Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000018.1 Hibiscus syriacus cultivar Beakdansim tig00000034_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: 70004
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4052 original size:20 final size:20
Alignment explanation
Indices: 4024--4069 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
4014 GGTGGAAGCT
*
4024 TTTGAAGAAAATTGAAAATA
1 TTTGCAGAAAATTGAAAATA
4044 TTTGCAGAAAATTGAAAATA
1 TTTGCAGAAAATTGAAAATA
4064 TTTGCA
1 TTTGCA
4070 CAACGATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.48, C:0.04, G:0.15, T:0.33
Consensus pattern (20 bp):
TTTGCAGAAAATTGAAAATA
Found at i:4785 original size:22 final size:22
Alignment explanation
Indices: 4728--4785 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 22
4718 AATTAACATA
4728 AGGGGTATCGGTACCTTTGGGAT
1 AGGGGTATC-GTACCTTTGGGAT
*
4751 A--GGTATCGATACCTTT-GTAT
1 AGGGGTATCG-TACCTTTGGGAT
4771 AGGGGTATCAGTACC
1 AGGGGTATC-GTACC
4786 CTATGGGGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
20 5 0.17
21 13 0.43
22 10 0.33
23 2 0.07
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.31
Consensus pattern (22 bp):
AGGGGTATCGTACCTTTGGGAT
Found at i:24856 original size:15 final size:15
Alignment explanation
Indices: 24826--24917 Score: 57
Period size: 15 Copynumber: 6.1 Consensus size: 15
24816 TTAAAAATGT
*
24826 TTTATGAAAAAT-AA
1 TTTATGTAAAATGAA
24840 TTTATGTAAAATGAA
1 TTTATGTAAAATGAA
* * *
24855 -TTATTTGAAAATTAT
1 TTTATGT-AAAATGAA
*
24870 TTTACGTAAAATGAA
1 TTTATGTAAAATGAA
* *
24885 TTATAT-AAAAATTG-T
1 TT-TATGTAAAA-TGAA
24900 TTTATGTAAAAATGAA
1 TTTATGT-AAAATGAA
24916 TT
1 TT
24918 ATATTTTTTA
Statistics
Matches: 57, Mismatches: 13, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
14 19 0.33
15 24 0.42
16 14 0.25
ACGTcount: A:0.47, C:0.01, G:0.10, T:0.42
Consensus pattern (15 bp):
TTTATGTAAAATGAA
Found at i:24879 original size:30 final size:30
Alignment explanation
Indices: 24828--24921 Score: 125
Period size: 30 Copynumber: 3.1 Consensus size: 30
24818 AAAAATGTTT
* *
24828 TATGAAAAATAATTTATGTAAAATGAATTA
1 TATGAAAATTATTTTATGTAAAATGAATTA
* *
24858 TTTGAAAATTATTTTACGTAAAATGAATTA
1 TATGAAAATTATTTTATGTAAAATGAATTA
* *
24888 TATAAAAATTGTTTTATGTAAAAATGAATTA
1 TATGAAAATTATTTTATGT-AAAATGAATTA
24919 TAT
1 TAT
24922 TTTTTAAAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 41 0.75
31 14 0.25
ACGTcount: A:0.48, C:0.01, G:0.10, T:0.41
Consensus pattern (30 bp):
TATGAAAATTATTTTATGTAAAATGAATTA
Found at i:24919 original size:15 final size:15
Alignment explanation
Indices: 24817--24919 Score: 61
Period size: 14 Copynumber: 6.9 Consensus size: 15
24807 ATAATTACTT
**
24817 TAAAAATGTTTTATG
1 TAAAAATGAATTATG
24832 -AAAAAT-AATTTATG
1 TAAAAATGAA-TTATG
*
24846 T-AAAATGAATTATT
1 TAAAAATGAATTATG
* * * *
24860 TGAAAATTATTTTACG
1 TAAAAATGA-ATTATG
*
24876 T-AAAATGAATTATA
1 TAAAAATGAATTATG
**
24890 TAAAAATTGTTTTATG
1 TAAAAA-TGAATTATG
24906 TAAAAATGAATTAT
1 TAAAAATGAATTAT
24920 ATTTTTTAAA
Statistics
Matches: 65, Mismatches: 16, Indels: 14
0.68 0.17 0.15
Matches are distributed among these distances:
14 25 0.38
15 24 0.37
16 16 0.25
ACGTcount: A:0.48, C:0.01, G:0.10, T:0.42
Consensus pattern (15 bp):
TAAAAATGAATTATG
Found at i:25225 original size:19 final size:19
Alignment explanation
Indices: 25203--25246 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
25193 TTTATTAACA
*
25203 TAATACTAAAATAT-TATAT
1 TAATA-TAAAATATATAGAT
*
25222 TAATATTAAATATATAGAT
1 TAATATAAAATATATAGAT
25241 TAATAT
1 TAATAT
25247 TAATCATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
TAATATAAAATATATAGAT
Found at i:25247 original size:19 final size:18
Alignment explanation
Indices: 25211--25249 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
25201 CATAATACTA
*
25211 AAATATTATATTAATATT
1 AAATATTAGATTAATATT
25229 AAATATATAGATTAATATT
1 AAATAT-TAGATTAATATT
25248 AA
1 AA
25250 TCATTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
AAATATTAGATTAATATT
Found at i:25270 original size:54 final size:52
Alignment explanation
Indices: 25212--25345 Score: 146
Period size: 54 Copynumber: 2.5 Consensus size: 52
25202 ATAATACTAA
*
25212 AATATTATATTAATATTAAATATATAGATTAATATTAATCATTATTAATAATTT
1 AATATTATATTAATATTAAAAATATAGA-TAATATTAATCATT-TTAATAATTT
** * *
25266 AATATTATTATTTTTA-TAAAAATAATAGATAATATTAATTATTTTAGTAATTT
1 AATATTA-TATTAATATTAAAAAT-ATAGATAATATTAATCATTTTAATAATTT
*
25319 ATTATATTTTATTAA-ATTAAAAATATA
1 A--ATATTATATTAATATTAAAAATATA
25346 ACATGATACA
Statistics
Matches: 67, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
53 14 0.21
54 37 0.55
55 16 0.24
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (52 bp):
AATATTATATTAATATTAAAAATATAGATAATATTAATCATTTTAATAATTT
