Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004173.1 Hibiscus syriacus cultivar Beakdansim tig00009128_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: 100793
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:765 original size:17 final size:19
Alignment explanation
Indices: 730--776 Score: 73
Period size: 17 Copynumber: 2.6 Consensus size: 19
720 TCCTAGTTGT
730 GGTATCGATACCAATCATG
1 GGTATCGATACCAATCATG
749 GGTATCGATA-C-ATCATG
1 GGTATCGATACCAATCATG
766 GGTATCG-TACC
1 GGTATCGATACC
777 CATTTTGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 2 0.07
17 14 0.52
18 1 0.04
19 10 0.37
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (19 bp):
GGTATCGATACCAATCATG
Found at i:4119 original size:27 final size:27
Alignment explanation
Indices: 4084--4146 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
4074 AATTCATGAC
* *
4084 TTCATAAATCACCAAAAAATTAACTAAA
1 TTCA-AAATAACCAAAAAATTAACAAAA
* * *
4112 TTCAAAATAATCAAATATTTAACAAAA
1 TTCAAAATAACCAAAAAATTAACAAAA
4139 TGTCAAAA
1 T-TCAAAA
4147 GTGTATACTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 19 0.66
28 10 0.34
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (27 bp):
TTCAAAATAACCAAAAAATTAACAAAA
Found at i:6982 original size:15 final size:15
Alignment explanation
Indices: 6959--6988 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6949 TGTACTTCTG
*
6959 TACTGAATCATTCAA
1 TACTAAATCATTCAA
6974 TACTAAATCATTCAA
1 TACTAAATCATTCAA
6989 AGATACGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.20, G:0.03, T:0.33
Consensus pattern (15 bp):
TACTAAATCATTCAA
Found at i:15983 original size:21 final size:20
Alignment explanation
Indices: 15946--15985 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
15936 TCAATTGATA
* *
15946 TAAAATATTTTATTATTATT
1 TAAAACATTTTAATATTATT
15966 TAAAACATATTTAATATTAT
1 TAAAACAT-TTTAATATTAT
15986 CTGAATATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TAAAACATTTTAATATTATT
Found at i:18386 original size:2 final size:2
Alignment explanation
Indices: 18379--18405 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18369 TATTCTCCAT
18379 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
18406 GATACTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22863 original size:15 final size:16
Alignment explanation
Indices: 22827--22863 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
22817 GAGAAGATTT
22827 GAAAGAGAAATGAAGA
1 GAAAGAGAAATGAAGA
22843 -AGAAGA-AAATGAAGA
1 GA-AAGAGAAATGAAGA
22858 GAAAGA
1 GAAAGA
22864 CATAGAGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.30, T:0.05
Consensus pattern (16 bp):
GAAAGAGAAATGAAGA
Found at i:25182 original size:37 final size:37
Alignment explanation
Indices: 25094--25196 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 37
25084 TTTTCATCCT
25094 ACTAGGATTCAAACTCCTAAAAATAGGATAGAATTTC
1 ACTAGGATTCAAACTCCTAAAAATAGGATAGAATTTC
* *
25131 GCTAGGATTCAAACTCCTAAAAATAGGATAG-AGTTC
1 ACTAGGATTCAAACTCCTAAAAATAGGATAGAATTTC
** * *
25167 TACTATTATTTAAACTCCTAAAGATAGGAT
1 -ACTAGGATTCAAACTCCTAAAAATAGGAT
25197 CCACAAGCAT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 4 0.07
37 54 0.93
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.29
Consensus pattern (37 bp):
ACTAGGATTCAAACTCCTAAAAATAGGATAGAATTTC
Found at i:25664 original size:2 final size:2
Alignment explanation
Indices: 25651--25727 Score: 131
Period size: 2 Copynumber: 39.5 Consensus size: 2
25641 CCTTATTATT
*
25651 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25693 TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25728 TTATTTATTA
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
1 2 0.03
2 69 0.97
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25777 original size:5 final size:5
Alignment explanation
Indices: 25763--25813 Score: 66
Period size: 5 Copynumber: 9.8 Consensus size: 5
25753 ATTTTTTGCG
* *
25763 TTATA TTATA ATATA TTATA TTATA TTCCTA TTATA TATATA TTATA TTAT
1 TTATA TTATA TTATA TTATA TTATA TT-ATA TTATA T-TATA TTATA TTAT
25814 TATTTTTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
5 31 0.77
6 9 0.22
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (5 bp):
TTATA
Found at i:25817 original size:11 final size:11
Alignment explanation
Indices: 25763--25858 Score: 56
Period size: 11 Copynumber: 8.6 Consensus size: 11
25753 ATTTTTTGCG
25763 TTATATTA-TA
1 TTATATTATTA
*
25773 ATATATTA-TA
1 TTATATTATTA
**
25783 TTATATTCCTA
