Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002481.1 Hibiscus syriacus cultivar Beakdansim tig00005067_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: 89270
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:14128 original size:13 final size:15
Alignment explanation
Indices: 14098--14134 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
14088 ATATACATTT
14098 AATAATAATAACATG
1 AATAATAATAACATG
14113 AATAATAA-AA-ATG
1 AATAATAATAACATG
14126 AATAA-AATA
1 AATAATAATA
14135 TCCATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 2 0.10
13 9 0.43
14 2 0.10
15 8 0.38
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (15 bp):
AATAATAATAACATG
Found at i:14524 original size:37 final size:37
Alignment explanation
Indices: 14474--14544 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
14464 GTGGTTGTGG
* *
14474 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATCTTTAGGAATTTAAATCCTAATAGAACTCT
* * *
14511 ATCCTATTTTTAGGAGTTTGAATCCTAATAGAAC
1 ATCCTATCTTTAGGAATTTAAATCCTAATAGAAC
14545 GAAAATGTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.39
Consensus pattern (37 bp):
ATCCTATCTTTAGGAATTTAAATCCTAATAGAACTCT
Found at i:15383 original size:105 final size:105
Alignment explanation
Indices: 15079--15526 Score: 658
Period size: 105 Copynumber: 4.3 Consensus size: 105
15069 GCATTGTTCC
* * **
15079 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAATTG-TTGTTGACA
* * * * * *
15143 ACCATTC-GTCCCTTCGTTGTGAAATTGAACTTGTGTTGTCTC
64 AGCA-GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
15185 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAG
*
15245 CAGCGGTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
15285 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAG
15350 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
15390 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGATAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAG
*
15455 CAGCGGTCCCTTCGTCTTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
15495 AAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
15527 CTATTCTCGA
Statistics
Matches: 316, Mismatches: 19, Indels: 15
0.90 0.05 0.04
Matches are distributed among these distances:
99 1 0.00
100 81 0.26
101 1 0.00
102 7 0.02
104 5 0.02
105 185 0.59
106 36 0.11
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:15400 original size:205 final size:210
Alignment explanation
Indices: 15079--15526 Score: 658
Period size: 205 Copynumber: 2.2 Consensus size: 210
15069 GCATTGTTCC
* *
15079 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAA
* * *
15144 CCATTCGTCCCTTCGTTGTGAAATTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAA
66 CCATGCGTCCCTTCGTCGTGAAATTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGCTGTGAA
*
15209 GTTGAAATTGACTCTGA-A-T-GAAATT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGGAGTTG
131 GTTGAAATTGACTCTGAGATTGGAAATTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
15270 AACTTGCGTTGTCTG
196 AACTTGCGTTGTCTG
** *
15285 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAGATTGGGAAGTTG-TTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGA-ACCGGGAAATTGTTTGTTGACA
* * * *
15348 AGCA-GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
65 ACCATGC-GTCCCTTCGTCGTGAAATTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGCTGTG
* * * *
15412 AAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGATAAGCAGCGGTCCCTTCGTCTTGAAG
129 AAGTTGAAATTGACTCTGAGATT-GGAAATTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAG
15477 TTGAACTTGCGTTGTCTG
193 TTGAACTTGCGTTGTCTG
*
15495 AAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