Found at i:25906 original size:20 final size:20
Alignment explanation
Indices: 25812--26180 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
25802 GATTTTCCAT
* ** *
25812 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
25832 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
25852 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
25872 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
25892 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
25912 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
25932 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
25952 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
25972 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
25992 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
26012 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
26032 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
26052 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
*
26072 AATCGCAACGCATATCCGTA
1 AATCGCAACGCGTATCCGTA
*
26092 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
26112 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
26132 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
26152 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
26172 AATCACAAC
1 AATCGCAAC
26181 ACTGAAATTT
Statistics
Matches: 307, Mismatches: 34, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
19 4 0.01
20 299 0.97
21 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:26905 original size:24 final size:24
Alignment explanation
Indices: 26866--26912 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
26856 AAATTTGGTC
26866 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
26890 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
26913 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:27104 original size:12 final size:12
Alignment explanation
Indices: 27087--27111 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27077 ATATAATCCT
27087 GAAGAAGAAAAA
1 GAAGAAGAAAAA
27099 GAAGAAGAAAAA
1 GAAGAAGAAAAA
27111 G
1 G
27112 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:29408 original size:19 final size:19
Alignment explanation
Indices: 29386--29673 Score: 329
Period size: 19 Copynumber: 16.4 Consensus size: 19
29376 CGGAAAATAC
*
29386 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
29405 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
29419 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
29439 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
29453 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
29472 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
29491 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
29505 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
29524 AAACGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
29543 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
29557 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
29576 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
29595 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
29614 AATCGCAA--CG-AA-G-G
1 AATCGCAATGCGAAATGAA
29628 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
29647 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
29666 AATCGCAA
1 AATCGCAA
29674 CGAGATAATC
Statistics
Matches: 231, Mismatches: 12, Indels: 52
0.78 0.04 0.18
Matches are distributed among these distances:
14 48 0.21
15 3 0.01
16 14 0.06
17 13 0.06
18 4 0.02
19 136 0.59
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:29473 original size:33 final size:33
Alignment explanation
Indices: 29386--29654 Score: 260
Period size: 33 Copynumber: 7.8 Consensus size: 33
29376 CGGAAAATAC
* *
29386 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
29419 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
29453 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
* * * * *
29491 AATCGCAACGAGAGAATCG-CAATGCGAAATGA-AA
1 AATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGAA
* *
29525 AA-CGCAATGCGAAATGAAAATCGCAACGACAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
29557 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
29595 AATCGCAATGCGAAATGAAAATCGCAACGA-AGG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGA-A
29628 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
29655 TGCGAAATGA
Statistics
Matches: 199, Mismatches: 18, Indels: 38
0.78 0.07 0.15
Matches are distributed among these distances:
31 7 0.04
32 10 0.05
33 85 0.43
34 34 0.17
35 5 0.03
36 3 0.02
37 2 0.01
38 42 0.21
39 6 0.03
40 5 0.03
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:29501 original size:52 final size:52
Alignment explanation
Indices: 29414--29654 Score: 362
