Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008003.1 Hibiscus syriacus cultivar Beakdansim tig00110462_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: 3297763
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 14
Found at i:2421887 original size:23 final size:23
Alignment explanation
Indices: 2421829--2421889 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
2421819 GACACGAAAG
* *
2421829 AAAAAAAAAAGAAAAAAAAGAAA
1 AAAAAAAAAAAAAAAAAAACAAA
2421852 AAAAAAAAAAAAAAAAAAACAAA
1 AAAAAAAAAAAAAAAAAAACAAA
* *
2421875 CAGAAAAAAAAAAAA
1 AAAAAAAAAAAAAAA
2421890 CGAAAGGAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.92, C:0.03, G:0.05, T:0.00
Consensus pattern (23 bp):
AAAAAAAAAAAAAAAAAAACAAA
Found at i:2422811 original size:15 final size:14
Alignment explanation
Indices: 2422764--2422822 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 14
2422754 ATCCATTAGT
*
2422764 TTTTAATATTATTA
1 TTTTAATTTTATTA
2422778 CTTTTAATTTCT-TTCA
1 -TTTTAATTT-TATT-A
2422794 TTTTAATTATTATTA
1 TTTTAATT-TTATTA
2422809 -TTT-ATTTTATTA
1 TTTTAATTTTATTA
2422821 TT
1 TT
2422823 ACGTTTGATA
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
12 6 0.16
13 4 0.11
14 3 0.08
15 20 0.53
16 5 0.13
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTAATTTTATTA
Found at i:2422966 original size:13 final size:13
Alignment explanation
Indices: 2422937--2422979 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2422927 AAAAATCCTA
2422937 TTTATAAATTTAAT
1 TTTATAAA-TTAAT
*
2422951 TTTATAAATTACT
1 TTTATAAATTAAT
* *
2422964 TTTAAAAATAAAT
1 TTTATAAATTAAT
2422977 TTT
1 TTT
2422980 GATATGTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 17 0.68
14 8 0.32
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (13 bp):
TTTATAAATTAAT
Found at i:2423228 original size:18 final size:18
Alignment explanation
Indices: 2423174--2423228 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
2423164 GTCCTTTCTG
* * *
2423174 ATATTTCCTAAAAAATAA
1 ATATTTTCTTAAAAATAT
*
2423192 ATATTTT-TTATAAATTAT
1 ATATTTTCTTA-AAAATAT
2423210 ATATTTTCTTAAAAATAT
1 ATATTTTCTTAAAAATAT
2423228 A
1 A
2423229 ATAAAATTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
17 2 0.07
18 25 0.83
19 3 0.10
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATTTTCTTAAAAATAT
Found at i:2424433 original size:94 final size:95
Alignment explanation
Indices: 2424328--2424575 Score: 287
Period size: 94 Copynumber: 2.6 Consensus size: 95
2424318 AATAAAATAT
* *
2424328 GCAACCTATTACGTTAAACTGGCTACCTTTGTTTAAAGGTAT-ATAATAACGTAAAC-TATAAAA
1 GCAACCTATTACGTTAAACTAGCTACCTTTGTTTAAAGGTATAATAATAATGTAAACGTA-AAAA
2424391 TATT-CAACATAACCAG-CTAAAATAAATAGGC
65 T-TTACAACATAA-CAGACTAAAATAAATAGGC
2424422 GCAACCTATTACGTTAAACTAGCTACCAGTTTG-TTAAAGGTATAATAAT-ATGTAAACGGTAAA
1 GCAACCTATTACGTTAAACTAGCTACC--TTTGTTTAAAGGTATAATAATAATGTAAAC-GTAAA
* * * *
2424485 AATTTACAACTTAACTGATTAAAATAAATAGGT
63 AATTTACAACATAACAGACTAAAATAAATAGGC
** *
2424518 GCAA-C-ATTACGTTAAACTAGCTATCGGGTTGTTTAAATGTATAATAATAATGTAAACG
1 GCAACCTATTACGTTAAACTAGCTA-C-CTTTGTTTAAAGGTATAATAATAATGTAAACG
2424576 GTAACTACCA
Statistics
Matches: 134, Mismatches: 9, Indels: 21
0.82 0.05 0.13
Matches are distributed among these distances:
94 47 0.35
95 39 0.29
96 46 0.34
97 2 0.01
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (95 bp):
GCAACCTATTACGTTAAACTAGCTACCTTTGTTTAAAGGTATAATAATAATGTAAACGTAAAAAT
TTACAACATAACAGACTAAAATAAATAGGC
Found at i:2424512 original size:96 final size:97
Alignment explanation
Indices: 2424328--2424579 Score: 308
Period size: 96 Copynumber: 2.6 Consensus size: 97
2424318 AATAAAATAT
* *
2424328 GCAACCTATTACGTTAAACTGGCTACC-TTTGTTTAAAGGTAT-ATAATAACGTAAAC--TATAA
1 GCAACCTATTACGTTAAACTAGCTACCGTTTGTTTAAAGGTATAATAATAATGTAAACGGTA-AA
2424389 AATATTCAACATAACCAGCTAAAATAAATAGGC
65 AATATTCAACATAACCAGCTAAAATAAATAGGC
2424422 GCAACCTATTACGTTAAACTAGCTACCAGTTTG-TTAAAGGTATAATAAT-ATGTAAACGGTAAA
1 GCAACCTATTACGTTAAACTAGCTACC-GTTTGTTTAAAGGTATAATAATAATGTAAACGGTAAA
* * * *
2424485 AAT-TTACAACTTAA-CTGATTAAAATAAATAGGT
65 AATATT-CAACATAACCAG-CTAAAATAAATAGGC
* * *
2424518 GCAA-C-ATTACGTTAAACTAGCTATCGGGTTGTTTAAATGTATAATAATAATGTAAACGGTAA
1 GCAACCTATTACGTTAAACTAGCTA-CCGTTTGTTTAAAGGTATAATAATAATGTAAACGGTAA
2424580 CTACCAATTT
Statistics
Matches: 139, Mismatches: 9, Indels: 18
0.84 0.05 0.11
Matches are distributed among these distances:
94 48 0.35
95 38 0.27
96 51 0.37
97 2 0.01
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (97 bp):
GCAACCTATTACGTTAAACTAGCTACCGTTTGTTTAAAGGTATAATAATAATGTAAACGGTAAAA
ATATTCAACATAACCAGCTAAAATAAATAGGC
Found at i:2424693 original size:72 final size:72
Alignment explanation
Indices: 2424587--2424832 Score: 263
Period size: 73 Copynumber: 3.4 Consensus size: 72
2424577 TAACTACCAA
* *
2424587 TTTGTTTAAAGGCATAATAATAATGTAA-ACGGTAAAATAAAATAGGCGCA-ACTTA-TTTAAAC
1 TTTGTTTAAAGGCATAATAATAATGTAACA-GGTAAAATAAAATAAGCGCATA-TTACGTTAAAC
2424649 TAGCTACATG
64 TAGCTACA-G
* * *
2424659 TTTGTTTAAAGGTATAATAATAATGTAACAGGTAAAA-AATAA-ATGCAACATATTACGTTAAAC
1 TTTGTTTAAAGGCATAATAATAATGTAACAGGTAAAATAA-AATAAGC-GCATATTACGTTAAAC
2424722 TAGCTAACAG
64 TAGCT-ACAG
* ** * * *
2424732 TTTGTTTAACGATATAATAATAATGTAACCA-ATAAAATAAAATAAGTGTATTATTACGTTAAAC
1 TTTGTTTAAAGGCATAATAATAATGTAA-CAGGTAAAATAAAATAAGCGCA-TATTACGTTAAAC
2424796 TAGCTACCAG
64 TAGCTA-CAG
2424806 -TTGTTTAAAGGCATAATAATAATGTAA
1 TTTGTTTAAAGGCATAATAATAATGTAA
2424833 ATTATAACAC
Statistics
Matches: 149, Mismatches: 14, Indels: 21
0.81 0.08 0.11
Matches are distributed among these distances:
71 5 0.03
72 41 0.28
73 73 0.49
74 30 0.20
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (72 bp):
TTTGTTTAAAGGCATAATAATAATGTAACAGGTAAAATAAAATAAGCGCATATTACGTTAAACTA
GCTACAG
Found at i:2426441 original size:2 final size:2
Alignment explanation
Indices: 2426434--2426477 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
2426424 AATCATATGA
* *
2426434 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2426476 AT
1 AT
2426478 CTAATTCATG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2427498 original size:18 final size:18
Alignment explanation
Indices: 2427416--2427508 Score: 96
Period size: 18 Copynumber: 4.9 Consensus size: 18
2427406 AGGGATTATC
*
2427416 AGTGGTCCTTCGGGACAAAT
1 AGTGGTCCTTCGAGAC--AT
* *
2427436 AATGGTCCTTCGGGACAT
1 AGTGGTCCTTCGAGACAT
* *
2427454 AGTGGTTCTTCGAAACAGT
1 AGTGGTCCTTCGAGACA-T
2427473 CAGTGGTCCTTCGAGACAT
1 -AGTGGTCCTTCGAGACAT
*
2427492 AGTGGTCATTCGAGACA
1 AGTGGTCCTTCGAGACA
2427509 AATATTCAGT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
18 31 0.49
19 2 0.03
20 30 0.48
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGAGACAT
Found at i:2427832 original size:4 final size:4
Alignment explanation
Indices: 2427825--2428699 Score: 1385
Period size: 4 Copynumber: 224.5 Consensus size: 4
2427815 TGATAATGAC
2427825 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT -ATGT ATGT
*
2427874 A-GT ATGT ATGT -TGT ATGT ATATT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT AT-GT ATGT ATGT ATGT ATGT ATGT ATGT
2427921 ATGT ATGT ATGT ATGT ATGT A--T ATGT ATGT -TGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
2427966 ATGT ATGT A-GT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG- GTGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2428012 ATGT ATGT ATGT ATGT ATGT ATGT ATGT -TGT ATGT A-GT AT-T ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2428057 ATGT ATGT ATGT ATGT ATGT AT-T ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2428104 -TGT ATGT ATGT A-GT ATGT A-GT ATGT ATGT ATGT ATGT ATGT ATG-
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2428148 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2428196 ATGT ATGT ATGT ATGT ATGT ATG- ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2428243 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-GT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2428290 ATGT ATGT A-GT ATGT ATGT ATGT ATGT ATGT ATGT ATG- ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2428336 ATGT ATGT ATGT ATGT ATGT ATGT ATGGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT AT-GT ATGT ATGT ATGT ATGT ATGT
*
2428385 ATGT ATGT ATGT ATGT ATGT ATGT A-CT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2428432 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-GT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2428479 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2428527 A--T ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-GT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2428572 ATGT ATGT ATGT ATGGGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT -TGT
1 ATGT ATGT ATGT AT--GT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * * *
2428621 ATGT ATGT ATGT ATGT GTGT ATGT GTGT GTGT GTGT -GGT GTGT GTGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* *
2428668 GTGT GTGT ATG- -TGT ATGT ATGT -TGT AGTGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-TGT AT