15527 CTATTCTCGA
Statistics
Matches: 217, Mismatches: 18, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
204 1 0.00
205 84 0.39
206 47 0.22
207 1 0.00
209 5 0.02
210 79 0.36
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (210 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAA
CCATGCGTCCCTTCGTCGTGAAATTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGCTGTGAA
GTTGAAATTGACTCTGAGATTGGAAATTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
AACTTGCGTTGTCTG
Found at i:15693 original size:36 final size:36
Alignment explanation
Indices: 15646--15721 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
15636 TGTTTGGAGA
* * *
15646 GAAACTGTCTCAAGGGAGATAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
15682 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
15718 GAAA
1 GAAA
15722 TGTTTTCAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
Found at i:15842 original size:104 final size:103
Alignment explanation
Indices: 15621--15938 Score: 487
Period size: 104 Copynumber: 3.1 Consensus size: 103
15611 TTCGTTAAAT
* ** * *
15621 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGATAAA-ATTC-GTTTCAAGGGA
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGATAAATTTTCTGTTTCGAGGGA
* * *
15684 AACTATCTCAAGCGAGATAAAATTCATTTCAAGGGAAA
66 AACTATCTCAAGAGAGAAAAAAATCATTTCAAGGGAAA
15722 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGATAAATTTTCTGTTTCGAGGGA
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGATAAATTTTCTGTTTCGAGGGA
15787 AACTATCTCAAGAGAGAAAAAAAATCATTTCAAGGGAAA
66 AACTATCTCAAGAGAG-AAAAAAATCATTTCAAGGGAAA
* *
15826 TGTTTTCAATGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGA-TAAATTTTCTGTTTCGAGGG
* * *
15891 AAACTATCTCAGGAGAGAGAAAAATAATTTCAAGGGAAA
65 AAACTATCTCAAGAGAGAAAAAAATCATTTCAAGGGAAA
15930 TGTTTTCAA
1 TGTTTTCAA
15939 GAGAAACTGT
Statistics
Matches: 200, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
101 45 0.22
102 3 0.01
103 25 0.12
104 92 0.46
105 35 0.17
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.31
Consensus pattern (103 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGATAAATTTTCTGTTTCGAGGGA
AACTATCTCAAGAGAGAAAAAAATCATTTCAAGGGAAA
Found at i:16173 original size:71 final size:74
Alignment explanation
Indices: 16021--16180 Score: 177
Period size: 72 Copynumber: 2.2 Consensus size: 74
16011 AAAAATAGCA
* * * *
16021 TTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGACAAATCTTGTTTTAA
1 TTGAGTGAAAT-AAAT-CCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAATCATATTTTAA
16086 GAAAAACAATC
64 GAAAAACAATC
* * *
16097 TTGAGTGAAATAAAT-CTTTTTTCGAG-AAAAACAGTGTCAAGTGAGACAAAGT-ATATTTTAAG
1 TTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAA-TCATATTTTAAG
16159 -AAAACAAAT-
65 AAAAAC-AATC
*
16168 TTGAGTGAGATAA
1 TTGAGTGAAATAA
16181 TCATCTGTAT
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
71 17 0.23
72 31 0.42
73 11 0.15
75 4 0.05
76 11 0.15
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (74 bp):
TTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAATCATATTTTAAGA
AAAACAATC
Found at i:22042 original size:37 final size:36
Alignment explanation
Indices: 21992--22089 Score: 115
Period size: 38 Copynumber: 2.6 Consensus size: 36
21982 GGATCTTATC
* *
21992 TTTAAGAATTTAAATCTTAGTAGAACTCTATCCTATT
1 TTTAA-AATTTAAATCTTAATAAAACTCTATCCTATT
* * *
22029 TTTAAAAGTTTAAAATCCTAATAAAATTTTATCCTATT
1 TTTAAAA-TTT-AAATCTTAATAAAACTCTATCCTATT
22067 TTTAAAAATTTAAATCTTAATAA
1 TTT-AAAATTTAAATCTTAATAA
22090 TACGAAAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
36 2 0.04
37 19 0.37
38 27 0.52
39 4 0.08