Period size: 52 Copynumber: 4.6 Consensus size: 52
29404 AAATCCCAAC
29414 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
29467 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
29519 ATGAAAAACGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* * * *
29571 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAA
*
29621 ACGAAGGAATCGCAATGCGAAATGAAAATCGCAA
1 ATGAA--AATCGCAATGCGAAATGAAAATCGCAA
29655 TGCGAAATGA
Statistics
Matches: 176, Mismatches: 9, Indels: 7
0.92 0.05 0.04
Matches are distributed among these distances:
50 8 0.05
51 6 0.03
52 146 0.83
53 16 0.09
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.13
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:29540 original size:71 final size:69
Alignment explanation
Indices: 29389--29673 Score: 293
Period size: 71 Copynumber: 4.1 Consensus size: 69
29379 AAAATACAAT
* *
29389 CGCAACGCGAAATGAAAATCCCAAC-ATGAA-AATCGCAATGCGGAAATGAAAATCGCAA--CG-
1 CGCAATGCGAAATGAAAATCGCAACGA--AAGAATCGCAA-GC-G-AATGAAAATCGCAATGCGA
* *
29449 -A-GAGAAT
61 AATGAAAAA
*
29456 CGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CG-A-GAGAATCGCAATGCGA
1 CGCAATGCGAAATGAAAATCGCAA--CGAAA-G--AATCGCAAGCGAATGAAAATCGCAATGCGA
29518 AATGAAAAA
61 AATGAAAAA
*
29527 CGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAAT
1 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAA-GCG-AATGAAAATCGCAATGCGAAAT
*
29592 GAAAAT
64 GAAAAA
*
29598 CGCAATGCGAAATGAAAATCGCAACGAAGGAATCGCAATGCGAAATGAAAATCGCAATGCGAAAT
1 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAA-GCG-AATGAAAATCGCAATGCGAAAT
*
29663 GAAAAT
64 GAAAAA
29669 CGCAA
1 CGCAA
29674 CGAGATAATC
Statistics
Matches: 191, Mismatches: 10, Indels: 30
0.83 0.04 0.13
Matches are distributed among these distances:
66 18 0.09
67 23 0.12
68 7 0.04
69 6 0.03
70 4 0.02
71 125 0.65
72 8 0.04
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.13
Consensus pattern (69 bp):
CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAAGCGAATGAAAATCGCAATGCGAAATGA
AAAA
Found at i:29655 original size:52 final size:49
Alignment explanation
Indices: 29386--29695 Score: 298
Period size: 52 Copynumber: 5.9 Consensus size: 49
29376 CGGAAAATAC
*
29386 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGCGAAATG-AAATCGCAAC--GAAAATCGCAATGC-GAAATGAA
* * * *
29439 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGCGA-AAT-GAAAT-CGCAACGAAAATCGCAATGCGAAATGAA
* * * * *
29491 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAAACGCAATGCGAAATGAA
1 AATCGCAACGCGA-AAT-GAAAT-CGCAACGAAAATCGCAATGCGAAATGAA
* * *
29543 AATCGCAACGAC-AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACG-CGA-AAT-GAAAT-CGCAACGAAAATCGCAATGCGAAATGAA
*
29595 AATCGCAATGCGAAATGAAAATCGCAACGAAGGAATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATG-AAATCGCAACGAA--AATCGCAATGCGAAATGAA
*
29647 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 AATCGCAACGCGAAATG-AAATCGCAACGA-A-AATCGCAATGCGAAAT
29696 TATAAACGCA
Statistics
Matches: 235, Mismatches: 13, Indels: 19
0.88 0.05 0.07
Matches are distributed among these distances:
50 8 0.03
51 7 0.03
52 183 0.78
53 27 0.11
54 6 0.03
55 4 0.02
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (49 bp):
AATCGCAACGCGAAATGAAATCGCAACGAAAATCGCAATGCGAAATGAA
Found at i:29811 original size:19 final size:19
Alignment explanation
Indices: 29702--29803 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
29692 AAATTATAAA
29702 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
29721 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
29741 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
*
29757 CG--TTGTGATTTTCATTT
1 CGCATTGCGATTTTCATTT
29774 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
29793 CGCATTGCGAT
1 CGCATTGCGAT
29804 AGTCATTTTT
Statistics
Matches: 73, Mismatches: 4, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
14 5 0.07
16 7 0.10
17 7 0.10
19 35 0.48
20 19 0.26
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:29929 original size:14 final size:14
Alignment explanation
Indices: 29910--29946 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
29900 CATCAATTAC
29910 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
29924 ACAAATCATCTTTT
1 ACAAATCAACTTTT
29938 ACAAATCAA
1 ACAAATCAA
29947 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:31951 original size:32 final size:33
Alignment explanation
Indices: 31897--31988 Score: 159
Period size: 32 Copynumber: 2.8 Consensus size: 33
31887 GCGAAACCAA
*
31897 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
31930 AATCGCAATGCG-AATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
31962 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
