGTTTGTTGAAAAAATGCCACTACA
1 TTTT-TATAAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGTTGAAAAAATGCCACTACA
* * *
892695 GATGAACCCTATTGCGGCATTTGTATAAAAATGCCACTAAAGTACTACTCTATTACGGCGTTTCT
65 GATGAACCCTATTGCGGCATTTATATAAAAACGCCACTAAAGTAATACTCTATTACGGCGTTTCT
**
892760 -TGAAAAACGCCACTAAAGATGA-ACCCTATTATGGCA
130 AT-AAAAACGCCACTAAAG-T-ACACCCTATTACAGCA
892796 TTTTTATAAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGTTGAAAAAATGCCACTACAG
1 TTTTTATAAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGTTGAAAAAATGCCACTACAG
* * * *
892861 ATGAACCCTATTGCGGCATTTATATAAAAACGTCGCTAAAGTAATACTCTATTGCGGCGTTTGTA
66 ATGAACCCTATTGCGGCATTTATATAAAAACGCCACTAAAGTAATACTCTATTACGGCGTTTCTA
* * * * *
892926 TAAAAACGCCGCTAAAGTACTACTCTGTTGCAGCG
131 TAAAAACGCCACTAAAGTAC-ACCCTATTACAGCA
** * *
892961 TTAGTATAAAAACGCCCCTAAAGTACTACTCTATTGTGGCGTTTGT
1 TTTTTATAAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGT
893007 ATAAAAACGC
Statistics
Matches: 187, Mismatches: 21, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
163 1 0.01
164 1 0.01
165 180 0.96
166 5 0.03
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (164 bp):
TTTTTATAAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGTTGAAAAAATGCCACTACAG
ATGAACCCTATTGCGGCATTTATATAAAAACGCCACTAAAGTAATACTCTATTACGGCGTTTCTA
TAAAAACGCCACTAAAGTACACCCTATTACAGCA
Found at i:892991 original size:82 final size:81
Alignment explanation
Indices: 892620--893105 Score: 473
Period size: 82 Copynumber: 5.9 Consensus size: 81
892610 ACATACCAAA
* * * * *
892620 CTATTGCGGCTTTTATATAAAAACGCCGCTAAAGTACTACTTTATTACGGCGTTTGTTGAAAAAA
1 CTATTGCGGCATTTGTATAAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGTTG-AAAAA
* *
892685 TGCCACTACAGATGAACC
65 CGCCACTAAAGAT-AACC
* * *
892703 CTATTGCGGCATTTGTATAAAAATGCCACTAAAGTACTACTCTATTACGGCGTTTCTTGAAAAAC
1 CTATTGCGGCATTTGTATAAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGTTGAAAAAC
892768 GCCACTAAAGATGAACC
66 GCCACTAAAGAT-AACC
** *
892785 CTATTATGGCATTTTTATAAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGTTGAAAAAA
1 CTATTGCGGCATTTGTATAAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGTTG-AAAAA
* *
892850 TGCCACTACAGATGAACC
65 CGCCACTAAAGAT-AACC
* * * *
892868 CTATTGCGGCATTTATATAAAAACGTCGCTAAAGTAATACTCTATTGCGGCGTTTGTAT-AAAAA
1 CTATTGCGGCATTTGTATAAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGT-TGAAAAA
* *
892932 CGCCGCTAAAG-TACTACT
65 CGCCACTAAAGATA--ACC
* * * * * *
892950 CTGTTGCAGCGTTAGTATAAAAACGCCCCTAAAGTACTACTCTATTGTGGCGTTTGTAT-AAAAA
1 CTATTGCGGCATTTGTATAAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGT-TGAAAAA
* *
893014 CGCCGCT-AAG-TACTACT
65 CGCCACTAAAGATA--ACC
* * * * * *
893031 CTTTTGCGGCGTTTGTTAAAAAAACGCCACTATAG-ATTACCCTATTGCGGCGTTT-TTGTAAAA
1 CTATTGCGGCATTTG-TATAAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGTTG-AAAA
* *
893094 ACACCGCTAAAG
64 ACGCCACTAAAG
893106 TTACCATTTT
Statistics
Matches: 350, Mismatches: 45, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
79 1 0.00
80 2 0.01
81 51 0.15
82 170 0.49
83 125 0.36
84 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (81 bp):
CTATTGCGGCATTTGTATAAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGTTGAAAAAC
GCCACTAAAGATAACC
Found at i:893905 original size:20 final size:20
Alignment explanation
Indices: 893811--894179 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
893801 GATTTTCCAT
* ** *
893811 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
893831 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
893851 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
893871 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
893891 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
893911 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
893931 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
893951 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
893971 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
893991 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
894011 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
894031 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
894051 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
894071 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
894091 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
894111 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
894131 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
894151 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
894171 AATCACAAC
1 AATCGCAAC
894180 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:894891 original size:24 final size:24
Alignment explanation
Indices: 894852--894898 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
894842 AAATTTGGTC
894852 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
894876 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
894899 GATGTTTCAG
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:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:895090 original size:12 final size:12
Alignment explanation
Indices: 895073--895097 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
895063 ATATAATCCT
895073 GAAGAAGAAAAA
1 GAAGAAGAAAAA
895085 GAAGAAGAAAAA
1 GAAGAAGAAAAA
895097 G
1 G
895098 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:897422 original size:19 final size:19
Alignment explanation
Indices: 897400--897706 Score: 351
Period size: 19 Copynumber: 17.4 Consensus size: 19
897390 ACGGAAATAC
*
897400 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
897419 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
897433 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
897453 AATCGCAA--CG---TGAG
1 AATCGCAATGCGAAATGAA