1 TTATATTATTA
25794 TTATA-TATATA
1 TTATATTAT-TA
25805 TTATATTATTA
1 TTATATTATTA
*
25816 TT-TTTTATCTA
1 TTATATTAT-TA
*
25827 TGTTTACTTATTTA
1 T-TATA-TTA-TTA
* *
25841 TTATTTTTTTA
1 TTATATTATTA
25852 TTATATT
1 TTATATT
25859 TTCCTAACGT
Statistics
Matches: 67, Mismatches: 11, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
10 21 0.31
11 30 0.45
12 6 0.09
13 3 0.04
14 6 0.09
15 1 0.01
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (11 bp):
TTATATTATTA
Found at i:26045 original size:21 final size:21
Alignment explanation
Indices: 26016--26067 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
26006 TACATTTTTA
*
26016 TATTT-TT-TTTTATATATA-
1 TATTTATTATTTTATTTATAC
26034 T-TTTATTATTTTATTTATAC
1 TATTTATTATTTTATTTATAC
26054 TATTTATTTATTTT
1 TATTTA-TTATTTT
26068 CATTATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 3 0.11
18 3 0.11
19 10 0.36
20 1 0.04
21 4 0.14
22 7 0.25
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (21 bp):
TATTTATTATTTTATTTATAC
Found at i:26080 original size:21 final size:20
Alignment explanation
Indices: 26023--26080 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
26013 TTATATTTTT
26023 TTTTA-TATATATTTTA-TTA
1 TTTTATTATAT-TTTTATTTA
*
26042 TTTTATTTATACTATTTATTTA
1 TTTTA-TTATA-TTTTTATTTA
26064 TTTTCATTATATTTTTA
1 TTTT-ATTATATTTTTA
26081 GTTTCTTTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
19 5 0.16
21 13 0.41
22 13 0.41
23 1 0.03
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTATTATATTTTTATTTA
Found at i:27320 original size:20 final size:20
Alignment explanation
Indices: 27295--27332 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
27285 ACCTTACTAA
27295 CTCTTTTCATTTT-TTTCCCT
1 CTCTTTT-ATTTTATTTCCCT
27315 CTCTTTTATTTTATTTCC
1 CTCTTTTATTTTATTTCC
27333 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.08, C:0.26, G:0.00, T:0.66
Consensus pattern (20 bp):
CTCTTTTATTTTATTTCCCT
Found at i:31717 original size:29 final size:28
Alignment explanation
Indices: 31685--31749 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
31675 TCCTATTATA
31685 TATATATATATA-TTATATTATTATTTTTT
1 TATATATATATACTTAT-TTATTA-TTTTT
* *
31714 TATATATGTTTACTTATTTATTATTTTT
1 TATATATATATACTTATTTATTATTTTT
31742 TAT-TATAT
1 TATATATAT
31750 TTTCCTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 4 0.12
28 8 0.25
29 16 0.50
30 4 0.12
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (28 bp):
TATATATATATACTTATTTATTATTTTT
Found at i:31717 original size:33 final size:33
Alignment explanation
Indices: 31660--31749 Score: 105
Period size: 33 Copynumber: 2.8 Consensus size: 33
31650 TTTTTTGCGT
*
31660 TATATTATATTATTTTCCTATTATATATATATA-
1 TATATTATATTATTTT-TTATTATATATATATAC
* * *
31693 TATATTATATTATTATTTTTTTATATATGTTTAC
1 TATATTATATTATT-TTTTATTATATATATATAC
31727 T-TATT-TATTATTTTTTATTATAT
1 TATATTATATTATTTTTTATTATAT
31750 TTTCCTAACG
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
31 10 0.20
32 7 0.14
33 30 0.60
34 3 0.06
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.64
Consensus pattern (33 bp):
TATATTATATTATTTTTTATTATATATATATAC
Found at i:31966 original size:28 final size:27
Alignment explanation
Indices: 31910--31967 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
31900 TTTTTATATT
* *
31910 TTTATATATATATTTTTTATTATTTTA
1 TTTATATATATATTTTTTATCATTATA
*
31937 TTTATACTATTTATTTATTT-TCATTATA
1 TTTATA-TATATATTT-TTTATCATTATA
31965 TTT
1 TTT
31968 TTAGTTTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 6 0.23
28 17 0.65
29 3 0.12
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTATATATATATTTTTTATCATTATA
Found at i:31970 original size:21 final size:21
Alignment explanation
Indices: 31826--31970 Score: 63
Period size: 22 Copynumber: 6.6 Consensus size: 21
31816 TTTAGTTAAT
* *
31826 ATTATATGTATATTTATTTTTC
1 ATTATATTTTTATTTA-TTTTC
31848 ATT-TATTTATTA-TTATTATTAC
1 ATTATATTT-TTATTTATT-TT-C
31870 TATT-TAGTATTTTATTATATTTTAC
1 -ATTATA-T-TTTTATT-TATTTT-C
*
31895 A-TACATTTTTATATT-TTTAT-
1 ATTATATTTTTAT-TTATTT-TC
31915 ATATATATTTTT-TATTATTTT-
1 AT-TATATTTTTAT-TTATTTTC
*
31936 ATTTATACTATTTATTTATTTTC
1 A-TTATA-TTTTTATTTATTTTC
31959 ATTATATTTTTA
1 ATTATATTTTTA
31971 GTTTCTTTGC
Statistics
Matches: 99, Mismatches: 6, Indels: 37
0.70 0.04 0.26
Matches are distributed among these distances:
20 3 0.03
21 27 0.27
22 42 0.42
23 10 0.10
24 6 0.06
25 7 0.07
26 4 0.04
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (21 bp):
ATTATATTTTTATTTATTTTC