2428700 TTGTTACTAA
Statistics
Matches: 824, Mismatches: 12, Indels: 70
0.91 0.01 0.08
Matches are distributed among these distances:
2 6 0.01
3 66 0.08
4 733 0.89
5 15 0.02
6 4 0.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:2428647 original size:2 final size:2
Alignment explanation
Indices: 2428634--2428681 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
2428624 TATGTATGTA
*
2428634 TG TG TG TA TG TG TG TG TG TG TG TG -G TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
2428675 TA TG TG T
1 TG TG TG T
2428682 ATGTATGTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.04, C:0.00, G:0.46, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2428664 original size:17 final size:17
Alignment explanation
Indices: 2428642--2428674 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2428632 TATGTGTGTA
2428642 TGTGTGTGTGTGTGTGG
1 TGTGTGTGTGTGTGTGG
2428659 TGTGTGTGTGTGTGTG
1 TGTGTGTGTGTGTGTG
2428675 TATGTGTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (17 bp):
TGTGTGTGTGTGTGTGG
Found at i:2428682 original size:6 final size:6
Alignment explanation
Indices: 2428611--2428685 Score: 53
Period size: 6 Copynumber: 12.2 Consensus size: 6
2428601 TATGTATGTA
* * * * *
2428611 TGTATG TTGTATG TATGTATG TATGTG TGTATG TGTGTG TGTGTG TG-GTG
1 TGTATG -TGTATG --TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
* *
2428661 TGTGTG TGTGTG TGTATG TGTATG T
1 TGTATG TGTATG TGTATG TGTATG T
2428686 ATGTTGTAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
5 5 0.08
6 42 0.71
7 6 0.10
8 6 0.10
ACGTcount: A:0.11, C:0.00, G:0.39, T:0.51
Consensus pattern (6 bp):
TGTATG
Found at i:2429475 original size:18 final size:18
Alignment explanation
Indices: 2429452--2429557 Score: 158
Period size: 18 Copynumber: 5.9 Consensus size: 18
2429442 CGTAGAAATT
* * *
2429452 TGTCCCGTATGACCACTA
1 TGTCCCGAAGGACCACTG
2429470 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTG
2429488 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTG
*
2429506 TGTTCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTG
*
2429524 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTG
*
2429542 TGTCCCGAAGAACCAC
1 TGTCCCGAAGGACCAC
2429558 AAATAATCCC
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 81 1.00
ACGTcount: A:0.25, C:0.33, G:0.24, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTG
Found at i:2431423 original size:2 final size:2
Alignment explanation
Indices: 2431416--2431461 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2431406 TCGATACTCA
2431416 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2431458 AT AT
1 AT AT
2431462 CTTTCTTACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2432266 original size:33 final size:33
Alignment explanation
Indices: 2432207--2432309 Score: 147
Period size: 33 Copynumber: 3.2 Consensus size: 33
2432197 ACAAAGGTTA
* *
2432207 CGAT-AATTGAAATAC-TAAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
2432238 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
* *
2432271 TGATAAATTTAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
*
2432304 TGATAA
1 CGATAA
2432310 TTGAAACAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
31 4 0.06
32 10 0.15
33 52 0.79
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.33
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTCCAAGTT
Found at i:2432331 original size:21 final size:21
Alignment explanation
Indices: 2432305--2432345 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2432295 TTCCAAGTTT
2432305 GATAATTGAAACAAAGTTTAC
1 GATAATTGAAACAAAGTTTAC
*
2432326 GATAATTGAAATAAAGTTTA
1 GATAATTGAAACAAAGTTTA
2432346 AAAATAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.32
Consensus pattern (21 bp):
GATAATTGAAACAAAGTTTAC
Found at i:2435752 original size:18 final size:18
Alignment explanation
Indices: 2435729--2435799 Score: 79
Period size: 18 Copynumber: 3.9 Consensus size: 18
2435719 GTAGGAAATT
*
2435729 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
2435747 TGTCCCGAAGGACCATTG
1 TGTCCCGAAGGACCACTA
* *
2435765 TGTCCCGAATGACAACTA
1 TGTCCCGAAGGACCACTA
* *
2435783 TGTCCTGAAAGACCACT
1 TGTCCCGAAGGACCACT
2435800 GATAATCCCT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:2435770 original size:36 final size:36
Alignment explanation
Indices: 2435729--2435797 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
2435719 GTAGGAAATT
* * *
2435729 TGTCCCGTAGGACCACTATGTCCCGAAGGACCATTG
1 TGTCCCGAAGGACAACTATGTCCCGAAAGACCATTG
* *
2435765 TGTCCCGAATGACAACTATGTCCTGAAAGACCA
1 TGTCCCGAAGGACAACTATGTCCCGAAAGACCA
2435798 CTGATAATCC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (36 bp):
TGTCCCGAAGGACAACTATGTCCCGAAAGACCATTG
Found at i:2436665 original size:19 final size:19
Alignment explanation
Indices: 2436641--2436694 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
2436631 TCCCTTAACA
2436641 TATGCATCGATGCACTCCT
1 TATGCATCGATGCACTCCT
*
2436660 TATGCATCGATGCACTCTT
1 TATGCATCGATGCACTCCT
2436679 TATGCATCGATGCACT
1 TATGCATCGATGCACT
2436695 AATTGCATTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (19 bp):
TATGCATCGATGCACTCCT
Found at i:2444371 original size:29 final size:29
Alignment explanation
Indices: 2444355--2444423 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 29
2444345 ATCCAGATTG
* *
2444355 TATTTCAAAATATAATTTGAAATATATAA
1 TATTTCAAAATATAATTTGAAACAGATAA
* *
2444384 TATTTCAAAATATAATTTGAAATATATAA
1 TATTTCAAAATATAATTTGAAACAGATAA
2444413 TATTTCAAAAT
1 TATTTCAAAAT
2444424 TTTATAACTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (29 bp):
TATTTCAAAATATAATTTGAAACAGATAA
Found at i:2444383 original size:14 final size:14
Alignment explanation
Indices: 2444364--2444413 Score: 66
Period size: 14 Copynumber: 3.5 Consensus size: 14
2444354 GTATTTCAAA
2444364 ATATAATTTGAAAT
1 ATATAATTTGAAAT
*
2444378 ATATAATATTTCAAA-
1 ATAT-A-ATTTGAAAT
2444393 ATATAATTTGAAAT
1 ATATAATTTGAAAT
2444407 ATATAAT
1 ATATAAT
2444414 ATTTCAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 7 0.23
14 12 0.39
15 5 0.16
16 7 0.23
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (14 bp):
ATATAATTTGAAAT
Found at i:2444396 original size:17 final size:16
Alignment explanation
Indices: 2444355--2444421 Score: 74
Period size: 13 Copynumber: 4.6 Consensus size: 16
2444345 ATCCAGATTG
2444355 TATTTCAAA-ATAT-A
1 TATTTCAAATATATAA
*
2444369 -ATTTGAAATATATAA
1 TATTTCAAATATATAA
2444384 TATTTCAAA-ATAT-A
1 TATTTCAAATATATAA
*
2444398 -ATTTGAAATATATAA
1 TATTTCAAATATATAA
2444413 TATTTCAAA
1 TATTTCAAA
2444422 ATTTTATAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
13 14 0.33
14 9 0.21
15 6 0.14
16 14 0.33
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (16 bp):
TATTTCAAATATATAA
Found at i:2453110 original size:22 final size:22
Alignment explanation
Indices: 2453083--2453142 Score: 59
Period size: 25 Copynumber: 2.6 Consensus size: 22
2453073 TTATCATAAA
2453083 TATTTAATAAAATAAATAATAT
1 TATTTAATAAAATAAATAATAT
* *
2453105 TATTTATCATAAAATTTAATATTAT
1 TATTTA--ATAAAA-TAAATAATAT
*
2453130 TATTT-TTAAAATA
1 TATTTAATAAAATA
2453143 TTAAAATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
21 1 0.03
22 11 0.35
24 6 0.19
25 13 0.42
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TATTTAATAAAATAAATAATAT
Found at i:2453309 original size:20 final size:19
Alignment explanation
Indices: 2453265--2453346 Score: 62
Period size: 19 Copynumber: 4.3 Consensus size: 19
2453255 AGTAATAGTG
*
2453265 TTATTA-TATTTTAAAATA
1 TTATTAGTATATTAAAATA
2453283 TTAATTAGTATATTAAAGATA
1 TT-ATTAGTATATTAAA-ATA
* *
2453304 TTATTAG-ATTATTATATTA
1 TTATTAGTA-TATTAAAATA
* *
2453323 ATATTAATATA-TAAATATA
1 TTATTAGTATATTAAA-ATA
2453342 TTATT
1 TTATT
2453347 TTTATGAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
18 5 0.10
19 20 0.40
20 20 0.40
21 5 0.10
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (19 bp):
TTATTAGTATATTAAAATA
Found at i:2453466 original size:18 final size:18
Alignment explanation
Indices: 2453411--2453494 Score: 62
Period size: 18 Copynumber: 4.4 Consensus size: 18
2453401 AAATAAAAAT
*
2453411 ATATCTTATATTATTATA
1 ATATTTTATATTATTATA
*
2453429 ATATAATTGATTATTTATTATA
1 ATAT--TTTA-TA-TTATTATA
*
2453451 ATATTTTATATTATTAGAA
1 ATATTTTATATTATTA-TA
* *
2453470 ATATTAATATATTTTTA-A
1 ATATT-TTATATTATTATA
2453488 ATATTTT
1 ATATTTT
2453495 TAATAATTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 13
0.73 0.10 0.18
Matches are distributed among these distances:
17 1 0.02
18 16 0.30
19 8 0.15
20 14 0.26
21 2 0.04
22 12 0.23
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.56
Consensus pattern (18 bp):
ATATTTTATATTATTATA
Found at i:2453466 original size:40 final size:37
Alignment explanation
Indices: 2453411--2453494 Score: 98
Period size: 40 Copynumber: 2.2 Consensus size: 37
2453401 AAATAAAAAT
* * *
2453411 ATATCTTATATTATTATAATATAATTGAT-TATTTATTATA