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (36 bp):
TTTAAAATTTAAATCTTAATAAAACTCTATCCTATT
Found at i:24588 original size:20 final size:19
Alignment explanation
Indices: 24558--24605 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
24548 CAAAACAAGT
* *
24558 AATAATAAGGTAAAGTATC
1 AATACTAAGGTAAAATATC
*
24577 GATACCTAAGGTAAAATATC
1 AATA-CTAAGGTAAAATATC
24597 AATACTAAG
1 AATACTAAG
24606 AGTTCAATAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (19 bp):
AATACTAAGGTAAAATATC
Found at i:25973 original size:18 final size:18
Alignment explanation
Indices: 25938--25983 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
25928 GTTTAATAGT
*
25938 ATTG-TAAAAATAACTAA
1 ATTGATAAAAAAAACTAA
*
25955 ATTGATAAAAAAAATTAA
1 ATTGATAAAAAAAACTAA
25973 A-T-ATAAAAAAA
1 ATTGATAAAAAAA
25984 TTACATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 9 0.35
17 5 0.19
18 12 0.46
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.26
Consensus pattern (18 bp):
ATTGATAAAAAAAACTAA
Found at i:26737 original size:2 final size:2
Alignment explanation
Indices: 26730--26758 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
26720 TTTAAAAATA
26730 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
26759 AGTTGTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32593 original size:63 final size:63
Alignment explanation
Indices: 32510--32646 Score: 193
Period size: 63 Copynumber: 2.2 Consensus size: 63
32500 TTGTACGTAT
* *
32510 CAACAGCCTGAACCTTTACCAAAGTCGGAAAACAATACTGATAACGCTGACTCTCATACTACC
1 CAACAGCCTGAACCTTTACCAAAGTCGAAAAACAATACTGATAACGCTGACTCTCATACCACC
* * * * * *
32573 CAACAGCCTGAACTTTTACCAAGGTCGAAAAATAATATTGATAATGCTGACTCTCATACCCCC
1 CAACAGCCTGAACCTTTACCAAAGTCGAAAAACAATACTGATAACGCTGACTCTCATACCACC
*
32636 CAGCAGCCTGA
1 CAACAGCCTGA
32647 GTCCTTGTCT
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.35, C:0.29, G:0.14, T:0.22
Consensus pattern (63 bp):
CAACAGCCTGAACCTTTACCAAAGTCGAAAAACAATACTGATAACGCTGACTCTCATACCACC
Found at i:40849 original size:21 final size:21
Alignment explanation
Indices: 40815--40854 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
40805 GATGTTGTAT
40815 AGCCGTTAGGGATG-TTTTGG
1 AGCCGTTAGGGATGATTTTGG
*
40835 AGCCGTTTGGGGATGATTTT
1 AGCCG-TTAGGGATGATTTT
40855 TCTACTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.38
Consensus pattern (21 bp):
AGCCGTTAGGGATGATTTTGG
Found at i:41021 original size:21 final size:20
Alignment explanation
Indices: 40957--41050 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
40947 GCAGCCTTCG
* * *
40957 TGCATGGATGCACAACAAGA
1 TGCATCGATGCACAGCAGGA
*
40977 TGCATCGATGCATAGCAGGA
1 TGCATCGATGCACAGCAGGA
**
40997 TGCATCGATGCACAGCCTTGA
1 TGCATCGATGCACAG-CAGGA
**
41018 TGCATCGATGCACAAAAGGA
1 TGCATCGATGCACAGCAGGA
* *
41038 TGAATTGATGCAC
1 TGCATCGATGCAC
41051 TAATTACATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 43 0.72
21 17 0.28
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.20
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:41261 original size:29 final size:31
Alignment explanation
Indices: 41229--41288 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
41219 AAACTTTGAA
41229 TAAATTCAATT-AAGTCCAAAAAC-ATTTTG
1 TAAATTCAATTCAAGTCCAAAAACTATTTTG
41258 TAAATTCAATTCAAGTCCAAAAACTATTTTG
1 TAAATTCAATTCAAGTCCAAAAACTATTTTG
41289 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACTATTTTG
Found at i:42726 original size:21 final size:21
Alignment explanation
Indices: 42692--42731 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
42682 TGTTGTATAT
42692 AGCCGTTAGGGATG-TTTTGG
1 AGCCGTTAGGGATGATTTTGG
*
42712 AGCCGTTTGGGGATGATTTT