31989 TGAGATTTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:31960 original size:12 final size:14
Alignment explanation
Indices: 31916--31971 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
31906 GCGAAATGAA
*
31916 AATCGCAACGACAG
1 AATCGCAACGAAAG
*
31930 AATCGCAATGCGAATGAA
1 AATCGCAA--CGAA--AG
31948 AATCGCAACGAAAG
1 AATCGCAACGAAAG
31962 AATCGCAACG
1 AATCGCAACG
31972 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 19 0.54
16 7 0.20
18 9 0.26
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:31986 original size:19 final size:19
Alignment explanation
Indices: 31860--31988 Score: 118
Period size: 19 Copynumber: 7.3 Consensus size: 19
31850 TAGTTTACTT
* *
31860 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
31880 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
31899 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
31918 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
31932 TCGCAATGCG-AATGAAAA
1 TCGCAACGCGAAATGAAAA
31950 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
31964 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
31983 TCGCAA
1 TCGCAA
31989 TGAGATTTTG
Statistics
Matches: 91, Mismatches: 7, Indels: 23
0.75 0.06 0.19
Matches are distributed among these distances:
14 16 0.18
15 1 0.01
16 12 0.13
17 7 0.08
18 8 0.09
19 35 0.38
20 12 0.13
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:32034 original size:33 final size:33
Alignment explanation
Indices: 31992--32080 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
31982 ATCGCAATGA
31992 GATTTTGGTTTCGCGTTGCGA-TCTTGTCGTTGC
1 GATTTTGGTTTCGCGTTGCGATTC-TGTCGTTGC
32025 GATTTTGGTTTCGCGTTGCGATTCTGTCGTTGC
1 GATTTTGGTTTCGCGTTGCGATTCTGTCGTTGC
**
32058 GATTTTCATTTCGCGTTGCGATT
1 GATTTTGGTTTCGCGTTGCGATT
32081 TTGGTTTCGC
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
33 51 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
GATTTTGGTTTCGCGTTGCGATTCTGTCGTTGC
Found at i:32043 original size:19 final size:19
Alignment explanation
Indices: 31992--32117 Score: 119
Period size: 19 Copynumber: 7.1 Consensus size: 19
31982 ATCGCAATGA
31992 GATTTTGGTTTCGCGTTGC
1 GATTTTGGTTTCGCGTTGC
*
32011 GATCTT-G--T--CGTTGC
1 GATTTTGGTTTCGCGTTGC
32025 GATTTTGGTTTCGCGTTGC
1 GATTTTGGTTTCGCGTTGC
*
32044 GATTCT-G--T--CGTTGC
1 GATTTTGGTTTCGCGTTGC
**
32058 GATTTTCATTTCGCGTTGC
1 GATTTTGGTTTCGCGTTGC
32077 GATTTTGGTTTCGCGTTGC
1 GATTTTGGTTTCGCGTTGC
* *
32096 GATTTTAAGTTTCGTGTTGC
1 GATTTT-GGTTTCGCGTTGC
32116 GA
1 GA
32118 AAGTAAACTA
Statistics
Matches: 87, Mismatches: 9, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
14 22 0.25
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 45 0.52
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
GATTTTGGTTTCGCGTTGC
Found at i:32320 original size:93 final size:93
Alignment explanation
Indices: 32161--32817 Score: 1284
Period size: 93 Copynumber: 7.1 Consensus size: 93
32151 TTGAATGGAT
32161 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
32226 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
32254 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
32319 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
32347 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
32411 AG-TTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
32438 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
32503 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
32531 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
32596 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
32624 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
32688 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
32716 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
32781 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
32809 AAATTTACT
1 AAATTTACT
32818 AAGCAATCTA
Statistics
Matches: 560, Mismatches: 1, Indels: 6
0.99 0.00 0.01
Matches are distributed among these distances:
91 64 0.11
92 146 0.26
93 350 0.62
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:32593 original size:185 final size:186
Alignment explanation
Indices: 32161--32817 Score: 1284
Period size: 185 Copynumber: 3.5 Consensus size: 186
32151 TTGAATGGAT
32161 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
32226 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
32291 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
32347 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
32411 AG-TTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
32475 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
32531 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
32596 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
32661 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