1 ATATTTTATATTATTAGAA-AT-ATTAATATATTT-TTA-A
2453451 ATATTTTATATTATTAGAAATATTAATATATTTTTAA
1 ATATTTTATATTATTAGAAATATTAATATATTTTTAA
2453488 ATATTTT
1 ATATTTT
2453495 TAATAATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
37 8 0.20
38 8 0.20
39 7 0.17
40 17 0.43
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.56
Consensus pattern (37 bp):
ATATTTTATATTATTAGAAATATTAATATATTTTTAA
Found at i:2453548 original size:22 final size:23
Alignment explanation
Indices: 2453499--2453551 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
2453489 TATTTTTAAT
2453499 AATTAATATTTTGATTAAAATGA
1 AATTAATATTTTGATTAAAATGA
* * * *
2453522 TATTAA-ATTTTTATTAATATTA
1 AATTAATATTTTGATTAAAATGA
2453544 AATTAATA
1 AATTAATA
2453552 AACTAAAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
AATTAATATTTTGATTAAAATGA
Found at i:2453750 original size:42 final size:42
Alignment explanation
Indices: 2453711--2453792 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
2453701 ACCAAACATT
** * *
2453711 GAAAAATATTTTTCGGGAAACGAATTATGTGAAGCAAACAAG
1 GAAAAATATTTTTCGAAAAACGAATTACGTGAAACAAACAAG
* *
2453753 GGAAAATATTTTTCGAAAAACGAGTTACGTGAAACAAACA
1 GAAAAATATTTTTCGAAAAACGAATTACGTGAAACAAACA
2453793 CTGTATTTCG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.23
Consensus pattern (42 bp):
GAAAAATATTTTTCGAAAAACGAATTACGTGAAACAAACAAG
Found at i:2454364 original size:26 final size:26
Alignment explanation
Indices: 2454317--2454366 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2454307 AATATTTAAA
*
2454317 TATATTTATTAATATTTCTAATAATT
1 TATATTTATTAATATTTATAATAATT
*
2454343 TATATTATTTTAATA-TTATAATAA
1 TATATT-TATTAATATTTATAATAA
2454367 AGTAATCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 14 0.67
27 7 0.33
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (26 bp):
TATATTTATTAATATTTATAATAATT
Found at i:2454506 original size:19 final size:18
Alignment explanation
Indices: 2454482--2454549 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 18
2454472 ATATTATTAA
2454482 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
2454501 ATTATTTAT-ATATTAAT
1 ATTATTAATAATAATAAT
2454518 ATTAATATAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
2454540 ATT-TTAATAA
1 ATTATTAATAA
2454550 GGATATATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
17 8 0.20
18 4 0.10
19 17 0.43
20 2 0.05
22 9 0.22
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:2454653 original size:31 final size:29
Alignment explanation
Indices: 2454568--2454697 Score: 79
Period size: 31 Copynumber: 4.3 Consensus size: 29
2454558 AAATATACTA
* *
2454568 ATTAATATTTTTA-AAATAAAATAT-AAC
1 ATTAATATTTTTATTAATAAAATATAAAT
* * * * *
2454595 ACTATTACTTTAATAAATAATTAATAT-AAT
1 ATTAATATTTTTATTAATAA--AATATAAAT
*
2454625 TTATAATATTTTTATTTCAATAAAATATACCAAT
1 AT-TAATATTTTTA-TT-AATAAAATATA--AAT
2454659 ATTAATATTTTTATTAATAAAATTATAAA-
1 ATTAATATTTTTATTAATAAAA-TATAAAT
*
2454688 AATAATATTT
1 ATTAATATTT
2454698 AATAATAAAT
Statistics
Matches: 80, Mismatches: 13, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
27 9 0.11
28 6 0.08
29 9 0.11
30 9 0.11
31 20 0.25
32 7 0.09
33 16 0.20
34 4 0.05
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (29 bp):
ATTAATATTTTTATTAATAAAATATAAAT
Found at i:2454963 original size:34 final size:34
Alignment explanation
Indices: 2454881--2454964 Score: 159
Period size: 34 Copynumber: 2.5 Consensus size: 34
2454871 TTTTCCAGAA
*
2454881 AAATGTAATTCATTCTACGGAAAACGTTTTCCAT
1 AAATGTAATTCATTTTACGGAAAACGTTTTCCAT
2454915 AAATGTAATTCATTTTACGGAAAACGTTTTCCAT
1 AAATGTAATTCATTTTACGGAAAACGTTTTCCAT
2454949 AAATGTAATTCATTTT
1 AAATGTAATTCATTTT
2454965 CCAGAATTCA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (34 bp):
AAATGTAATTCATTTTACGGAAAACGTTTTCCAT
Found at i:2454974 original size:14 final size:13
Alignment explanation
Indices: 2454955--2455042 Score: 50
Period size: 14 Copynumber: 6.2 Consensus size: 13
2454945 CCATAAATGT
*
2454955 AATTCATTTTCCAG
1 AATTCAATTT-CAG
2454969 AATTCAAATTTCAG
1 AATTC-AATTTCAG
* *
2454983 TAATTCATTTTTCAT
1 -AATTCA-ATTTCAG
2454998 AATTCAAATTTCAG
1 AATTC-AATTTCAG
* * *
2455012 TAATTCATTTTTTAA
1 -AATTCA-ATTTCAG
2455027 AATTCAATTTCCAG
1 AATTCAATTT-CAG
2455041 AA
1 AA
2455043 AACTAATTAC
Statistics
Matches: 56, Mismatches: 11, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
13 3 0.05
14 29 0.52
15 24 0.43
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (13 bp):
AATTCAATTTCAG
Found at i:2454987 original size:15 final size:15
Alignment explanation
Indices: 2454969--2455018 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
2454959 CATTTTCCAG
2454969 AATTCAAATTTCAGT
1 AATTCAAATTTCAGT
**
2454984 AATTCATTTTTCA-T
1 AATTCAAATTTCAGT
2454998 AATTCAAATTTCAGT
1 AATTCAAATTTCAGT
2455013 AATTCA
1 AATTCA
2455019 TTTTTTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 12 0.40
15 18 0.60
ACGTcount: A:0.38, C:0.14, G:0.04, T:0.44
Consensus pattern (15 bp):
AATTCAAATTTCAGT
Found at i:2455001 original size:29 final size:29
Alignment explanation
Indices: 2454953--2455037 Score: 127
Period size: 29 Copynumber: 3.0 Consensus size: 29
2454943 TTCCATAAAT
* *
2454953 GTAATTCATTTTCCAGAATTCAAATTTCA
1 GTAATTCATTTTTCAAAATTCAAATTTCA
*
2454982 GTAATTCATTTTTCATAATTCAAATTTCA
1 GTAATTCATTTTTCAAAATTCAAATTTCA
*
2455011 GTAATTCATTTTTTAAAATTC-AATTTC
1 GTAATTCATTTTTCAAAATTCAAATTTC
2455038 CAGAAAACTA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 6 0.12
29 46 0.88
ACGTcount: A:0.34, C:0.14, G:0.05, T:0.47
Consensus pattern (29 bp):
GTAATTCATTTTTCAAAATTCAAATTTCA
Found at i:2474815 original size:10 final size:10
Alignment explanation
Indices: 2474797--2474826 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2474787 CATTTAAAGG
*
2474797 ACTATAATTC
1 ACTAAAATTC
2474807 ACTAAAATTC
1 ACTAAAATTC
2474817 ACTAAAATTC
1 ACTAAAATTC
2474827 GATGTCTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (10 bp):
ACTAAAATTC
Found at i:2493936 original size:16 final size:16
Alignment explanation
Indices: 2493915--2493947 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2493905 TAATAAATAA
2493915 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
2493931 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
2493947 A
1 A
2493948 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:2494081 original size:16 final size:16
Alignment explanation
Indices: 2494021--2494077 Score: 78
Period size: 16 Copynumber: 3.6 Consensus size: 16
2494011 AAATAAACGC
2494021 ACATAAACGAACACGA
1 ACATAAACGAACACGA
* *
2494037 ACATAAACAAATACGA
1 ACATAAACGAACACGA
* *
2494053 ACATAAATGGACACGA
1 ACATAAACGAACACGA
2494069 ACATAAACG
1 ACATAAACG
2494078 GACATAAACG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.56, C:0.21, G:0.12, T:0.11
Consensus pattern (16 bp):
ACATAAACGAACACGA
Found at i:2494328 original size:11 final size:11
Alignment explanation
Indices: 2494312--2494352 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
2494302 TTGAGAGTCG
2494312 AGCTCGATTCA
1 AGCTCGATTCA
*
2494323 AGCTCGATTCTG
1 AGCTCGATTC-A
2494335 AGCTCGATTCA
1 AGCTCGATTCA
2494346 AGCTCGA
1 AGCTCGA
2494353 CATTGCCCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:2495228 original size:14 final size:14
Alignment explanation
Indices: 2495211--2495266 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
2495201 AATGAACATA
2495211 AACGAACATAACCG
1 AACGAACATAACCG
2495225 AACGAACAT-A---
1 AACGAACATAACCG
*
2495235 AACGAACATAATCG
1 AACGAACATAACCG
2495249 AACGAACATAACCG
1 AACGAACATAACCG
2495263 AACG
1 AACG
2495267 TTCACGAACG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.52, C:0.25, G:0.14, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:2495265 original size:10 final size:10
Alignment explanation
Indices: 2495204--2495251 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
2495194 ATAAATGAAT
2495204 GAACATAAAC
1 GAACATAAAC
2495214 GAACATAACCGAAC
1 GAACAT-A---AAC
2495228 GAACATAAAC
1 GAACATAAAC
*
2495238 GAACATAATC
1 GAACATAAAC
2495248 GAAC
1 GAAC
2495252 GAACATAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:2495276 original size:24 final size:24
Alignment explanation
Indices: 2495204--2495265 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
2495194 ATAAATGAAT
*
2495204 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAATCGAAC
2495228 GAACATAAACGAACATAATCGAAC
1 GAACATAAACGAACATAATCGAAC
*
2495252 GAACATAACCGAAC
1 GAACATAAACGAAC
2495266 GTTCACGAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.53, C:0.24, G:0.13, T:0.10
Consensus pattern (24 bp):
GAACATAAACGAACATAATCGAAC
Found at i:2498667 original size:20 final size:21
Alignment explanation
Indices: 2498642--2498693 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2498632 TTTTCCCAAT
*
2498642 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
2498662 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
2498683 TCGCAATGCGA
1 TCGCAATGCGA