897467 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
897486 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
897505 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
897519 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
897538 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
897557 AATCG-AA--CAGACAT---
1 AATCGCAATGC-GAAATGAA
*
897571 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
897590 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
897609 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
897628 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
897647 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
897661 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
897680 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
897699 AATCGCAA
1 AATCGCAA
897707 CGAGATAATC
Statistics
Matches: 249, Mismatches: 11, Indels: 56
0.79 0.03 0.18
Matches are distributed among these distances:
14 46 0.18
15 3 0.01
16 16 0.06
17 15 0.06
18 4 0.02
19 152 0.61
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:897520 original size:52 final size:52
Alignment explanation
Indices: 897428--897706 Score: 347
Period size: 52 Copynumber: 5.2 Consensus size: 52
897418 AAATCCCAAC
* *
897428 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGTGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAAAATCGCAATGCGAA
*
897481 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAA
897533 ATGAAAATCGCAATGCGAAATGAAAATCG-AAC-AGACATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGA-A-AATCGCAATGCGAA
* *
897585 ATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAA
897642 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAA
897694 ATGAAAATCGCAA
1 ATGAAAATCGCAA
897707 CGAGATAATC
Statistics
Matches: 212, Mismatches: 5, Indels: 19
0.90 0.02 0.08
Matches are distributed among these distances:
50 3 0.01
51 3 0.01
52 151 0.71
53 18 0.08
54 1 0.00
55 6 0.03
57 26 0.12
58 2 0.01
59 2 0.01
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAA
Found at i:897551 original size:71 final size:71
Alignment explanation
Indices: 897467--897706 Score: 348
Period size: 71 Copynumber: 3.4 Consensus size: 71
897457 GCAACGTGAG
*
897467 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
897532 AATGAA
66 AATGAA
* *
897538 AATCGCAATGCGAAATGAAAATCG-AA--CAGACAT---AATCGCAATGCGAAATTAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAA--CG-AA--AGAATCGCA
*
897597 ATACGAAATGAA
60 ATGCGAAATGAA
897609 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
897674 AATGAA
66 AATGAA
897680 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
897707 CGAGATAATC
Statistics
Matches: 150, Mismatches: 7, Indels: 24
0.83 0.04 0.13
Matches are distributed among these distances:
66 8 0.05
68 3 0.02
69 5 0.03
70 2 0.01
71 113 0.75
72 2 0.01
73 6 0.04
74 3 0.02
76 8 0.05
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAA
Found at i:897649 original size:142 final size:137
Alignment explanation
Indices: 897400--897738 Score: 506
Period size: 142 Copynumber: 2.4 Consensus size: 137
897390 ACGGAAATAC
* * *
897400 AATCGCAACGCGAAATGAAAATCCCAACATGAA-AATCGCAATGCGGAAATGAAAATCGC-AACG
1 AATCGCAATGCGAAATGAAAAT-CGAACA-GAATAATCGCAATGC-GAAATTAAAATCGCAAACG
* *
897463 TGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAAT
63 TGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAAT
897528 GCGAAATGAA
128 GCGAAATGAA
897538 AATCGCAATGCGAAATGAAAATCGAACAGACATAATCGCAATGCGAAATTAAAATCGCAATACGA
1 AATCGCAATGCGAAATGAAAATCGAACAGA-ATAATCGCAATGCGAAATTAAAATCGCAA-ACG-
897603 AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
63 --TGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
897668 ATGCGAAATGAA
126 ATGCGAAATGAA
897680 AATCGCAATGCGAAATGAAAATCGCAAC-GAGATAATCGCAATGCGAAATTATAAA-CGCA
1 AATCGCAATGCGAAATGAAAATCG-AACAGA-ATAATCGCAATGCGAAATTA-AAATCGCA
897739 TTGCGATTTT
Statistics
Matches: 186, Mismatches: 6, Indels: 14
0.90 0.03 0.07
Matches are distributed among these distances:
136 2 0.01
137 19 0.10
138 33 0.18
139 3 0.02
142 123 0.66
143 6 0.03
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (137 bp):
AATCGCAATGCGAAATGAAAATCGAACAGAATAATCGCAATGCGAAATTAAAATCGCAAACGTGA
AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCG
AAATGAA
Found at i:897844 original size:19 final size:19
Alignment explanation
Indices: 897735--897836 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
897725 AAATTATAAA
897735 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
897754 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
897774 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
897790 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
897807 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
897826 CGCATTGCGAT
1 CGCATTGCGAT
897837 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:897968 original size:14 final size:14
Alignment explanation
Indices: 897949--897985 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
897939 CATCAATTAC
897949 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
897963 ACAAATCATCTTTT
1 ACAAATCAACTTTT
897977 ACAAATCAA
1 ACAAATCAA
897986 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:897997 original size:12 final size:12
Alignment explanation
Indices: 897980--898052 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
897970 ATCTTTTACA
897980 AATCAATTAAAC
1 AATCAATTAAAC
*
897992 AATCAA--AAATTG
1 AATCAATTAAA--C
**
898004 AATCAACTTTTAC
1 AATCAA-TTAAAC
898017 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
898030 AATCAA-AAAAC
1 AATCAATTAAAC
898041 AATCAATTAAAC
1 AATCAATTAAAC
898053 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:898014 original size:38 final size:38
Alignment explanation