Found at i:32064 original size:5 final size:5
Alignment explanation
Indices: 32041--32091 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
32031 TTTGTATATA
* * * *
32041 TATTT TATCTT CA-TT TATTT TATTT TATTT TATTC AATTT CATTT TATTT
1 TATTT TAT-TT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT
32091 T
1 T
32092 TTTGTTTCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
4 3 0.08
5 31 0.84
6 3 0.08
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.71
Consensus pattern (5 bp):
TATTT
Found at i:32072 original size:15 final size:15
Alignment explanation
Indices: 32041--32091 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
32031 TTTGTATATA
32041 TATTTTATCTTCA-TT
1 TATTTTAT-TTCATTT
*
32056 TATTTTATTTTATTT
1 TATTTTATTTCATTT
**
32071 TATTCAATTTCATTT
1 TATTTTATTTCATTT
32086 TATTTT
1 TATTTT
32092 TTTGTTTCAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 3 0.10
15 26 0.90
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.71
Consensus pattern (15 bp):
TATTTTATTTCATTT
Found at i:33016 original size:46 final size:46
Alignment explanation
Indices: 32958--33109 Score: 295
Period size: 46 Copynumber: 3.3 Consensus size: 46
32948 GGGTGGTCGA
*
32958 CTCTACAACTCCTAAGAGTAGAGGTTAAACCTCTGAGGAAGGTCAT
1 CTCTACAACTCCTGAGAGTAGAGGTTAAACCTCTGAGGAAGGTCAT
33004 CTCTACAACTCCTGAGAGTAGAGGTTAAACCTCTGAGGAAGGTCAT
1 CTCTACAACTCCTGAGAGTAGAGGTTAAACCTCTGAGGAAGGTCAT
33050 CTCTACAACTCCTGAGAGTAGAGGTTAAACCTCTGAGGAAGGTCAT
1 CTCTACAACTCCTGAGAGTAGAGGTTAAACCTCTGAGGAAGGTCAT
33096 CTCTACAACTCCTG
1 CTCTACAACTCCTG
33110 TGCCTAACAG
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
46 105 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (46 bp):
CTCTACAACTCCTGAGAGTAGAGGTTAAACCTCTGAGGAAGGTCAT
Found at i:35325 original size:20 final size:21
Alignment explanation
Indices: 35300--35339 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
35290 TTTTACCACA
*
35300 ATTCAT-CTAGTATCGATACT
1 ATTCATCCTAGTATCAATACT
35320 ATTCATCCTAGTATCAATAC
1 ATTCATCCTAGTATCAATAC
35340 CTAGTCCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.38
Consensus pattern (21 bp):
ATTCATCCTAGTATCAATACT
Found at i:35827 original size:11 final size:10
Alignment explanation
Indices: 35805--35845 Score: 59
Period size: 9 Copynumber: 4.2 Consensus size: 10
35795 ATCTTGGAAT
35805 GAAGAATGAA
1 GAAGAATGAA
35815 GAAGAATTGAA
1 GAAGAA-TGAA
35826 GAAGAA-GAA
1 GAAGAATGAA
35835 GAA-AATGAA
1 GAAGAATGAA
35844 GA
1 GA
35846 GAACGGAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 2 0.07
9 11 0.38
10 6 0.21
11 10 0.34
ACGTcount: A:0.61, C:0.00, G:0.29, T:0.10
Consensus pattern (10 bp):
GAAGAATGAA
Found at i:35832 original size:17 final size:18
Alignment explanation
Indices: 35804--35837 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
35794 GATCTTGGAA
35804 TGAAGAATGAAGAAGAAT
1 TGAAGAATGAAGAAGAAT
35822 TGAAGAA-GAAGAAGAA
1 TGAAGAATGAAGAAGAA
35838 AATGAAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.59, C:0.00, G:0.29, T:0.12
Consensus pattern (18 bp):
TGAAGAATGAAGAAGAAT
Found at i:40828 original size:21 final size:20
Alignment explanation
Indices: 40782--40836 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
40772 CCAAAGTGAG
* * *
40782 TAGTATCGATACTCTATTTG
1 TAGTATCGATACCCTAGTTC
40802 TAGTATCGATACCCTAAGTTC
1 TAGTATCGATACCCT-AGTTC
*
40823 TAGTATCCATACCC
1 TAGTATCGATACCC
40837 CTATGAGTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (20 bp):
TAGTATCGATACCCTAGTTC
Found at i:40927 original size:21 final size:21
Alignment explanation
Indices: 40888--40928 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40878 TGGGGCACAA
**
40888 TATCGATACTGTCACCCTGAG
1 TATCGATACTCCCACCCTGAG
*
40909 TATCGATACTCCCATCCTGA
1 TATCGATACTCCCACCCTGA
40929 AACCTTAATT
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:0.24, C:0.32, G:0.15, T:0.29
Consensus pattern (21 bp):
TATCGATACTCCCACCCTGAG
Found at i:42068 original size:60 final size:60
Alignment explanation
Indices: 41994--42121 Score: 213
Period size: 60 Copynumber: 2.1 Consensus size: 60
41984 TTTTCGAAAC
*
41994 GTGGATCTTCTAAGTTTTGACCTAATTGAGA-CAATACCATATGATATCTCTTGATTTTAT
1 GTGGATCTTATAAGTTTTGACCTAATTGAGACCAA-ACCATATGATATCTCTTGATTTTAT
**
42054 GTGGATCTTATAAGTTTTGACCTAATTGCTACCAAACCATATGATATCTCTTGATTTTAT
1 GTGGATCTTATAAGTTTTGACCTAATTGAGACCAAACCATATGATATCTCTTGATTTTAT
42114 GTGGATCT
1 GTGGATCT
42122 ACTTTATTAT
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