2498694 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:2498706 original size:41 final size:41
Alignment explanation
Indices: 2498679--2498810 Score: 133
Period size: 41 Copynumber: 3.2 Consensus size: 41
2498669 GCGAATTGGG
* * *
2498679 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
* * *
2498720 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAAT-AC
** * * *
2498762 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
*
2498801 ATAATCGCAA
1 AAAATCGCAA
2498811 TGCGATTTTC
Statistics
Matches: 74, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.42
41 39 0.53
42 2 0.03
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
Found at i:2498707 original size:20 final size:20
Alignment explanation
Indices: 2498682--2498796 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
2498672 AATTGGGAAA
*
2498682 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
2498702 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
2498723 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
2498743 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
2498763 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
2498783 TTCGCAACGCGATA
1 ATCGCAACGCGATA
2498797 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:2499330 original size:20 final size:20
Alignment explanation
Indices: 2499271--2499334 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
2499261 GCTATTTTAG
*
2499271 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAT
*
2499291 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
2499311 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
2499331 TTTC
1 TTTC
2499335 AGAAACTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:2500675 original size:18 final size:18
Alignment explanation
Indices: 2500654--2500698 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2500644 TCCACTTCGG
*
2500654 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
2500672 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
2500690 GAGCCATCA
1 GAGCCATCA
2500699 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2501234 original size:19 final size:20
Alignment explanation
Indices: 2501180--2501246 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
2501170 TAGTTTACTT
* *
2501180 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
2501200 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
2501220 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
2501239 TCGCAACG
1 TCGCAACG
2501247 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:2501254 original size:14 final size:14
Alignment explanation
Indices: 2501235--2501292 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2501225 ATGCGAAATG
2501235 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2501249 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
2501265 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
2501281 AAAATCGCAACG
1 AAAATCGCAACG
2501293 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2501277 original size:32 final size:33
Alignment explanation
Indices: 2501219--2501309 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
2501209 GGAAATGGCT
*
2501219 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
2501252 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
2501284 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
2501310 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:2501303 original size:19 final size:19
Alignment explanation
Indices: 2501180--2501314 Score: 85
Period size: 19 Copynumber: 7.6 Consensus size: 19
2501170 TAGTTTACTT
* **
2501180 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
2501200 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
2501220 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2501239 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
2501253 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
2501271 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
2501285 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2501304 TCGCAATGCGA
1 TCGCAACGCGA
2501315 TTTGTGTTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 25
0.72 0.09 0.20
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.12
19 27 0.29
20 24 0.26
21 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2501345 original size:14 final size:14
Alignment explanation
Indices: 2501326--2501383 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2501316 TTGTGTTTCG
2501326 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2501340 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
2501356 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
2501372 CGTTGCGATTTT
1 CGTTGCGATTTT
2501384 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2501360 original size:32 final size:33
Alignment explanation
Indices: 2501321--2501399 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
2501311 GCGATTTGTG
2501321 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
2501353 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
2501386 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
2501400 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:2501398 original size:19 final size:19
Alignment explanation
Indices: 2501340--2501457 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
2501330 GCGATTTTGT
2501340 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
2501358 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
2501372 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
2501391 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
2501411 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
2501430 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
2501450 TGTTGCGA
1 CGTTGCGA
2501458 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:2503325 original size:14 final size:14
Alignment explanation
Indices: 2503306--2503341 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2503296 ATTGTTTAAT
2503306 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2503320 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2503334 TGATTTGT
1 TGATTTGT
2503342 TTAATCGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2503467 original size:14 final size:14
Alignment explanation
Indices: 2503448--2503501 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
2503438 CGAAATGGCT
2503448 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
2503462 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
2503481 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
2503495 ATCGCAA
1 ATCGCAA
2503502 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:2503519 original size:33 final size:33
Alignment explanation
Indices: 2503429--2503506 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
2503419 AAAACAGACT
* ***
2503429 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
2503462 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
2503495 ATCGCAATGCGA
1 ATCGCAATGCGA
2503507 TTTTCATTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:2503550 original size:20 final size:20
Alignment explanation
Indices: 2503525--2503582 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
2503515 TCGCATTGCG
*
2503525 ATTTTCTCGTTGCGATAGCC
1 ATTTTCACGTTGCGATAGCC
2503545 ATTTTCACGTTGCGATAGCC
1 ATTTTCACGTTGCGATAGCC
*
2503565 ATTTTCGCGTTGCGATAG
1 ATTTTCACGTTGCGATAG
2503583 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCACGTTGCGATAGCC
Found at i:2504811 original size:12 final size:12
Alignment explanation
Indices: 2504794--2504818 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2504784 ATATAATCCT
2504794 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2504806 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2504818 G
1 G
2504819 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:2507163 original size:33 final size:33
Alignment explanation
Indices: 2507110--2507236 Score: 175
Period size: 33 Copynumber: 3.8 Consensus size: 33
2507100 GGAAATTACT
* *
2507110 ATCGCAATACAAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
2507143 ATCGTAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
2507175 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
2507209 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
2507237 CGAATTTAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
32 1 0.01
33 79 0.98
34 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2507196 original size:66 final size:66
Alignment explanation
Indices: 2507111--2507243 Score: 221
Period size: 66 Copynumber: 2.0 Consensus size: 66
2507101 GAAATTACTA
* *
2507111 TCGCAATACAAAATGAAAATCGCAACGAGAGAATCGTAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATACAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
2507176 T
66 T
* * *
2507177 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATACAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
2507242 T
66 T
2507243 T