32716 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
32781 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
32818 AAGCAATCTA
Statistics
Matches: 468, Mismatches: 1, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
184 157 0.34
185 208 0.44
186 103 0.22
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:32655 original size:277 final size:278
Alignment explanation
Indices: 32161--32817 Score: 1298
Period size: 277 Copynumber: 2.4 Consensus size: 278
32151 TTGAATGGAT
32161 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
32226 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
32291 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
32356 TTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAG-TTAGCAG
196 TTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
32420 AATTGGCAGCAACCGAAC
261 AATTGGCAGCAACCGAAC
32438 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
32503 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
32568 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
32633 TTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
196 TTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
32698 AATTGGCAGCAACCGAAC
261 AATTGGCAGCAACCGAAC
32716 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
32781 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
32818 AAGCAATCTA
Statistics
Matches: 378, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
277 252 0.67
278 126 0.33
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (278 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
TTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
AATTGGCAGCAACCGAAC
Found at i:34543 original size:14 final size:14
Alignment explanation
Indices: 34524--34613 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
34514 TTGAAATGAA
34524 AATCGCAACGAGAG
1 AATCGCAACGAGAG
34538 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
34555 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
34571 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
34590 AATCGCAACGAGAG
1 AATCGCAACGAGAG
34604 AATCGCAACG
1 AATCGCAACG
34614 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:34561 original size:33 final size:33
Alignment explanation
Indices: 34516--34630 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
34506 TCTTTTGGTT
34516 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
34549 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
34582 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
34615 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
34631 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:34562 original size:19 final size:18
Alignment explanation
Indices: 34523--34635 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
34513 GTTGAAATGA
34523 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
34538 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
34555 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
34571 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
34588 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
34604 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
34621 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
34636 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:34666 original size:14 final size:14
Alignment explanation
Indices: 34647--34701 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
34637 TTTGGTTTCG
34647 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
34661 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
34680 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
34694 CGTTGCGA
1 CGTTGCGA
34702 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:34679 original size:33 final size:33
Alignment explanation
Indices: 34631--34701 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
34621 AAAATCGCAA
**
34631 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
34664 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
34697 TGCGA
1 TGCGA
34702 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:34709 original size:33 final size:33
Alignment explanation
Indices: 34642--34723 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
34632 GCGATTTTGG
***
34642 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
34675 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
34708 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
34724 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:34728 original size:20 final size:20
Alignment explanation
Indices: 34654--34742 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
34644 TCGCGTTGCG
34654 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