1 AGCCG-TTAGGGATGATTTT
42732 TCTACTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.38
Consensus pattern (21 bp):
AGCCGTTAGGGATGATTTTGG
Found at i:42877 original size:21 final size:21
Alignment explanation
Indices: 42852--42907 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
42842 TACACAACAG
42852 GATGCATCGATGCAAAGCCTT
1 GATGCATCGATGCAAAGCCTT
42873 GATGCATCGATGCAAAGCCTT
1 GATGCATCGATGCAAAGCCTT
42894 GATGCATCGATGCA
1 GATGCATCGATGCA
42908 CAGAAGGATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (21 bp):
GATGCATCGATGCAAAGCCTT
Found at i:42994 original size:22 final size:23
Alignment explanation
Indices: 42963--43005 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
42953 ATGGATACAA
42963 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCGATGCACTAG
*
42986 TGCA-GGTGCATGGATGCACT
1 TGCATGGTGCATCGATGCACT
43006 TTGACACCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (23 bp):
TGCATGGTGCATCGATGCACTAG
Found at i:43106 original size:29 final size:29
Alignment explanation
Indices: 43085--43143 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 29
43075 AAACTTTGAA
43085 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
43114 TAAATTCAATTCAAGTCCAAAAACCATTTG
1 TAAATTCAATTCAAGTCCAAAAA-CATTTG
43144 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.39
30 15 0.54
31 2 0.07
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.32
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:43132 original size:30 final size:30
Alignment explanation
Indices: 43085--43142 Score: 100
Period size: 29 Copynumber: 1.9 Consensus size: 30
43075 AAACTTTGAA
43085 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
43114 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATT-AAGTCCAAAAACCATTT
43143 GCCTTAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.41
30 11 0.41
31 5 0.19
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:45265 original size:176 final size:174
Alignment explanation
Indices: 44971--45309 Score: 515
Period size: 176 Copynumber: 1.9 Consensus size: 174
44961 AAATTAAATA
*
44971 TTTTTAATTCAAAAAAACATTATAATTAATTTAAATAATATAATTATAAAATAAAAATTTTATAT
1 TTTTTAATTCAAAAAAACATTACAATTAATTTAAATAATATAATTATAAAATAAAAATTTTATAT
* *
45036 AAATTTTTTAATTAATTATATTGATTAAGTTTAAAAGTTATTGGATCTTAAATTA-TAATTGGGG
66 -AATTTTTTAATTAATAATATTGATTAAGTTTAAAAGTTATTGAATCTTAAATTATTAATT-GGG
*
45100 TTTTAAATGGTTTGGGCTTAG-CCCATATGTTATAATATTTAATATT
129 TTTTAAATGGTTT-GGCTAAGCCCCATATGTTATAATATTTAATATT
**
45146 TTTTTAATTCAAAAAATAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTTA
1 TTTTTAATTCAAAAAA-ACATTACAATTAATTTAAAT-A-ATATAATTATAAAATAAAAATTTTA
* *
45211 TAT-ATTTTTTAATTAA-AATATTGATTTAGGTTTAAAAGTTATTGAATTTTAAATTATTAATTG
63 TATAATTTTTTAATTAATAATATTGA-TTAAGTTTAAAAGTTATTGAATCTTAAATTATTAATTG
45274 GGTTTTAAATGGTTTGGCTAAGCCCCATATGTTATA
127 GGTTTTAAATGGTTTGGCTAAGCCCCATATGTTATA
45310 TAATATATTT
Statistics
Matches: 150, Mismatches: 8, Indels: 11
0.89 0.05 0.07
Matches are distributed among these distances:
175 29 0.19
176 87 0.58
177 6 0.04
178 28 0.19
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (174 bp):
TTTTTAATTCAAAAAAACATTACAATTAATTTAAATAATATAATTATAAAATAAAAATTTTATAT
AATTTTTTAATTAATAATATTGATTAAGTTTAAAAGTTATTGAATCTTAAATTATTAATTGGGTT
TTAAATGGTTTGGCTAAGCCCCATATGTTATAATATTTAATATT
Found at i:45354 original size:9 final size:9
Alignment explanation
Indices: 45340--45364 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
45330 TTTAATTTCG
45340 GTTAATTCA
1 GTTAATTCA
45349 GTTAATTCA
1 GTTAATTCA
45358 GTTAATT
1 GTTAATT
45365 AATCGATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.48