1 T
2507244 AATTTCGCGT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.17
Consensus pattern (66 bp):
TCGCAATACAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:2507201 original size:19 final size:19
Alignment explanation
Indices: 2507110--2507240 Score: 67
Period size: 19 Copynumber: 7.7 Consensus size: 19
2507100 GGAAATTACT
* *
2507110 ATCGCAATACAAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2507129 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
2507143 ATCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
2507162 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
2507176 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
2507195 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
2507209 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2507228 ATCGCAACGCGAA
1 ATCGCAATGCGAA
2507241 TTTAATTTCG
Statistics
Matches: 81, Mismatches: 16, Indels: 30
0.64 0.13 0.24
Matches are distributed among these distances:
14 26 0.32
15 3 0.04
16 6 0.07
17 5 0.06
18 3 0.04
19 38 0.47
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2507258 original size:19 final size:20
Alignment explanation
Indices: 2507236--2507278 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
2507226 AAATCGCAAC
2507236 GCGAATTTAATTT-CGCGTT
1 GCGAATTTAATTTCCGCGTT
* *
2507255 GCGATTTTCATTTCCGCGTT
1 GCGAATTTAATTTCCGCGTT
2507275 GCGA
1 GCGA
2507279 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.40
Consensus pattern (20 bp):
GCGAATTTAATTTCCGCGTT
Found at i:2507438 original size:14 final size:14
Alignment explanation
Indices: 2507419--2507455 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2507409 CATCAATTAA
2507419 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2507433 ACAAATCACCTTTT
1 ACAAATCAACTTTT
2507447 ACAAATCAA
1 ACAAATCAA
2507456 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:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2508846 original size:21 final size:21
Alignment explanation
Indices: 2508780--2508846 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2508770 GTGAATCGGG
*
2508780 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
2508800 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
2508822 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
2508843 CTCT
1 CTCT
2508847 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:2508865 original size:42 final size:41
Alignment explanation
Indices: 2508780--2508902 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
2508770 GTGAATCGGG
* * * *
2508780 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
2508822 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
2508864 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
2508903 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:2510969 original size:33 final size:33
Alignment explanation
Indices: 2510912--2511010 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
2510902 ACGAGATAAT
*
2510912 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
* *
2510946 TAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
2510979 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
2511011 GCGAAATAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 44 0.77
34 13 0.23
ACGTcount: A:0.39, C:0.26, G:0.22, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:2511004 original size:19 final size:19
Alignment explanation
Indices: 2510887--2511052 Score: 136
Period size: 20 Copynumber: 9.1 Consensus size: 19
2510877 TCTTTTGGTT
*
2510887 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
2510906 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
2510926 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
2510944 G--AT-AGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
2510960 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
2510978 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2510993 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
2511013 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
2511032 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
2511051 GA
1 GA
2511053 TTTTTGTTTC
Statistics
Matches: 119, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
14 18 0.15
15 4 0.03
16 2 0.02
17 1 0.01
18 5 0.04
19 42 0.35
20 45 0.38
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:2511084 original size:19 final size:19
Alignment explanation
Indices: 2511048--2511092 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
2511038 AAAATCGCAA
*
2511048 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
2511067 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
2511086 TGTGATT
1 TGCGATT
2511093 CTCTCGTTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.07, C:0.13, G:0.24, T:0.56
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:2511669 original size:20 final size:20
Alignment explanation
Indices: 2511644--2511696 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2511634 GCGCTATGTA
2511644 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
2511664 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
2511684 TATCTCGTTGCGA
1 AATCGCGTTGCGA
2511697 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:2511730 original size:20 final size:20
Alignment explanation
Indices: 2511705--2511758 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
2511695 GATTTTGTAT
*
2511705 TATCGCATTTCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
2511725 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
2511745 TATCGCATTGCGAT
1 TATCGCATTGCGAT
2511759 TTTCCCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:2511869 original size:21 final size:21
Alignment explanation
Indices: 2511829--2511869 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2511819 ACTGTATACC
**
2511829 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
2511850 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
2511870 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:2518945 original size:27 final size:27
Alignment explanation
Indices: 2518907--2518964 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
2518897 TGTTGCTGCG
* *
2518907 GTACTTATATTTTTGTGAGTATATAAA
1 GTACTTATATTTTGGTGACTATATAAA
2518934 GTACTTATATTTTGGTGACTATATAAA
1 GTACTTATATTTTGGTGACTATATAAA
2518961 GTAC
1 GTAC
2518965 CGAAGTCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.45
Consensus pattern (27 bp):
GTACTTATATTTTGGTGACTATATAAA
Found at i:2526332 original size:2 final size:2
Alignment explanation
Indices: 2526325--2526371 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2526315 TGAAAATACT
2526325 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2526367 TC TC T
1 TC TC T
2526372 GTGCTTATTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2530591 original size:23 final size:23
Alignment explanation
Indices: 2530530--2530617 Score: 72
Period size: 23 Copynumber: 3.7 Consensus size: 23
2530520 ACAAAAGTTT
2530530 TATAAATTAATTTATAAAACGT-TAAA
1 TATAAATTAA-TTA-AAAA--TATAAA
* ** *
2530556 TCATAAAGT-ATTAAACGTATAAT
1 T-ATAAATTAATTAAAAATATAAA
2530579 TATAAATTAATTAAAAATATAAA
1 TATAAATTAATTAAAAATATAAA
*
2530602 TATAATTTAATTAAAA
1 TATAAATTAATTAAAA
2530618 TACAATATTT
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
22 7 0.14
23 30 0.60
24 2 0.04
25 3 0.06
26 2 0.04
27 6 0.12
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (23 bp):
TATAAATTAATTAAAAATATAAA
Found at i:2542199 original size:39 final size:39
Alignment explanation
Indices: 2542156--2542233 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
2542146 AGTTTTGGGG
2542156 ATAAAGGCGTTTAAGCACCAAATTAAACCTTAAAACTAA
1 ATAAAGGCGTTTAAGCACCAAATTAAACCTTAAAACTAA
* *
2542195 ATAAAGGTGTTTAAGTACCAAATTAAACCTTAAAACTAA
1 ATAAAGGCGTTTAAGCACCAAATTAAACCTTAAAACTAA
2542234 GTTTAGATAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.26
Consensus pattern (39 bp):
ATAAAGGCGTTTAAGCACCAAATTAAACCTTAAAACTAA
Found at i:2547770 original size:13 final size:14
Alignment explanation
Indices: 2547752--2547784 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2547742 GATTAATACG
*
2547752 TTTTTTAAATTAT-
1 TTTTTTAAATAATC
2547765 TTTTTTAAATAATC
1 TTTTTTAAATAATC
2547779 TTTTTT
1 TTTTTT
2547785 GAACATTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTTAAATAATC
Found at i:2549507 original size:12 final size:12
Alignment explanation
Indices: 2549459--2549500 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
2549449 AGCTGTGAAG
*
2549459 AAGGAAAAAGGG
1 AAGGAAAAAGGA
2549471 AAGGAAAAAGGA
1 AAGGAAAAAGGA
2549483 AAGG--AAAGGA
1 AAGGAAAAAGGA
2549493 AAGGAAAA
1 AAGGAAAA
2549501 GAAAAAGCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 10 0.37
12 17 0.63
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (12 bp):
AAGGAAAAAGGA
Found at i:2549507 original size:22 final size:22
Alignment explanation
Indices: 2549465--2549505 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2549455 GAAGAAGGAA