34674 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
34687 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
34707 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
34727 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
34743 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:34864 original size:33 final size:33
Alignment explanation
Indices: 34822--34892 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
34812 AATACTAACT
*
34822 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
34855 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
34888 TGAAA
1 TGAAA
34893 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:35125 original size:22 final size:22
Alignment explanation
Indices: 35073--35127 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
35063 TGGTTGTGAG
**
35073 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
35095 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
35117 GGATTTCTTCG
1 GGATTTCTTCG
35128 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:35298 original size:20 final size:20
Alignment explanation
Indices: 35273--35465 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
35263 CTTTAAATAT
35273 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
35293 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
35315 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
35334 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
35354 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
35374 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
35394 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
35414 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
35434 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
35454 CGCGTTGCGATT
1 CGCGTTGCGATT
35466 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:35460 original size:60 final size:60
Alignment explanation
Indices: 35273--35465 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
35263 CTTTAAATAT
**
35273 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
35334 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
35394 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
35454 CGCGTTGCGATT
1 CGCGTTGCGATT
35466 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:35546 original size:20 final size:20
Alignment explanation
Indices: 35521--35572 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
35511 AAGAATCGCG
*
35521 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
35541 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
35561 TTGCGATTCTGG
1 TTGCGATTCTGG
35573 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:35838 original size:15 final size:15
Alignment explanation
Indices: 35815--35846 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
35805 ATAGTAAAAT
*
35815 AAAATAATATTTTTC
1 AAAAAAATATTTTTC
35830 AAAAAAATATTTTTC
1 AAAAAAATATTTTTC
35845 AA
1 AA
35847 TTATTAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAAAAATATTTTTC
Found at i:35886 original size:24 final size:24
Alignment explanation
Indices: 35859--35905 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
35849 ATTAAACACA
35859 CCCTAAGTTTGATTAAATGACTAG
1 CCCTAAGTTTGATTAAATGACTAG
35883 CCCTAAGTTTGATTAAATGACTA
1 CCCTAAGTTTGATTAAATGACTA
35906 ACAACGGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (24 bp):
CCCTAAGTTTGATTAAATGACTAG
Found at i:35931 original size:41 final size:41
Alignment explanation
Indices: 35885--35966 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
35875 ATGACTAGCC
*
35885 CTAAGTTTGATTAAATGACTAACAACGGAGAGAGGTAGAGA
1 CTAAGTTTGATTAAACGACTAACAACGGAGAGAGGTAGAGA
* *
35926 CTAAGTTTGATTAAACGACTAGCGACGGAGAGAGGTAGAGA
1 CTAAGTTTGATTAAACGACTAACAACGGAGAGAGGTAGAGA
35967 ATCGGGGCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.39, C:0.11, G:0.29, T:0.21
Consensus pattern (41 bp):
CTAAGTTTGATTAAACGACTAACAACGGAGAGAGGTAGAGA
Found at i:36107 original size:31 final size:31
Alignment explanation
Indices: 36071--36137 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
36061 TAATTTGTAG
** * *
36071 TCATTTTTGTTTCGTTTTAATTAAGATATGA
1 TCATTTTCATTTCATTTTAATTAAGATATAA
*
36102 TCATTTTCATTTTATTTTAATTAAGATATAA
1 TCATTTTCATTTCATTTTAATTAAGATATAA
36133 TCATT
1 TCATT
36138 GAAACGTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (31 bp):
TCATTTTCATTTCATTTTAATTAAGATATAA
Found at i:38363 original size:18 final size:17
Alignment explanation
Indices: 38328--38367 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
38318 TAACTTAAAT
38328 AAATTAATAATTACAAC
1 AAATTAATAATTACAAC
38345 ATAATTAATAATTTA-AAC
1 A-AATTAATAA-TTACAAC
38363 AAATT
1 AAATT
38368 TTAACATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 5 0.24
18 13 0.62
19 3 0.14