Consensus pattern (9 bp):
GTTAATTCA
Found at i:49620 original size:63 final size:64
Alignment explanation
Indices: 49542--49680 Score: 156
Period size: 63 Copynumber: 2.2 Consensus size: 64
49532 CGGATCCTGG
* * *
49542 CAGGTCGGGTAAAATCGGATACAGGTCA-AGTCAGGTAAATTTGACACCAG-TCCAGATCAGGTT
1 CAGGTCAGGTCAAATCAG-TACAGGTCATAGTCAGGTAAATTTGACACCAGATCCAGATCAGGTT
* * * ** ** *
49605 CAGGTCAGGTCAAATCAGTTCGGGTGATTTTCAGGTTGATTTGACACCAGATCCAGATCGGGTT
1 CAGGTCAGGTCAAATCAGTACAGGTCATAGTCAGGTAAATTTGACACCAGATCCAGATCAGGTT
49669 CAGGTCAGGTCA
1 CAGGTCAGGTCA
49681 TTTTCAGTTC
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
62 6 0.10
63 33 0.52
64 24 0.38
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.25
Consensus pattern (64 bp):
CAGGTCAGGTCAAATCAGTACAGGTCATAGTCAGGTAAATTTGACACCAGATCCAGATCAGGTT
Found at i:50685 original size:200 final size:206
Alignment explanation
Indices: 49981--50714 Score: 1006
Period size: 212 Copynumber: 3.5 Consensus size: 206
49971 ATTTAATAAT
*
49981 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATAAAACAATACACAATGATGAG
1 TAAATTGAA-AAATATGAAATTACAAATAAAAATTTAAATAAATTAAAC-A-ACACAAT-A--AG
* * *
50046 GGATCAAATCGAAATAATTTTAAATTGTGAAGTTGAAATTAATACAAAAAAATACTAAATTATAC
60 GGATCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* * *
50111 CCATTTAAAAAGTTATGGGCCAATTAAAAAAATAGAATTAAGTAAT-AGTATGGATCAATTCATG
125 CCATTTAAAAAGTTA-GGGCCAATT-TAAAAATAGAAATAAGTAATAAGTATGGGTCAATTCATG
50175 CAAATAAAATTTGGAGGAC
188 CAAATAAAATTTGGAGGAC
*
50194 TAAATTGAAAAAATATGAAATTACAAAT-AAAATTTAAATAAATTAAACAACACACTTTGATGAG
1 TAAATTG-AAAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACA-----ATAAG
* *
50258 GGATCAAATCAAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTGTAC
60 GGATCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
*
50323 CCATTTAAAAAGTTATGGGCCAATTT-AAAATAGAAATAAGTAATAAGTATGGGTCAGTTTCAAA
125 CCATTTAAAAAGTTA-GGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCA-ATTC--A
50387 TGCAAATAAAATTTGGAGGAC
186 TGCAAATAAAATTTGGAGGAC
*
50408 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAACACAA-AAGGGATC
1 TAAATTGAA-AAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACAATAAGGGATC
* * *
50472 AAATCGAAATAATTTTAAATTTTGAGGTTAAAATTAATA-AAAAAAGTACTAAATTATACCCATT
65 AAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCCATT
*
50536 T-AAAAGTTA-GACCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTCAGGTGCAAAT
130 TAAAAAGTTAGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTCA--TGCAAAT
50599 -AAATTTGGAGGAC
193 AAAATTTGGAGGAC
* * * *
50612 TAAA-TGAATAA-ATGAAATTACAAATAAAAA-TTAAATATATTAAACAACACAA-AATGGATCG
1 TAAATTGAAAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACAATAAGGGATCA
*
50673 AATCAAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAA
66 AATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAA
50715 TTTATACTCA
Statistics
Matches: 481, Mismatches: 24, Indels: 44
0.88 0.04 0.08
Matches are distributed among these distances:
200 65 0.14
201 22 0.05
202 2 0.00
203 5 0.01
204 17 0.04
205 18 0.04
206 30 0.06
207 8 0.02
208 25 0.05
209 42 0.09
210 23 0.05
211 11 0.02
212 110 0.23
213 27 0.06
214 49 0.10
215 27 0.06
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (206 bp):
TAAATTGAAAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACAATAAGGGATCA
AATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCCATTT
AAAAAGTTAGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTCATGCAAATAAA
ATTTGGAGGAC
Found at i:50805 original size:2 final size:2
Alignment explanation
Indices: 50800--50909 Score: 64
Period size: 2 Copynumber: 54.5 Consensus size: 2
50790 AAAACAACTA