60 61 0.95
61 3 0.05
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (60 bp):
GTGGATCTTATAAGTTTTGACCTAATTGAGACCAAACCATATGATATCTCTTGATTTTAT
Found at i:45188 original size:18 final size:18
Alignment explanation
Indices: 45162--45206 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
45152 TAATGATGTC
*
45162 TATTGGCACCCCATTGCT
1 TATTAGCACCCCATTGCT
45180 TATTAGCACCCCATTGCT
1 TATTAGCACCCCATTGCT
45198 TATTAGCAC
1 TATTAGCAC
45207 TAGCTTGACG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.22, C:0.31, G:0.13, T:0.33
Consensus pattern (18 bp):
TATTAGCACCCCATTGCT
Found at i:47569 original size:31 final size:31
Alignment explanation
Indices: 47533--47596 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
47523 GTGAATTATA
47533 TTTAACGCGGTCCCTAGTCCGCGTTATATCT
1 TTTAACGCGGTCCCTAGTCCGCGTTATATCT
47564 TTTAACGCGGTCCCTAGTCCGCGTTATATCT
1 TTTAACGCGGTCCCTAGTCCGCGTTATATCT
47595 TT
1 TT
47597 ATCTGAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.16, C:0.28, G:0.19, T:0.38
Consensus pattern (31 bp):
TTTAACGCGGTCCCTAGTCCGCGTTATATCT
Found at i:48803 original size:17 final size:18
Alignment explanation
Indices: 48762--48800 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
48752 ATTATATTAA
48762 TAAAATA-TTAAATAAAG
1 TAAAATACTTAAATAAAG
*
48779 TAAAATACTTAAATAAAT
1 TAAAATACTTAAATAAAG
48797 TAAA
1 TAAA
48801 TACATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (18 bp):
TAAAATACTTAAATAAAG
Found at i:48861 original size:10 final size:10
Alignment explanation
Indices: 48842--48872 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
48832 CTTAAGCAGA
*
48842 GAGAGTATTT
1 GAGAGAATTT
48852 GAGAGAATTT
1 GAGAGAATTT
48862 GAGAGAATTT
1 GAGAGAATTT
48872 G
1 G
48873 GTGTGATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:50113 original size:37 final size:37
Alignment explanation
Indices: 50047--50120 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
50037 ATCTAAATCA
* *
50047 GTCTCAACCTTCCTTCTTTACCGGCAAATTTGCTCCG
1 GTCTCAACCTTCATTCTATACCGGCAAATTTGCTCCG
* * *
50084 GTCTCGACCTTCATTCTATACTGGTAAATTTGCTCCG
1 GTCTCAACCTTCATTCTATACCGGCAAATTTGCTCCG
50121 ATGGGTAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.18, C:0.31, G:0.15, T:0.36
Consensus pattern (37 bp):
GTCTCAACCTTCATTCTATACCGGCAAATTTGCTCCG
Found at i:52399 original size:12 final size:12
Alignment explanation
Indices: 52384--52417 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
52374 TAAAAGTAAC
52384 AGTAAAAATTTT
1 AGTAAAAATTTT
*
52396 AGTAAAATTTTTT
1 AGTAAAA-ATTTT
52409 AGTAAAAAT
1 AGTAAAAAT
52418 AGTTAATTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (12 bp):
AGTAAAAATTTT
Found at i:52597 original size:32 final size:32
Alignment explanation
Indices: 52520--52612 Score: 91
Period size: 32 Copynumber: 3.0 Consensus size: 32
52510 TAATGCCTTG
* * * * *
52520 GGGGCCTTAGAGCCTA-CCTAATGAATACCTT
1 GGGGCCTAAGAGCCTACCCAAAGGAACACCTC
* * *
52551 GGGGCCTGACAGCCTACCCAAAGGAACATCTC
1 GGGGCCTAAGAGCCTACCCAAAGGAACACCTC
*
52583 GGGGCCTAAGAGCCTACCC-AAGGGACACCT
1 GGGGCCTAAGAGCCTACCCAAAGGAACACCT
52613 TAGGTCTGTA
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
31 23 0.46
32 27 0.54
ACGTcount: A:0.27, C:0.31, G:0.26, T:0.16
Consensus pattern (32 bp):
GGGGCCTAAGAGCCTACCCAAAGGAACACCTC
Found at i:53790 original size:19 final size:20
Alignment explanation
Indices: 53749--53799 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
53739 GAAACCCCTT
*
53749 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
53769 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
53788 TGAAGATACATG
1 TGAAAATACATG
53800 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:56185 original size:20 final size:20
Alignment explanation
Indices: 56160--56252 Score: 87
Period size: 21 Copynumber: 4.5 Consensus size: 20
56150 TTTTCCCAAT
*
56160 TCGCAATGTGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
56180 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
56200 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
56221 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
56242 TCGCAATGCGA
1 TCGCAATGCGA
56253 TACTGACTAT
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 26 0.46
21 31 0.54
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:56206 original size:21 final size:20
Alignment explanation
Indices: 56177--56252 Score: 89
Period size: 21 Copynumber: 3.7 Consensus size: 20
56167 GTGAATAAGT
56177 AAATCGCAACGCGAATTGGG