Indices: 897966--898038 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
897956 AACTTTTACA
*
897966 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
898004 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
898039 ACAATCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:899922 original size:14 final size:14
Alignment explanation
Indices: 899903--899959 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
899893 GCGAAATGAA
*
899903 AATCGCAACGACAG
1 AATCGCAACGAAAG
899917 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
899934 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
899950 AATCGCAACG
1 AATCGCAACG
899960 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:899930 original size:33 final size:33
Alignment explanation
Indices: 899884--899976 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
899874 GCGAAACCAA
*
899884 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
899917 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
899950 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
899977 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:899941 original size:19 final size:19
Alignment explanation
Indices: 899847--899981 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
899837 ATAGTTACTT
* *
899847 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
899867 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
899886 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
899905 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
899919 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
899938 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
899952 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
899971 TCGCAATGCGA
1 TCGCAACGCGA
899982 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:899999 original size:19 final size:18
Alignment explanation
Indices: 899977--900105 Score: 94
Period size: 19 Copynumber: 7.3 Consensus size: 18
899967 AAAATCGCAA
899977 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
899996 TGCGATCTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
* *
900010 TGCGATTTTCATTTCGCAT
1 TGCGATTTT-GTTTCGCGT
*
900029 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
900043 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
900062 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
900081 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT--GTTTCGCGT
900101 TGCGA
1 TGCGA
900106 AAGTAAACTA
Statistics
Matches: 86, Mismatches: 13, Indels: 21
0.72 0.11 0.17
Matches are distributed among these distances:
14 21 0.24
16 2 0.02
17 2 0.02
18 1 0.01
19 47 0.55
20 13 0.15
ACGTcount: A:0.10, C:0.18, G:0.26, T:0.46
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:900025 original size:33 final size:33
Alignment explanation
Indices: 899977--900068 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
899967 AAAATCGCAA
**
899977 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTC-TGTCGT
*
900010 TGCGATTTTCATTTCGCATTGCGATTCTGTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
900043 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTCATTTCGCGTTGCGATT
900069 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 52 0.96
34 2 0.04
ACGTcount: A:0.10, C:0.20, G:0.25, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
Found at i:900448 original size:92 final size:93
Alignment explanation
Indices: 900148--900617 Score: 912
Period size: 93 Copynumber: 5.1 Consensus size: 93
900138 CTTGATGGAT
900148 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
900213 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
900241 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
900306 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
900334 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACA-TGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
900398 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
900426 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTG-TAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
900489 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
900517 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAA-AATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
900581 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
900609 AAATTTACT
1 AAATTTACT
900618 AAGCAATCTA
Statistics
Matches: 374, Mismatches: 0, Indels: 7
0.98 0.00 0.02
Matches are distributed among these distances:
91 88 0.24
92 140 0.37
93 146 0.39
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:900558 original size:183 final size:186
Alignment explanation
Indices: 900148--900617 Score: 912
Period size: 183 Copynumber: 2.5 Consensus size: 186
900138 CTTGATGGAT
900148 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
900213 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
900278 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
900334 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACA-TGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
900398 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
900463 TA-TATTTCACAGTG-TAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
900517 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAA-AATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
900581 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
900618 AAGCAATCTA
Statistics
Matches: 283, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
183 133 0.47
184 19 0.07
185 82 0.29
186 49 0.17
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:902339 original size:14 final size:14
Alignment explanation
Indices: 902320--902409 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
902310 TTGAAATGAA
902320 AATCGCAACGAGAG
1 AATCGCAACGAGAG