* * *
50800 AT AT AT AT AT AT AA AT AT AT AT A- AT AT AA ACT AT AT AGT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT
* * * * *
50843 AT AT AA AGT AT AT GT -T AT AT AT AA AA AT AT AG AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
50885 AT GT AT A- AA AT AT AA ACT AT AT AT A
1 AT AT AT AT AT AT AT AT A-T AT AT AT A
50910 CCATGTATAA
Statistics
Matches: 83, Mismatches: 18, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
1 3 0.04
2 76 0.92
3 4 0.05
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.41
Consensus pattern (2 bp):
AT
Found at i:50848 original size:20 final size:18
Alignment explanation
Indices: 50805--50883 Score: 85
Period size: 18 Copynumber: 4.4 Consensus size: 18
50795 AACTAATATA
50805 TATATATAAATATATA--
1 TATATATAAATATATAGT
50821 TA-ATATAAACTATATAGTT
1 TATATATAAA-TATATAG-T
50840 TATATATAAAGTATAT-GT
1 TATATATAAA-TATATAGT
* *
50858 TATATATAAAAATATAGA
1 TATATATAAATATATAGT
50876 TATATATA
1 TATATATA
50884 TATGTATAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
15 7 0.13
16 8 0.15
17 4 0.07
18 20 0.37
19 3 0.06
20 12 0.22
ACGTcount: A:0.52, C:0.01, G:0.05, T:0.42
Consensus pattern (18 bp):
TATATATAAATATATAGT
Found at i:50879 original size:25 final size:25
Alignment explanation
Indices: 50804--50935 Score: 71
Period size: 26 Copynumber: 5.4 Consensus size: 25
50794 CAACTAATAT
* * *
50804 ATATATATAAATATATATAATATAA
1 ATATATATATATATATAAAATATAG
* *
50829 ACTATATAGTTTATATAT-AAA-GT--
1 A-TATATA-TATATATATAAAATATAG
*
50852 ATATGT-TATATATA-AAAATATAG
1 ATATATATATATATATAAAATATAG
* *
50875 ATATATATATATGTATAAAATATAA
1 ATATATATATATATATAAAATATAG
* * *
50900 ACTATATATACCATGTATAAACTATA-
1 A-TATATATA-TATATATAAAATATAG
50926 ATACTATATA
1 ATA-TATATA
50936 GTTTATGAAC
Statistics
Matches: 84, Mismatches: 12, Indels: 21
0.72 0.10 0.18
Matches are distributed among these distances:
20 10 0.12
21 1 0.01
22 4 0.05
23 6 0.07
24 7 0.08
25 13 0.15
26 23 0.27
27 20 0.24
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.39
Consensus pattern (25 bp):
ATATATATATATATATAAAATATAG
Found at i:50891 original size:26 final size:28
Alignment explanation
Indices: 50862--50935 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 28
50852 ATATGTTATA
* *
50862 TATAAAAATATAGA-TATATATA-TATG
1 TATAAAAATATAAACTATATATACCATG
50888 TAT-AAAATATAAACTATATATACCATG
1 TATAAAAATATAAACTATATATACCATG
*
50915 TAT-AAACTATAATACTATATA
1 TATAAAAATATAA-ACTATATA
50936 GTTTATGAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
25 9 0.21
26 11 0.26
27 14 0.33
28 8 0.19
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (28 bp):
TATAAAAATATAAACTATATATACCATG
Found at i:50907 original size:28 final size:28
Alignment explanation
Indices: 50875--50935 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
50865 AAAAATATAG
*
50875 ATATATATATATGTATAAAATATAA-ACT
1 ATATATA-ACATGTATAAAATATAATACT
* *
50903 ATATATACCATGTATAAACTATAATACT
1 ATATATAACATGTATAAAATATAATACT
50931 ATATA
1 ATATA
50936 GTTTATGAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 14 0.48
28 15 0.52
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (28 bp):
ATATATAACATGTATAAAATATAATACT
Found at i:51075 original size:47 final size:47
Alignment explanation
Indices: 50984--51075 Score: 109
Period size: 47 Copynumber: 2.0 Consensus size: 47
50974 TTATACAAAT
* *
50984 TATATGAATTATATATAAACTATACAATTTATAAATGTATTACTATA
1 TATATGAATTATATATAAACTATACAATATATAAATATATTACTATA
*
51031 TATATGAATTATAGT-T-AACTATGAACTATATATAAATATA-TACTA
1 TATATGAATTATA-TATAAACTAT--ACAATATATAAATATATTACTA
51076 GGTTGATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
46 6 0.15