1 AAATCGCAACGCGAATTGGG
* ** *
56197 AAATTCGCAATGCGAATAAGT
1 AAA-TCGCAACGCGAATTGGG
56218 AAATCGCAACGCGAATTGGG
1 AAATCGCAACGCGAATTGGG
*
56238 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
56253 TACTGACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.17
Consensus pattern (20 bp):
AAATCGCAACGCGAATTGGG
Found at i:56214 original size:41 final size:41
Alignment explanation
Indices: 56157--56252 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
56147 CGATTTTCCC
*
56157 AATTCGCAATGTGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
56198 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
56239 AAATCGCAATGCGA
1 AATTCGCAATGCGA
56253 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.20
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:56265 original size:41 final size:41
Alignment explanation
Indices: 56179--56313 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
56169 GAATAAGTAA
* * *
56179 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
56220 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
56261 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
56302 TTCGCAACGCGA
1 ATCGCAACGCGA
56314 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:56266 original size:20 final size:20
Alignment explanation
Indices: 56241--56335 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
56231 AATTGGGAAA
*
56241 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
56261 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
56282 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
56302 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
56322 TTCGCAACGCGATA
1 ATCGCAACGCGATA
56336 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:58207 original size:18 final size:18
Alignment explanation
Indices: 58163--58207 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
58153 TCCACTTCGG
*
58163 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
58181 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
*
58199 TAGCCATCA
1 GAGCCATCA
58208 TCTGATCGAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.27, C:0.42, G:0.13, T:0.18
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:58734 original size:19 final size:20
Alignment explanation
Indices: 58680--58746 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
58670 TAGTTTACTT
* *
58680 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
58700 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
58720 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
58739 TCGCAACG
1 TCGCAACG
58747 ACAAAAGCGC
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:58757 original size:14 final size:14
Alignment explanation
Indices: 58735--58824 Score: 81
Period size: 14 Copynumber: 5.9 Consensus size: 14
58725 ATGCGAAATG
58735 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
58749 AAAAGCGCAACGCGAA
1 AAAATCGCAA--CGAC
58765 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
58781 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
58797 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
58813 AAAATCGCAACG
1 AAAATCGCAACG
58825 CGAAACACAA
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
14 29 0.47
16 16 0.26
18 17 0.27
ACGTcount: A:0.48, C:0.26, G:0.19, T:0.08
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:58777 original size:32 final size:32
Alignment explanation
Indices: 58719--58829 Score: 195
Period size: 32 Copynumber: 3.4 Consensus size: 32
58709 GGAAATGGCT
*
58719 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
*
58752 AGCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
58784 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
58816 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
58830 CACAAATCGC
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 61 0.81
33 14 0.19
ACGTcount: A:0.47, C:0.24, G:0.20, T:0.09
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:58858 original size:19 final size:19
Alignment explanation
Indices: 58836--58989 Score: 123
Period size: 19 Copynumber: 8.6 Consensus size: 19
58826 GAAACACAAA
58836 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
58855 TCGCGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
58871 T--CGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
*
58887 TCGCGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
58903 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* ***