* *
2549465 AAAGGGAAGGAAAAAGGAAAGG
1 AAAGGAAAGGAAAAAGAAAAGG
2549487 AAAGGAAAGG-AAAAGAAAA
1 AAAGGAAAGGAAAAAGAAAA
2549506 AGCAGAAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (22 bp):
AAAGGAAAGGAAAAAGAAAAGG
Found at i:2551331 original size:2 final size:2
Alignment explanation
Indices: 2551324--2551379 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
2551314 ACCGACTTAA
2551324 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2551366 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
2551380 GATCTATCAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2562018 original size:22 final size:22
Alignment explanation
Indices: 2561990--2562072 Score: 130
Period size: 22 Copynumber: 3.8 Consensus size: 22
2561980 GGGTTTACGC
* * *
2561990 GGTCCTTCGGGACATATACAGA
1 GGTCCTTCGAGACAAATACATA
2562012 GGTCCTTCGAGACAAATACATA
1 GGTCCTTCGAGACAAATACATA
2562034 GGTCCTTCGAGACAAATACATA
1 GGTCCTTCGAGACAAATACATA
*
2562056 GGTCCTTCGGGACAAAT
1 GGTCCTTCGAGACAAAT
2562073 TTCACATGCC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 57 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (22 bp):
GGTCCTTCGAGACAAATACATA
Found at i:2562515 original size:21 final size:21
Alignment explanation
Indices: 2562489--2562529 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2562479 TAAATTTTTG
*
2562489 TGCATCGGTGCACTGTAGCAA
1 TGCATCGGTACACTGTAGCAA
2562510 TGCATCGGTACACTGTAGCA
1 TGCATCGGTACACTGTAGCA
2562530 CTGTTCATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (21 bp):
TGCATCGGTACACTGTAGCAA
Found at i:2568288 original size:23 final size:23
Alignment explanation
Indices: 2568256--2568314 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
2568246 AAGGGCAAAT
* *
2568256 AGTAAAGGCTGCTGTGAAGTAGC
1 AGTAAGGGCTGCTGTGAAGAAGC
2568279 AGTAAGGGCTGCTGTGAAGAAGC
1 AGTAAGGGCTGCTGTGAAGAAGC
2568302 AGTAAGGGCTGCT
1 AGTAAGGGCTGCT
2568315 TCCACTGCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.29, C:0.14, G:0.37, T:0.20
Consensus pattern (23 bp):
AGTAAGGGCTGCTGTGAAGAAGC
Found at i:2575159 original size:30 final size:30
Alignment explanation
Indices: 2575124--2575219 Score: 85
Period size: 29 Copynumber: 3.3 Consensus size: 30
2575114 TTTGTTTCAG
2575124 TTTAGTCCTATAAATTCATGTTTATGCTAT
1 TTTAGTCCTATAAATTCATGTTTATGCTAT
* * *
2575154 TTTAGTCCTTTAACTTTC-TATTT-TGCTAT
1 TTTAGTCCTATAA-ATTCATGTTTATGCTAT
* *
2575183 TTTAG-CCATGTAAGTTCATGTTTTAT-C-AT
1 TTTAGTCC-TATAAATTCATG-TTTATGCTAT
2575212 TTTAGTCC
1 TTTAGTCC
2575220 CCGAAATTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
28 5 0.09
29 23 0.43
30 22 0.41
31 4 0.07
ACGTcount: A:0.22, C:0.16, G:0.10, T:0.52
Consensus pattern (30 bp):
TTTAGTCCTATAAATTCATGTTTATGCTAT
Found at i:2575648 original size:31 final size:31
Alignment explanation
Indices: 2575613--2575680 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
2575603 ATGTAAATGT
2575613 AAATTTCAAAATTTTCATTTGTATTCAATTC
1 AAATTTCAAAATTTTCATTTGTATTCAATTC
2575644 AAATTTCAAAATTTTCATTTGTATTCAATTC
1 AAATTTCAAAATTTTCATTTGTATTCAATTC
2575675 AAATTT
1 AAATTT
2575681 TTAGTTAATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.37, C:0.12, G:0.03, T:0.49
Consensus pattern (31 bp):
AAATTTCAAAATTTTCATTTGTATTCAATTC
Found at i:2579257 original size:14 final size:14
Alignment explanation
Indices: 2579238--2579277 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
2579228 CAAAGAAAAT
2579238 CAAAGAGAAAGAAA
1 CAAAGAGAAAGAAA
2579252 CAAAGAG-AA-AAA
1 CAAAGAGAAAGAAA
2579264 C-AAGCAGAAAGAAA
1 CAAAG-AGAAAGAAA
2579278 AAGGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
11 3 0.13
12 6 0.26
13 4 0.17
14 10 0.43
ACGTcount: A:0.70, C:0.10, G:0.20, T:0.00
Consensus pattern (14 bp):
CAAAGAGAAAGAAA
Found at i:2581064 original size:23 final size:23
Alignment explanation
Indices: 2581038--2581106 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 23
2581028 CACCACAGCT
* *
2581038 CATATAAATGTACCGAAGTGCCA
1 CATAGAAATGCACCGAAGTGCCA
* * *
2581061 CATAGAATTGCACCGTAGTGCCG
1 CATAGAAATGCACCGAAGTGCCA
* ** *
2581084 CGTAGAGTTGCACCGTAGTGCCA
1 CATAGAAATGCACCGAAGTGCCA
2581107 TATAATAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.22
Consensus pattern (23 bp):
CATAGAAATGCACCGAAGTGCCA
Found at i:2581293 original size:103 final size:103
Alignment explanation
Indices: 2581122--2581339 Score: 418
Period size: 103 Copynumber: 2.1 Consensus size: 103
2581112 TAATGTCCAT
*
2581122 AAGGACCATATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
2581187 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCAAAAGAATACATATATGTCCCG
2581225 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
2581290 GACTTCACACATGTTCAAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCAAAAGAATACATATATGTCCCG
2581328 AAGGACCACATA
1 AAGGACCACATA
2581340 GACCCTCGAC
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 113 1.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCAAAAGAATACATATATGTCCCG
Found at i:2586091 original size:23 final size:23
Alignment explanation
Indices: 2586065--2586122 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
2586055 ATATAAATGT
*
2586065 ACCGAAGTGCCACATAGAATTGC
1 ACCGTAGTGCCACATAGAATTGC
* * * *
2586088 ACCGTAGTACCGCGTAGAGTTGC
1 ACCGTAGTGCCACATAGAATTGC
2586111 ACCGTAGTGCCA
1 ACCGTAGTGCCA
2586123 TATAATAATG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (23 bp):
ACCGTAGTGCCACATAGAATTGC
Found at i:2586306 original size:103 final size:100
Alignment explanation
Indices: 2586138--2586352 Score: 385
Period size: 103 Copynumber: 2.1 Consensus size: 100
2586128 TAATGTCCAT
*
2586138 AAGGACCACATATCATTCTTTAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
1 AAGGACCACATATCATTCTTGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
2586203 TTCACACATGTTCCAAAGAATACATATATGTCCCG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCG
*
2586238 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTACCA
1 AAGGACCACATATCATT-CTT--GAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
2586303 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
63 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
2586341 AAGGACCACATA
1 AAGGACCACATA
2586353 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 2, Indels: 3
0.96 0.02 0.03
Matches are distributed among these distances:
100 17 0.15
101 3 0.03
103 90 0.82
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.27
Consensus pattern (100 bp):
AAGGACCACATATCATTCTTGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:2588805 original size:4 final size:4
Alignment explanation
Indices: 2588727--2588796 Score: 115
Period size: 4 Copynumber: 17.5 Consensus size: 4
2588717 ATCGAGAAAA
*
2588727 ACAT ACAT -CAAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAC
1 ACAT ACAT AC-AT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2588775 ACAT ACAT ACAT ACAT ACAT AC
1 ACAT ACAT ACAT ACAT ACAT AC
2588797 GCATACATAT
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
3 1 0.02
4 60 0.97
5 1 0.02
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:2589201 original size:35 final size:36
Alignment explanation
Indices: 2589123--2589259 Score: 170
Period size: 35 Copynumber: 3.8 Consensus size: 36
2589113 TCTCGAAATA
* * *
2589123 AAATGTTGTCTCGCTAGAGACAACTTCTTTTGAAAAAC
1 AAATTTTGTCTCGCTTGAGACAA-TT-TTCTGAAAAAC
2589161 AAATTTTGTCTCGCTTGAGACAATTTTCT-AAAAAC
1 AAATTTTGTCTCGCTTGAGACAATTTTCTGAAAAAC
*
2589196 AAATTTTGTCTCGTTTGAGACAA-TTTCTTGAAAAAC
1 AAATTTTGTCTCGCTTGAGACAATTTTC-TGAAAAAC
* * *
2589232 AAATTTCGTCTCACTTGAGACACTTTTC
1 AAATTTTGTCTCGCTTGAGACAATTTTC
2589260 CTTTGAGATA
Statistics
Matches: 88, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
34 4 0.05
35 29 0.33
36 28 0.32
37 6 0.07
38 21 0.24
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.36
Consensus pattern (36 bp):
AAATTTTGTCTCGCTTGAGACAATTTTCTGAAAAAC
Found at i:2589249 original size:71 final size:73
Alignment explanation
Indices: 2589123--2589259 Score: 197
Period size: 71 Copynumber: 1.9 Consensus size: 73
2589113 TCTCGAAATA
* * *
2589123 AAATGTTGTCTCGCTAGAGACAACTTCTTTTGAAAAACAAATTTTGTCTCGCTTGAGACAATTTT
1 AAATGTTGTCTCGCTAGAGACAACTTCTCTTGAAAAACAAATTTCGTCTCACTTGAGACAATTTT
2589188 CTAAAAAC
66 CTAAAAAC
* * * *
2589196 AAATTTTGTCTCGTTTGAGACAA-TT-TCTTGAAAAACAAATTTCGTCTCACTTGAGACACTTTT
1 AAATGTTGTCTCGCTAGAGACAACTTCTCTTGAAAAACAAATTTCGTCTCACTTGAGACAATTTT
2589259 C
66 C
2589260 CTTTGAGATA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
71 35 0.61
72 2 0.04
73 20 0.35
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.36
Consensus pattern (73 bp):
AAATGTTGTCTCGCTAGAGACAACTTCTCTTGAAAAACAAATTTCGTCTCACTTGAGACAATTTT
CTAAAAAC
Found at i:2589369 original size:36 final size:36
Alignment explanation
Indices: 2589294--2589396 Score: 100
Period size: 36 Copynumber: 2.8 Consensus size: 36
2589284 GTTTCACATT
* **
2589294 AAACAAA-GTTGATCTCACTTGAGATCGTTTTCTCTAA