47 19 0.49
48 14 0.36
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (47 bp):
TATATGAATTATATATAAACTATACAATATATAAATATATTACTATA
Found at i:51101 original size:17 final size:17
Alignment explanation
Indices: 51081--51194 Score: 70
Period size: 17 Copynumber: 6.2 Consensus size: 17
51071 TACTAGGTTG
*
51081 ATATTTATATATGAACT
1 ATATTTACATATGAACT
*
51098 ATATTTACATATAAACT
1 ATATTTACATATGAACT
* *
51115 ATATAATATATACT-AACT
1 ATAT-TTACATA-TGAACT
*
51133 -TAGTTTACATATAAACTATAGTT
1 ATA-TTTACATATGAAC------T
51156 AATATTTACATATGAACT
1 -ATATTTACATATGAACT
*
51174 ATAATTACATATGAACT
1 ATATTTACATATGAACT
51191 ATAT
1 ATAT
51195 ATGTAAACTA
Statistics
Matches: 76, Mismatches: 9, Indels: 24
0.70 0.08 0.22
Matches are distributed among these distances:
16 1 0.01
17 48 0.63
18 11 0.14
19 1 0.01
23 1 0.01
24 12 0.16
25 2 0.03
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.41
Consensus pattern (17 bp):
ATATTTACATATGAACT
Found at i:51227 original size:2 final size:2
Alignment explanation
Indices: 51222--51290 Score: 70
Period size: 2 Copynumber: 33.5 Consensus size: 2
51212 TACATATGAC
*
51222 AT AT AT AT AT AT AT AT AT AG AT AT AT -T AT AT AT ACT AT AGT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A-T AT
*
51264 GAT AT TT AT AT ACT AT AT AT AT AT AT A
1 -AT AT AT AT AT A-T AT AT AT AT AT AT A
51291 AACTATATGT
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
1 2 0.04
2 49 0.86
3 6 0.11
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:51390 original size:16 final size:16
Alignment explanation
Indices: 51369--51471 Score: 109
Period size: 16 Copynumber: 6.2 Consensus size: 16
51359 GTTTATTAGT
51369 ATATATAAACTATATA
1 ATATATAAACTATATA
* *
51385 ATATATAGACTATATGGT
1 ATATATAAACTATAT--A
*
51403 ATATATAAACTATACA
1 ATATATAAACTATATA
*
51419 TTATATATAACTATATA
1 ATATATA-AACTATATA
*
51436 TTATATAAACTATAGT-
1 ATATATAAACTATA-TA
*
51452 ATATATAAACTATATT
1 ATATATAAACTATATA
51468 ATAT
1 ATAT
51472 GTTCAGTATA
Statistics
Matches: 74, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
15 1 0.01
16 44 0.59
17 16 0.22
18 13 0.18
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.41
Consensus pattern (16 bp):
ATATATAAACTATATA
Found at i:51479 original size:27 final size:26
Alignment explanation
Indices: 51449--51545 Score: 85
Period size: 27 Copynumber: 3.7 Consensus size: 26
51439 TATAAACTAT
51449 AGTATATATAAACTATATTATATGTTC
1 AGTATATATAAA-TATATTATATGTTC
* *
51476 AGTATATATAACCTATAGTATATG---
1 AGTATATATAA-ATATATTATATGTTC
*
51500 -GTATATACAAATATATTATATAGTTC
1 AGTATATATAAATATATTATAT-GTTC
51526 ATTAGTATATATAAATATAT
1 ---AGTATATATAAATATAT
51546 ATTAATTTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
22 9 0.16
23 10 0.18
27 21 0.38
30 15 0.27
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.42
Consensus pattern (26 bp):
AGTATATATAAATATATTATATGTTC
Found at i:51546 original size:10 final size:10
Alignment explanation
Indices: 51531--51567 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
51521 AGTTCATTAG
51531 TATATATAAA
1 TATATATAAA
*
51541 TATATATTAA
1 TATATATAAA
*
51551 TTTATATAAA
1 TATATATAAA
51561 TATATAT
1 TATATAT
51568 TAATCGAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
TATATATAAA
Found at i:51549 original size:20 final size:20
Alignment explanation
Indices: 51526--51571 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
51516 TATATAGTTC
*
51526 ATTAGTATATATAAATATAT
1 ATTAATATATATAAATATAT
*
51546 ATTAATTTATATAAATATAT
1 ATTAATATATATAAATATAT
51566 ATTAAT
1 ATTAAT
51572 CGAAAGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
ATTAATATATATAAATATAT