58920 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGATTTTCATT
**
58939 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
*
58959 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
58979 TCGTGTTGCGA
1 TCGCGTTGCGA
58990 AAGTAAACTA
Statistics
Matches: 110, Mismatches: 14, Indels: 21
0.76 0.10 0.14
Matches are distributed among these distances:
14 19 0.17
15 3 0.03
16 6 0.05
17 2 0.02
18 14 0.13
19 37 0.34
20 29 0.26
ACGTcount: A:0.12, C:0.20, G:0.25, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:58877 original size:14 final size:14
Alignment explanation
Indices: 58858--58915 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
58848 TTTCATTTCG
58858 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
58872 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
58888 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
58904 CGTTGCGATTTT
1 CGTTGCGATTTT
58916 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:58889 original size:32 final size:33
Alignment explanation
Indices: 58839--58931 Score: 170
Period size: 32 Copynumber: 2.8 Consensus size: 33
58829 ACACAAATCG
58839 CGTTGCGATTTTCATTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTTTGT
58872 CGTTGCGA-TTTCATTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTTTGT
*
58904 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT
58932 AGCCATTTCC
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.55
33 26 0.45
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTTTGT
Found at i:58950 original size:20 final size:19
Alignment explanation
Indices: 58916--58970 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
58906 TTGCGATTTT
*
58916 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
58935 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
58955 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
58971 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:60855 original size:14 final size:14
Alignment explanation
Indices: 60836--60871 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
60826 ATTGTTTAAT
60836 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
60850 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
60864 TGATTTGT
1 TGATTTGT
60872 TTAATTGATG
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:61010 original size:19 final size:19
Alignment explanation
Indices: 60988--61055 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
60978 ATCGCAACAA
60988 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
61007 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
61026 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
61040 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
61056 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:61106 original size:20 final size:20
Alignment explanation
Indices: 61081--61130 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
61071 GCGATATTCT
61081 CGTTGCGATAACCATTTTCG
1 CGTTGCGATAACCATTTTCG
61101 CGTTGCGATAACCATTTTCG
1 CGTTGCGATAACCATTTTCG
*
61121 CATTGCGATA
1 CGTTGCGATA
61131 GTCAAATGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAACCATTTTCG
Found at i:61517 original size:14 final size:14
Alignment explanation
Indices: 61498--61533 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
61488 ATTGTTTAAT
61498 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
61512 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
61526 TGATTTGT
1 TGATTTGT
61534 TTAATTGATG
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:62834 original size:24 final size:24
Alignment explanation
Indices: 62778--62836 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
62768 AGTCAGTATT
* *
62778 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
62802 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
62826 CGAATTTTGAT
1 CGAAATTTGAT
62837 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:63028 original size:12 final size:12
Alignment explanation
Indices: 63011--63035 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
63001 ATATAATCCT
63011 GAAGAAGAAAAA
1 GAAGAAGAAAAA
63023 GAAGAAGAAAAA
1 GAAGAAGAAAAA
63035 G
1 G
63036 TCACCGAAGA
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:65349 original size:19 final size:19
Alignment explanation
Indices: 65327--65424 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
65317 GGAAATTACT
65327 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