1 AAACAAATGTTG-TCTCACTTGA-AACAATTTCTCTAA
* * * **
2589331 AAATAATTTTTGTCTCGTTTGAAACAATTTCTCTAA
1 AAACAAATGTTGTCTCACTTGAAACAATTTCTCTAA
*
2589367 AAACAAATGTTGTCTCACTTGAGACAATTT
1 AAACAAATGTTGTCTCACTTGAAACAATTT
2589397 TCCAAATTAT
Statistics
Matches: 51, Mismatches: 14, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
36 35 0.69
37 13 0.25
38 3 0.06
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.38
Consensus pattern (36 bp):
AAACAAATGTTGTCTCACTTGAAACAATTTCTCTAA
Found at i:2589759 original size:30 final size:30
Alignment explanation
Indices: 2589706--2589779 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
2589696 TTTTGACTCA
* * *
2589706 TTTCTTTTGAAACACCTATCTTTGAGTTAG
1 TTTCTATTGAAACACCTACCTTTGAGATAG
* *
2589736 TTTCTCTTGAAACACAC-ACCTTTGAGATCG
1 TTTCTATTGAAACAC-CTACCTTTGAGATAG
*
2589766 TTTCTATTAAAACA
1 TTTCTATTGAAACA
2589780 AATTTTGTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
30 36 0.97
31 1 0.03
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (30 bp):
TTTCTATTGAAACACCTACCTTTGAGATAG
Found at i:2589827 original size:96 final size:97
Alignment explanation
Indices: 2589723--2589910 Score: 231
Period size: 96 Copynumber: 1.9 Consensus size: 97
2589713 TGAAACACCT
* *
2589723 ATCTTTGAGTTAGTTTCTCTTGAAAC-ACACACCTTTGAGATC-GTTTCTATT-AAAAC-AAATT
1 ATCTTTGAGTT-GTTTCTCTTGAAACAAAAAACCTTTGAG-TCGGTTTCT-TTGAAAACAAAATT
*
2589784 TTGTCTCCCTAGAGACAGTTTCTCTTGAAAAAAAA
63 TTGTCTCCCTAGAGACAGTTTCCCTTGAAAAAAAA
* * *
2589819 ATCTTTGAGTTGTTTCTTTTGAAACAAAAAATCTTTGAGTCGGTTTCTTTGGAAACAAAATTTTG
1 ATCTTTGAGTTGTTTCTCTTGAAACAAAAAACCTTTGAGTCGGTTTCTTTGAAAACAAAATTTTG
** * *
2589884 TCTCTTTTGAGACATTTTCCCTTGAAA
66 TCTCCCTAGAGACAGTTTCCCTTGAAA
2589911 CCATAATCAC
Statistics
Matches: 78, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
95 17 0.22
96 31 0.40
97 30 0.38
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (97 bp):
ATCTTTGAGTTGTTTCTCTTGAAACAAAAAACCTTTGAGTCGGTTTCTTTGAAAACAAAATTTTG
TCTCCCTAGAGACAGTTTCCCTTGAAAAAAAA
Found at i:2589850 original size:30 final size:31
Alignment explanation
Indices: 2589801--2589878 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
2589791 CCTAGAGACA
* *
2589801 GTTTCTCTTGAAA-AAAAAATCTTTGAGT-T
1 GTTTCTTTTGAAACAAAAAATCTTTGAGTCG
2589830 GTTTCTTTTGAAACAAAAAATCTTTGAGTCG
1 GTTTCTTTTGAAACAAAAAATCTTTGAGTCG
*
2589861 GTTTCTTTGGAAACAAAA
1 GTTTCTTTTGAAACAAAA
2589879 TTTTGTCTCT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 12 0.27
30 15 0.34
31 17 0.39
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (31 bp):
GTTTCTTTTGAAACAAAAAATCTTTGAGTCG
Found at i:2590258 original size:40 final size:40
Alignment explanation
Indices: 2590203--2590298 Score: 138
Period size: 40 Copynumber: 2.4 Consensus size: 40
2590193 AGATGGCCAT
*
2590203 AACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAG
1 AACTCTTCATCACGTATGAGCAGTGTCATCCCCCGACCAG
* *
2590243 AACTCTTCATTACGTATGAGCAGTGTCATCCCTCGACCAG
1 AACTCTTCATCACGTATGAGCAGTGTCATCCCCCGACCAG
** *
2590283 ATTTCCTCATCACGTA
1 AACTCTTCATCACGTA
2590299 GGAACCGAGT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (40 bp):
AACTCTTCATCACGTATGAGCAGTGTCATCCCCCGACCAG
Found at i:2590269 original size:134 final size:135
Alignment explanation
Indices: 2589940--2590270 Score: 452
Period size: 135 Copynumber: 2.5 Consensus size: 135
2589930 CTAGTCGTCC
* * * * *
2589940 TCATCACGTAAGAACCGTGTCATCCCCTGACCAGACCTCCTCATTATGTAGGAGCAGTGTCACAC
1 TCATCACGTATGAGCCGTGTCATCCCCTGACCAGAACTCTTCATTACGTAGGAGCAGTGTCACAC
**
2590005 CTAGATAACCAACCGTCCTCATCGCGTAGGAACCGTGTTATCACCCTTCCTAAAGATGGCCAAGA
66 CTAGATAACCAACCGTCCTCATAACGTAGGAACCGTGTTATCACCCTTCCTAAAGATGGCCAAGA
2590070 ACTCT
131 ACTCT
* * * * * *
2590075 TCATCACGTATGAGCAGTGTCATTCCTTGACCAGATCTCTTCATCACGTAGGAGCCGTGTCA-AC
1 TCATCACGTATGAGCCGTGTCATCCCCTGACCAGAACTCTTCATTACGTAGGAGCAGTGTCACAC
* * *
2590139 CATAGATAACCAGA-TGTCTTCATAACGTAGGAACCGTGTTATCGCCCTTCCTAAAGATGGCC-A
66 C-TAGATAACCA-ACCGTCCTCATAACGTAGGAACCGTGTTATCACCCTTCCTAAAGATGGCCAA
*
2590202 TAACTCT
129 GAACTCT
* *
2590209 TCATCACGTATGAGCCGTGTCATCCCCCGACCAGAACTCTTCATTACGTATGAGCAGTGTCA
1 TCATCACGTATGAGCCGTGTCATCCCCTGACCAGAACTCTTCATTACGTAGGAGCAGTGTCA
2590271 TCCCTCGACC
Statistics
Matches: 170, Mismatches: 24, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
134 64 0.38
135 105 0.62
136 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (135 bp):
TCATCACGTATGAGCCGTGTCATCCCCTGACCAGAACTCTTCATTACGTAGGAGCAGTGTCACAC
CTAGATAACCAACCGTCCTCATAACGTAGGAACCGTGTTATCACCCTTCCTAAAGATGGCCAAGA
ACTCT
Found at i:2592557 original size:30 final size:30
Alignment explanation
Indices: 2592522--2592617 Score: 94
Period size: 29 Copynumber: 3.3 Consensus size: 30
2592512 TTTGTTTCAG
2592522 TTTAGTCCTATAAATTCATGTTTATGCTAT
1 TTTAGTCCTATAAATTCATGTTTATGCTAT
* *
2592552 TTTAGTCCTTTAACTTTC-TGTTT-TGCTAT
1 TTTAGTCCTATAA-ATTCATGTTTATGCTAT
* *
2592581 TTTAG-CCATGTAAGTTCATGTTTTAT-C-AT
1 TTTAGTCC-TATAAATTCATG-TTTATGCTAT
2592610 TTTAGTCC
1 TTTAGTCC
2592618 CCGAAATTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
28 5 0.09
29 24 0.43
30 23 0.41
31 4 0.07
ACGTcount: A:0.21, C:0.16, G:0.11, T:0.52
Consensus pattern (30 bp):
TTTAGTCCTATAAATTCATGTTTATGCTAT
Found at i:2597963 original size:32 final size:31
Alignment explanation
Indices: 2597917--2597995 Score: 117
Period size: 32 Copynumber: 2.6 Consensus size: 31
2597907 CAGGGGTGAG
* *
2597917 ATTGGTCGCTATGCAGTCGGGGCGAAGCAGGT
1 ATTGGTCGCCATGCAGTCGGGGCGAAG-AAGT
2597949 ATTGGTCGCCATGCAGTCGGGGCGAAGAAGT
1 ATTGGTCGCCATGCAGTCGGGGCGAAGAAGT
2597980 A--GGTCGCCATGCAGTC
1 ATTGGTCGCCATGCAGTC
2597996 TGTTGAAGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
29 15 0.33
31 4 0.09
32 26 0.58
ACGTcount: A:0.20, C:0.22, G:0.38, T:0.20
Consensus pattern (31 bp):
ATTGGTCGCCATGCAGTCGGGGCGAAGAAGT
Found at i:2598247 original size:27 final size:29
Alignment explanation
Indices: 2598191--2598260 Score: 117
Period size: 27 Copynumber: 2.4 Consensus size: 29
2598181 ATTTTAACCC
2598191 ATTATATTAAAGTTGTGTGGTTGTAAGAGT
1 ATTATATTAAAG-TGTGTGGTTGTAAGAGT
2598221 ATTATATTAAAGTG-G-GGTTGTAAGAGT
1 ATTATATTAAAGTGTGTGGTTGTAAGAGT
2598248 ATTATATTAAAGT
1 ATTATATTAAAGT
2598261 ATAAAATATT
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
27 25 0.62
28 1 0.03
29 2 0.05
30 12 0.30
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.41
Consensus pattern (29 bp):
ATTATATTAAAGTGTGTGGTTGTAAGAGT
Found at i:2598531 original size:13 final size:14
Alignment explanation
Indices: 2598513--2598544 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2598503 TATTTATAAA
2598513 AAAATAATATT-TT
1 AAAATAATATTATT
2598526 AAAAT-ATATTATT
1 AAAATAATATTATT
2598539 AAAATA
1 AAAATA
2598545 CAATATACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAATAATATTATT
Found at i:2599078 original size:275 final size:271
Alignment explanation
Indices: 2598573--2599157 Score: 856
Period size: 275 Copynumber: 2.1 Consensus size: 271
2598563 TATAAGTAAC
* * *
2598573 TATTGATTTTACGAACCCTAAACCCTAAAATATTTTGGTTATTGCTGAAAACCTTTATAAATTCA
1 TATTGATTTTATGAACCCTAAACCCTAAAATATTTTAGTTATTGCTGAAAACCTATATAAATTCA
*
2598638 TGGTATGTTGAGGGAAATGAAAGTGGTAGAGGATGGTGATATCTACCATGATGGTGGTTACAAAT
66 TGGTATGTTGAGGGAAATGAAAGGGGTAGAGGATGGTGATATCTACCATGATGGTGGTTACAAAT
* *
2598703 TTGTTTTTTATAAGAAGAAATTGTTTGGATGGAGAATTGTTAGGGTTCAGGGTTTAAAGTCCAGA
131 TTGTTTTTTATAAGAAGAAATTGATTGGAGGGAGAA---TTA-GGTTCAGGGTTTAAAGTCCAGA
* *
2598768 GTTTAGAGTTTTAGCAACAACCAAAATATTTTAGGGTTTAGGGTTCACAAAATCAATAGTTACTT
192 GTTTAGAGTTTTAGCAACAACCAAAATATTTTAGGGTTTAGAGTGCACAAAATCAATAGTTACTT
2598833 ATATTATTTGTTGTA
257 ATATTATTTGTTGTA
* * *
2598848 TATTGATTTTGTGAACCCTAAACCCTAAAATATTTTAGTTGTTGCTGAGAACCTATATAAATTCA
1 TATTGATTTTATGAACCCTAAACCCTAAAATATTTTAGTTATTGCTGAAAACCTATATAAATTCA
*
2598913 TGGTATGTTGAGGGCAATGAAAGGGGTAGAGGATGGTGATATCTACCATGATGGTGGTTACAAAT
66 TGGTATGTTGAGGGAAATGAAAGGGGTAGAGGATGGTGATATCTACCATGATGGTGGTTACAAAT
** *
2598978 TTG-TTTTTATAAGAAGAAATTGATTGGAGGGAGAA-T-GG-TCAGGGTTTAAAGTTTAGGGTTT
131 TTGTTTTTTATAAGAAGAAATTGATTGGAGGGAGAATTAGGTTCAGGGTTTAAAGTCCAGAGTTT
*
2599039 AGGGTTTTTAGCAACAACCAAAATATTTTAGGGTTTAGGGTTTATAGTGCACAAAATCAATAGTT
196 AGAG-TTTTAGCAACAACCAAAATATTTTAGGGTTTA--G-----AGTGCACAAAATCAATAGTT
*
2599104 ACTTATATTATTTGTTGTG
253 ACTTATATTATTTGTTGTA
* *
2599123 TACTGATTTTATGAACCTTAAACCCT-AAATATTTT
1 TATTGATTTTATGAACCCTAAACCCTAAAATATTTT
2599158 TGGTTGTTAC
Statistics
Matches: 282, Mismatches: 20, Indels: 17
0.88 0.06 0.05
Matches are distributed among these distances:
267 23 0.08
268 34 0.12
270 2 0.01
274 39 0.14
275 184 0.65
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.37
Consensus pattern (271 bp):
TATTGATTTTATGAACCCTAAACCCTAAAATATTTTAGTTATTGCTGAAAACCTATATAAATTCA
TGGTATGTTGAGGGAAATGAAAGGGGTAGAGGATGGTGATATCTACCATGATGGTGGTTACAAAT
TTGTTTTTTATAAGAAGAAATTGATTGGAGGGAGAATTAGGTTCAGGGTTTAAAGTCCAGAGTTT
AGAGTTTTAGCAACAACCAAAATATTTTAGGGTTTAGAGTGCACAAAATCAATAGTTACTTATAT
TATTTGTTGTA
Found at i:2599264 original size:55 final size:56