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATTAATAATTACAAC
Found at i:42334 original size:43 final size:43
Alignment explanation
Indices: 42270--42524 Score: 402
Period size: 43 Copynumber: 5.9 Consensus size: 43
42260 ACTGTTACAA
*
42270 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* *
42313 CAGGTCCCTTTGCTGTTTGCAATGGTAAGCCTTACAGTTTCCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* * *
42356 CAAGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
*
42399 CAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
***
42442 CAGGTTTTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* *
42485 CAGGTCCCTTTGTTGTGTACAAGGGTAAGCCTTACAGTTT
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT
42525 GAAAAGTTGT
Statistics
Matches: 193, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 193 1.00
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (43 bp):
CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
Found at i:43514 original size:18 final size:20
Alignment explanation
Indices: 43486--43522 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
43476 TCGAACCAAA
43486 AAAAAACTAATT-AGTATTT
1 AAAAAACTAATTGAGTATTT
43505 AAAAAA-TAATTGAGTATT
1 AAAAAACTAATTGAGTATT
43523 AATAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.35
Consensus pattern (20 bp):
AAAAAACTAATTGAGTATTT
Found at i:48111 original size:59 final size:59
Alignment explanation
Indices: 48003--48118 Score: 153
Period size: 59 Copynumber: 2.0 Consensus size: 59
47993 TTAAATGATC
* * *
48003 ATTTTATAATTTTTAATAACTGGAGGACTCAACAAAATAAAACTCTATAATAAAAAATT
1 ATTTTATAACTTTTAATAACTCGAGGACTCAACAAAATAAAACTATATAATAAAAAATT
* * * *
48062 ATTTTATAACTTTTAATAA-TCGAGATACTCAACAAAATAATAGTATATAATTAAAAA
1 ATTTTATAACTTTTAATAACTCGAG-GACTCAACAAAATAAAACTATATAATAAAAAA
48119 CCATTTCTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
58 4 0.08
59 45 0.92
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.34
Consensus pattern (59 bp):
ATTTTATAACTTTTAATAACTCGAGGACTCAACAAAATAAAACTATATAATAAAAAATT
Found at i:51320 original size:42 final size:42
Alignment explanation
Indices: 51261--51345 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
51251 CTGGCAATCC
*
51261 CTGTATTAATACCATTTTATGTATTTTAATATGTCAACAATT
1 CTGTATTAATACCATTTTATGTATTTTAATAAGTCAACAATT
* * *
51303 CTGTATTAATATCATTTTATGTATTTTGATAAGTTAACAATT
1 CTGTATTAATACCATTTTATGTATTTTAATAAGTCAACAATT
51345 C
1 C
51346 GTGTTACATA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.33, C:0.11, G:0.08, T:0.48
Consensus pattern (42 bp):
CTGTATTAATACCATTTTATGTATTTTAATAAGTCAACAATT
Found at i:52537 original size:44 final size:44
Alignment explanation
Indices: 52472--52556 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
52462 TGATCATTGT
* * *
52472 TGAATGTGTTGTCTAGTACATTTGTTTCTGCGAGTCTTTGTCAA
1 TGAATGTGTTATATAGTACATTTGTTGCTGCGAGTCTTTGTCAA
*
52516 TGAATGTGTTATATA-TAACATTTGTTGCTGTGAGTCTTTGT
1 TGAATGTGTTATATAGT-ACATTTGTTGCTGCGAGTCTTTGT
52557 TGGGGTATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
43 1 0.03
44 35 0.97
ACGTcount: A:0.20, C:0.11, G:0.22, T:0.47
Consensus pattern (44 bp):
TGAATGTGTTATATAGTACATTTGTTGCTGCGAGTCTTTGTCAA
Found at i:56306 original size:23 final size:23
Alignment explanation
Indices: 56247--56317 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
56237 AATCTATTTA
*
56247 TATGACATATTTTTTATTTATCTT
1 TATGACACA-TTTTTATTTATCTT
* * *
56271 TAAGATACGTTTTTATTTATCTT
1 TATGACACATTTTTATTTATCTT
**
56294 TATGACACATTTTCCTTTATCTT
1 TATGACACATTTTTATTTATCTT
56317 T
1 T
56318 TGGCATATTT
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
23 33 0.87
24 5 0.13
ACGTcount: A:0.24, C:0.13, G:0.06, T:0.58
Consensus pattern (23 bp):
TATGACACATTTTTATTTATCTT
Found at i:60013 original size:35 final size:34
Alignment explanation
Indices: 59927--60014 Score: 97
Period size: 34 Copynumber: 2.6 Consensus size: 34
59917 ATTTCACATT
***
59927 TAGCCCAATTCACGTTTTATGTGCATTTTAGCCA
1 TAGCCCAATTCACGTTTTATGTGCATGGAAGCCA
* * *
59961 TAGCCTAATTCACGTTTTATGTGCACTGGAATCTGA
1 TAGCCCAATTCACGTTTTATGTGCA-TGGAAGC-CA
59997 -AGCCCAATTCACGTTTTA
1 TAGCCCAATTCACGTTTTA
60015 ATTTGATGAG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
34 24 0.53
35 20 0.44
36 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (34 bp):
TAGCCCAATTCACGTTTTATGTGCATGGAAGCCA
Found at i:61352 original size:23 final size:23
Alignment explanation
Indices: 61326--61369 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
61316 AGGCTAGAAC
* *
61326 CAGAAAGGTTGGGGTAGGGGAGG
1 CAGAAAGGTCGGGGAAGGGGAGG
61349 CAGAAAGGTCGGGGAAGGGGA
1 CAGAAAGGTCGGGGAAGGGGA
61370 TGGGGTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.07, G:0.55, T:0.09
Consensus pattern (23 bp):
CAGAAAGGTCGGGGAAGGGGAGG
Done.