65346 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
65360 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
65379 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
65393 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
65412 ATCGCAACGCGAA
1 ATCGCAATGCGAA
65425 TTTAATTTCG
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.50
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:65369 original size:33 final size:33
Alignment explanation
Indices: 65327--65420 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
65317 GGAAATTACT
65327 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
65360 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
65393 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
65421 CGAATTTAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:65442 original size:19 final size:20
Alignment explanation
Indices: 65420--65458 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
65410 AAATCGCAAC
65420 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
65439 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
65459 ACGATTCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.15, C:0.18, G:0.21, T:0.46
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:65622 original size:14 final size:14
Alignment explanation
Indices: 65603--65639 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
65593 CATCAATTAA
*
65603 ACAAATCAACTTTT
1 ACAAATCAACTTTC
*
65617 ACAAATCACCTTTC
1 ACAAATCAACTTTC
65631 ACAAATCAA
1 ACAAATCAA
65640 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (14 bp):
ACAAATCAACTTTC
Found at i:67062 original size:21 final size:21
Alignment explanation
Indices: 66996--67062 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
66986 GTGAATCGGG
*
66996 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
67016 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
67038 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
67059 CTCT
1 CTCT
67063 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:69161 original size:20 final size:19
Alignment explanation
Indices: 69116--69274 Score: 88
Period size: 19 Copynumber: 8.8 Consensus size: 19
69106 TCTTTTGGTT
69116 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* * *
69135 GATAATGAGAATTGCAACGCG
1 GA-AATGAAAATCGCAACG-A
** *
69156 GAAATGACTATCGCAATGA
1 GAAATGAAAATCGCAACGA
*
69175 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** * *
69189 GAAATGACTATCGCGATGA
1 GAAATGAAAATCGCAACGA
* *
69208 G--A-G--AATCACAACGC
1 GAAATGAAAATCGCAACGA
*
69222 GAAATG-AAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
69240 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
69259 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
69275 TGCGATTTTG
Statistics
Matches: 107, Mismatches: 21, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
14 16 0.15
16 4 0.04
17 4 0.04
18 16 0.15
19 39 0.36
20 26 0.24
21 2 0.02
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:69198 original size:33 final size:33
Alignment explanation
Indices: 69141--69236 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 33
69131 ACGAGATAAT
*
69141 GAGAATTGCAACGCGGAAATGACTATCGCAATGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAATGA
*
69175 GAGAATCGCAACGCGAAATGACTATCGCGATGA
1 GAGAATCGCAACGCGAAATGACTATCGCAATGA
* *
69208 GAGAATCACAACGCGAAATGA-AATCGCAA
1 GAGAATCGCAACGCGAAATGACTATCGCAA
69237 CGCGAAATGA
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
32 6 0.11
33 38 0.67
34 13 0.23
ACGTcount: A:0.41, C:0.20, G:0.25, T:0.15
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAATGA
Found at i:69252 original size:19 final size:19
Alignment explanation
Indices: 69211--69279 Score: 113
Period size: 19 Copynumber: 3.7 Consensus size: 19
69201 GCGATGAGAG
*
69211 AATCACAACGCGAAATG-A
1 AATCGCAACGCGAAATGAA
69229 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
69248 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
69267 AATCGCAATGCGA
1 AATCGCAACGCGA
69280 TTTTGGTTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
18 16 0.33
19 32 0.67
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:69308 original size:19 final size:19
Alignment explanation
Indices: 69275--69341 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
69265 AAAATCGCAA
**
69275 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
69294 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
** *
69313 TGCGATAGTTATTTCCGCTT