902334 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
902351 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
902367 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
902386 AATCGCAACGAGAG
1 AATCGCAACGAGAG
902400 AATCGCAACG
1 AATCGCAACG
902410 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:902357 original size:33 final size:33
Alignment explanation
Indices: 902312--902426 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
902302 TCTTTTGGTT
902312 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
902345 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
902378 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
902411 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
902427 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:902358 original size:19 final size:18
Alignment explanation
Indices: 902319--902431 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
902309 GTTGAAATGA
902319 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
902334 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
902351 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
902367 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
902384 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
902400 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
902417 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
902432 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:902462 original size:14 final size:14
Alignment explanation
Indices: 902443--902497 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
902433 TTTGGTTTCG
902443 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
902457 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
902476 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
902490 CGTTGCGA
1 CGTTGCGA
902498 CAGTCATTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:902657 original size:33 final size:33
Alignment explanation
Indices: 902618--902685 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
902608 TACTAACTTG
*
902618 AAATCGCAACGAGAGAATAGCAACGCGAAATGA
1 AAATCGCAACGACAGAATAGCAACGCGAAATGA
* *
902651 AAATCGCAACGACAGAATCGTAACGCGAAATGA
1 AAATCGCAACGACAGAATAGCAACGCGAAATGA
902684 AA
1 AA
902686 TCTAAGTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.49, C:0.19, G:0.22, T:0.10
Consensus pattern (33 bp):
AAATCGCAACGACAGAATAGCAACGCGAAATGA
Found at i:902917 original size:22 final size:22
Alignment explanation
Indices: 902865--902919 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
902855 TGGTTGTGAG
**
902865 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
902887 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
902909 GGATTTCTTCG
1 GGATTTCTTCG
902920 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:903090 original size:20 final size:20
Alignment explanation
Indices: 903065--903258 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
903055 CTTTAAATAT
903065 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
903085 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
903107 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
903126 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
903146 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
903166 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
903186 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
903206 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
903226 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
903246 CGCGTTGCGATTT
1 CGCGTTGCGATTT
903259 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:903252 original size:60 final size:60
Alignment explanation
Indices: 903065--903258 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
903055 CTTTAAATAT
**
903065 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
903126 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
903186 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
903246 CGCGTTGCGATTT
1 CGCGTTGCGATTT
903259 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:903275 original size:21 final size:20
Alignment explanation
Indices: 903251--903327 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
903241 ATATTCGCGT
903251 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
903272 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
903292 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
903314 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
903328 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:903338 original size:20 final size:20
Alignment explanation
Indices: 903313--903364 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
903303 AAGAATCGCG
*
903313 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
903333 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
903353 TTGCGATTCTGG
1 TTGCGATTCTGG
903365 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:903840 original size:26 final size:27
Alignment explanation
Indices: 903792--903846 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
903782 TCAAGGTTTA
*
903792 AAAAGTTAAAAAATATATAATTAA-AT
1 AAAAGTTAAAAAATAGATAATTAAGAT
*
903818 AAAATTTAAAAAATAAGAT-ATTAAGAT
1 AAAAGTTAAAAAAT-AGATAATTAAGAT
903845 AA
1 AA
903847 GGGAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.29
Consensus pattern (27 bp):
AAAAGTTAAAAAATAGATAATTAAGAT
Found at i:908910 original size:20 final size:20
Alignment explanation
Indices: 908865--908910 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
908855 GACCAACAAA
*
908865 ATCGCAATGCGATCGCTAAT
1 ATCGCAACGCGATCGCTAAT
* *
908885 -TCGCAACGCGATCTCTATT
1 ATCGCAACGCGATCGCTAAT
908904 ATCGCAA
1 ATCGCAA
908911 ATTCGCGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATCGCTAAT
Done.