Alignment explanation
Indices: 2599198--2599310 Score: 201
Period size: 56 Copynumber: 2.0 Consensus size: 56
2599188 CAATTTCTTC
*
2599198 TTGTAAAAAC-AATATGTAACCACCATCATGGTAGATATCACCATCCTCTACCTCT
1 TTGTAAAAACAAATATGTAACCACCATCATGGTAGATATCACCATCCTCTACCCCT
*
2599253 TTGTAAAAACAAATTTGTAACCACCATCATGGTAGATATCACCATCCTCTACCCCT
1 TTGTAAAAACAAATATGTAACCACCATCATGGTAGATATCACCATCCTCTACCCCT
2599309 TT
1 TT
2599311 CATTGCTCTC
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
55 10 0.18
56 45 0.82
ACGTcount: A:0.34, C:0.27, G:0.09, T:0.30
Consensus pattern (56 bp):
TTGTAAAAACAAATATGTAACCACCATCATGGTAGATATCACCATCCTCTACCCCT
Found at i:2600025 original size:27 final size:29
Alignment explanation
Indices: 2599994--2600063 Score: 108
Period size: 27 Copynumber: 2.4 Consensus size: 29
2599984 ATATTTATAT
*
2599994 ACTTTAATATAATACTCTTACAACC-C-C
1 ACTTTAATATAATACTCTTACAACCACAA
2600021 ACTTTAATATAATACTCTTACAACCACATA
1 ACTTTAATATAATACTCTTACAACCACA-A
2600051 ACTTTAATATAAT
1 ACTTTAATATAAT
2600064 GGGTTAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 25 0.64
28 1 0.03
30 13 0.33
ACGTcount: A:0.41, C:0.23, G:0.00, T:0.36
Consensus pattern (29 bp):
ACTTTAATATAATACTCTTACAACCACAA
Found at i:2600292 original size:29 final size:31
Alignment explanation
Indices: 2600259--2600335 Score: 104
Period size: 32 Copynumber: 2.5 Consensus size: 31
2600249 ACCTTCAACA
* *
2600259 GACTGAATGGCGACC-TAC-TTCTTCGCCCC
1 GACTGCATGGCGACCATACATGCTTCGCCCC
*
2600288 GACTGCATGACGACCAATACATGCTTCGCCCC
1 GACTGCATGGCGACC-ATACATGCTTCGCCCC
2600320 GACTGCATGGCGACCA
1 GACTGCATGGCGACCA
2600336 ATCTCACCCC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 13 0.32
31 4 0.10
32 24 0.59
ACGTcount: A:0.22, C:0.36, G:0.22, T:0.19
Consensus pattern (31 bp):
GACTGCATGGCGACCATACATGCTTCGCCCC
Found at i:2603966 original size:14 final size:14
Alignment explanation
Indices: 2603949--2603980 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
2603939 TTTGTGAAAA
2603949 TCAATTTGAAATTT
1 TCAATTTGAAATTT
2603963 TCAATTTGAAATTT
1 TCAATTTGAAATTT
2603977 TCAA
1 TCAA
2603981 CTTATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (14 bp):
TCAATTTGAAATTT
Found at i:2605280 original size:22 final size:22
Alignment explanation
Indices: 2605254--2605297 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2605244 TTTTTCCTCT
*
2605254 TTTAAGTTCTTCTGTTTTGGAA
1 TTTAAGTTCTTCTATTTTGGAA
* *
2605276 TTTAATTTTTTCTATTTTGGAA
1 TTTAAGTTCTTCTATTTTGGAA
2605298 GTTGAACTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.20, C:0.07, G:0.14, T:0.59
Consensus pattern (22 bp):
TTTAAGTTCTTCTATTTTGGAA
Found at i:2606466 original size:181 final size:183
Alignment explanation
Indices: 2606132--2606491 Score: 661
Period size: 181 Copynumber: 2.0 Consensus size: 183
2606122 AGCTTCAAGT
2606132 AGCAACTTTTCATGTGAATTTTGCTTCAGGGAATCATTCGTTGAGTTGAAGTTTTCATTGCTTTT
1 AGCAACTTTTCATGTGAATTTTGCTTCAGGGAATCATTCGTTGAGTTGAAGTTTTCATTGCTTTT
2606197 TTGAGTTCTGATATATTTTATTAGCATTACATGTGTGGTGACCTACGTGAACATGCTATTTCAGA
66 TTGAGTTCTGA-ATATTTTATTAGCATTACATGTGTGGTGACCTACGTGAACATGCTATTTCAGA
2606262 TGATAAAAGAACTCAAACTTGCACGGATGTCAGTGAGGCAACCCGGCATCTTGA
130 TGATAAAAGAACTCAAACTTGCACGGATGTCAGTGAGGCAACCCGGCATCTTGA
*
2606316 AGCAACTTTTCATGTGAATTTTGCTTCAGGGCATCATTCGTTGAGTTGAAGTTTTCATTGC-TTT
1 AGCAACTTTTCATGTGAATTTTGCTTCAGGGAATCATTCGTTGAGTTGAAGTTTTCATTGCTTTT
*
2606380 TTGAGTTCTG-ATATTTTATTAGCATTACATGTGTGTTGACCTACGTGAACATGCTATTTCAGAT
66 TTGAGTTCTGAATATTTTATTAGCATTACATGTGTGGTGACCTACGTGAACATGCTATTTCAGAT
* *
2606444 GATAAAAGTACTCAACCTTGCACGGATGTCAGTGAGGCAACCCGGCAT
131 GATAAAAGAACTCAAACTTGCACGGATGTCAGTGAGGCAACCCGGCAT
2606492 GGTTTAGAAT
Statistics
Matches: 172, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
181 99 0.58
183 13 0.08
184 60 0.35
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (183 bp):
AGCAACTTTTCATGTGAATTTTGCTTCAGGGAATCATTCGTTGAGTTGAAGTTTTCATTGCTTTT
TTGAGTTCTGAATATTTTATTAGCATTACATGTGTGGTGACCTACGTGAACATGCTATTTCAGAT
GATAAAAGAACTCAAACTTGCACGGATGTCAGTGAGGCAACCCGGCATCTTGA
Found at i:2607041 original size:19 final size:18
Alignment explanation
Indices: 2606979--2607042 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 18
2606969 TATTAATAGA
2606979 ATTATAAAAATATT-TTAAT
1 ATTATAAAAATATTATT--T
*
2606998 ATTTTAAAAATATAATATTT
1 ATTATAAAAATAT--TATTT
*
2607018 TTTATAAATAATATTATTT
1 ATTATAAA-AATATTATTT
2607037 ATTATA
1 ATTATA
2607043 TTTAATATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 22 0.59
20 7 0.19
21 6 0.16
22 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTATAAAAATATTATTT
Found at i:2607064 original size:16 final size:16
Alignment explanation
Indices: 2606994--2607064 Score: 54
Period size: 16 Copynumber: 4.2 Consensus size: 16
2606984 AAAAATATTT
*
2606994 TAATA-TTTTAAAAATA
1 TAATATTTTTAATAA-A
*
2607010 TAATATTTTTTATAAA
1 TAATATTTTTAATAAA
**
2607026 TAATATTATTTATTATATT
1 TAATATT-TTTA--ATAAA
*
2607045 TAATATTTGTAATAAA
1 TAATATTTTTAATAAA
2607061 TAAT
1 TAAT
2607065 TAAAAAAATT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
16 20 0.47
17 10 0.23
18 3 0.07
19 10 0.23
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (16 bp):
TAATATTTTTAATAAA
Found at i:2607771 original size:58 final size:58
Alignment explanation
Indices: 2607665--2607775 Score: 136
Period size: 58 Copynumber: 1.9 Consensus size: 58
2607655 TATAATATTG
* * * **
2607665 ATTCTAAATTGATCCTTAAATTTTTTAATATTTCAATTTTATCCCTAAATTATGACTC
1 ATTCTAAATTGATCCTTAAACTTTTGAAGATTTCAATTCCATCCCTAAATTATGACTC
*
2607723 ATTCTAAATT-AGTCCTTAAACTTTTGAAGA-TTCTAATTCCATCTCTAAATTAT
1 ATTCTAAATTGA-TCCTTAAACTTTTGAAGATTTC-AATTCCATCCCTAAATTAT
2607776 AACACCCTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
57 4 0.09
58 41 0.91
ACGTcount: A:0.33, C:0.16, G:0.05, T:0.46
Consensus pattern (58 bp):
ATTCTAAATTGATCCTTAAACTTTTGAAGATTTCAATTCCATCCCTAAATTATGACTC
Found at i:2608431 original size:97 final size:97
Alignment explanation
Indices: 2608319--2608512 Score: 291
Period size: 97 Copynumber: 2.0 Consensus size: 97
2608309 TCAGATATAA
** *
2608319 ATTTGATTTAAAAAATTGACTGGTCCTATATAAACCTAATTTAATTATGTTCAAATCAACAATGA
1 ATTTGATTTAAAAAATTGACTAATCCGATATAAACCTAATTTAATTATGTTCAAATCAACAATGA
* *
2608384 ACCAATTTAATGCTCGATTCAACCTGACTTAT
66 ACCAATTTAATACTCAATTCAACCTGACTTAT
* * *
2608416 ATTTGAATTT-AAAAATTGACTAATCCGATATAGACCTAGTTTAATTATGTTCAAATCGACAATG
1 ATTTG-ATTTAAAAAATTGACTAATCCGATATAAACCTAATTTAATTATGTTCAAATCAACAATG
*
2608480 AACCAATTTAATACTTAATTCAACCTGACTTAT
65 AACCAATTTAATACTCAATTCAACCTGACTTAT
2608513 CATAGATTTG
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
97 83 0.95
98 4 0.05
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (97 bp):
ATTTGATTTAAAAAATTGACTAATCCGATATAAACCTAATTTAATTATGTTCAAATCAACAATGA
ACCAATTTAATACTCAATTCAACCTGACTTAT
Found at i:2610518 original size:15 final size:15
Alignment explanation
Indices: 2610500--2610554 Score: 74
Period size: 15 Copynumber: 3.6 Consensus size: 15
2610490 TAACCGGTTT
2610500 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
2610515 CGGTTTTTTAAAAAAC
1 CGG-TTTTAAAAAAAC
*
2610531 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
2610546 CGATTTTAA
1 CGGTTTTAA
2610555 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
15 20 0.59
16 14 0.41
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.31
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:2610527 original size:16 final size:16
Alignment explanation
Indices: 2610503--2610552 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
2610493 CCGGTTTCGG
2610503 TTTTAAAAAAACCGGT
1 TTTTAAAAAAACCGGT
*
2610519 TTTTTAAAAAACCGG-
1 TTTTAAAAAAACCGGT
* *
2610534 TTATAAAAAAACCGAT
1 TTTTAAAAAAACCGGT
2610550 TTT
1 TTT
2610553 AATATTCCAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (16 bp):
TTTTAAAAAAACCGGT
Found at i:2610973 original size:13 final size:13
Alignment explanation
Indices: 2610952--2610981 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2610942 AAGTTCGATA
*
2610952 AATTTAAATACTT
1 AATTGAAATACTT
2610965 AATTGAAATACTT
1 AATTGAAATACTT
2610978 AATT
1 AATT
2610982 AACTCAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:2611088 original size:32 final size:33
Alignment explanation
Indices: 2610992--2611090 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
2610982 AACTCAACAT
* * *
2610992 AATTAAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
2611025 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
2611058 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
2611090 A
1 A
2611091 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:2611109 original size:21 final size:21
Alignment explanation
Indices: 2611085--2611124 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2611075 ACTTCAAGTT
2611085 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
2611106 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
2611125 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Done.