1 TGCGATTTTTATTT-CGCGT
69333 TGCGATTTT
1 TGCGATTTT
69342 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 29 0.73
20 11 0.28
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.49
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:69955 original size:20 final size:20
Alignment explanation
Indices: 69862--69955 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
69852 CTCTAAGTAA
*
69862 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
69882 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
69902 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
69923 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
69943 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
69956 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:69974 original size:41 final size:41
Alignment explanation
Indices: 69883--70017 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
69873 AAAGTCAGTA
* * * ** *
69883 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
69923 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
69965 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
70006 TCGCGTTGCGAT
1 TCGCGTTGCGAT
70018 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:69988 original size:20 final size:20
Alignment explanation
Indices: 69944--70036 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
69934 ATAGTCAGTA
* **
69944 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
69965 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
69985 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
70006 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
70026 TCGCATTGCGA
1 TCGCATTGCGA
70037 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:70018 original size:41 final size:41
Alignment explanation
Indices: 69944--70039 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
69934 ATAGTCAGTA
*
69944 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
69985 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
70026 TCGCATTGCGAATT
1 TCGCATTGCGAATT
70040 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:78896 original size:66 final size:63
Alignment explanation
Indices: 78789--78911 Score: 149
Period size: 66 Copynumber: 1.9 Consensus size: 63
78779 TTTGTTGAAG
* * * *
78789 GTGCATCGATGCACATGGAGTGTATCGATGCATTCATTTAAAATAAATAAACATCGAATGCCATT
1 GTGCATCGATGCACAAGGAGTGCATCGATGCATGCA-TTAAAAT--ACAAACATCGAATGCCATT
78854 A
63 A
*
78855 GTGCATCGATGCATAAGGAGTGCATCGATGCACCTGC-TTAAAATACAAACATCGAAT
1 GTGCATCGATGCACAAGGAGTGCATCGATGCA--TGCATTAAAATACAAACATCGAAT
78912 AGGATTTCTG
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
64 12 0.24
66 36 0.72
68 2 0.04
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCACAAGGAGTGCATCGATGCATGCATTAAAATACAAACATCGAATGCCATTA
Found at i:79531 original size:22 final size:22
Alignment explanation
Indices: 79506--79557 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
79496 ATATTAGTCC
79506 TTCGGGATGTATCCAGTGGTCA
1 TTCGGGATGTATCCAGTGGTCA
* * *
79528 TTCGAGACGTATCCAGTGGTCC
1 TTCGGGATGTATCCAGTGGTCA
79550 TTCGGGAT
1 TTCGGGAT
79558 ATAGTGGTCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.17, C:0.21, G:0.31, T:0.31
Consensus pattern (22 bp):
TTCGGGATGTATCCAGTGGTCA
Found at i:86459 original size:22 final size:22
Alignment explanation
Indices: 86434--86490 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
86424 GGGTATATTA
*
86434 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACATATCCAGTG
86456 GTCCTTCGGGACATATCCAGTG
1 GTCCTTCGGGACATATCCAGTG
*
86478 ATCCTTCGGGACA
1 GTCCTTCGGGACA
86491 AATACTGAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.26
Consensus pattern (22 bp):
GTCCTTCGGGACATATCCAGTG
Found at i:92350 original size:3 final size:3
Alignment explanation
Indices: 92342--92382 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
92332 TCTAATCAAC
*
92342 TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
92383 GTTGTTGTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:97213 original size:22 final size:22
Alignment explanation
Indices: 97160--97213 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
97150 TTCAACTGTT
* * *
97160 ATAACTCCCGAAATTATATCAT
1 ATAACTCCTGAAATTAAATCAA
* *
97182 GTAACCCCTGAAATTAAATCAA
1 ATAACTCCTGAAATTAAATCAA
97204 ATAACTCCTG
1 ATAACTCCTG
97214 TAACTCCTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.28
Consensus pattern (22 bp):
ATAACTCCTGAAATTAAATCAA
Done.