Found at i:52253 original size:23 final size:24
Alignment explanation
Indices: 52227--52277 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
52217 AATATTTTTT
52227 ATTTATATAAATTAAACTATA-TA
1 ATTTATATAAATTAAACTATATTA
*
52250 ATTTATATAAATTAAATTATATTA
1 ATTTATATAAATTAAACTATATTA
52274 ATTT
1 ATTT
52278 TCTTTTGCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
ATTTATATAAATTAAACTATATTA
Found at i:52574 original size:16 final size:16
Alignment explanation
Indices: 52548--52697 Score: 212
Period size: 16 Copynumber: 9.4 Consensus size: 16
52538 CGAATCATTT
* *
52548 ACAGATCAGGTTAAAA
1 ACAGGTCAGGTTGAAA
* *
52564 ACAAGTCAGGTTAAAA
1 ACAGGTCAGGTTGAAA
* *
52580 ATAGGTCAGATTGAAA
1 ACAGGTCAGGTTGAAA
*
52596 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTGAAA
*
52612 AGAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
52628 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
52644 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
*
52660 ACATGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
52676 ACAGGTCAGGTTG-AA
1 ACAGGTCAGGTTGAAA
52691 ACAGGTC
1 ACAGGTC
52698 GGGTAATACC
Statistics
Matches: 120, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
15 9 0.08
16 111 0.93
ACGTcount: A:0.41, C:0.12, G:0.27, T:0.20
Consensus pattern (16 bp):
ACAGGTCAGGTTGAAA
Found at i:56099 original size:31 final size:30
Alignment explanation
Indices: 56064--56140 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 30
56054 AGTTACATCA
56064 GGGACCATATTGCAAACAGACTAAATGTTTG
1 GGGACCATATTGCAAACAGACTAAATG-TTG
* *
56095 GGGACCATATTGAAAACATACTAAATGTTG
1 GGGACCATATTGCAAACAGACTAAATGTTG
**
56125 GGAGACTGTATTGCAA
1 GG-GACCATATTGCAA
56141 GTTTTAAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 5 0.12
31 35 0.88
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.26
Consensus pattern (30 bp):
GGGACCATATTGCAAACAGACTAAATGTTG
Found at i:56266 original size:14 final size:12
Alignment explanation
Indices: 56237--56262 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
56227 ATAAAAAAAA
56237 TTAAAAATAATT
1 TTAAAAATAATT
56249 TTAAAAATAATT
1 TTAAAAATAATT
56261 TT
1 TT
56263 TTAATTAGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TTAAAAATAATT
Found at i:56690 original size:30 final size:30
Alignment explanation
Indices: 56656--56718 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
56646 TATAAAATAA
*
56656 TTTAATTATA-TTCAATATTCAATATTCAAT
1 TTTAATTATACTTCAA-AATCAATATTCAAT
* *
56686 TTTAATTATACTTTAAAATCAATATTTAAT
1 TTTAATTATACTTCAAAATCAATATTCAAT
56716 TTT
1 TTT
56719 TCATTATGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 25 0.86
31 4 0.14
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (30 bp):
TTTAATTATACTTCAAAATCAATATTCAAT
Found at i:57013 original size:31 final size:31
Alignment explanation
Indices: 56964--57041 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
56954 CTTTTAAAAC
** *
56964 TTGCAATACAATCTCCCAACATTTAGTCCGT
1 TTGCAATATGATCCCCCAACATTTAGTCCGT
* *
56995 TTTCAATATGATCCCCCAACATTTAGTTCGT
1 TTGCAATATGATCCCCCAACATTTAGTCCGT
*
57026 TTGCAATATGGTCCCC
1 TTGCAATATGATCCCC
57042 GACGTAACTG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.35
Consensus pattern (31 bp):
TTGCAATATGATCCCCCAACATTTAGTCCGT
Found at i:57715 original size:21 final size:21
Alignment explanation
Indices: 57691--57736 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
57681 CGCAAGGCAG
*
57691 TTTCGAAAATCGCAACGCGAT
1 TTTCCAAAATCGCAACGCGAT
* * *
57712 TTTCCAAATTTGCGACGCGAT
1 TTTCCAAAATCGCAACGCGAT
57733 TTTC
1 TTTC
57737 AAATCCGTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (21 bp):
TTTCCAAAATCGCAACGCGAT
Found at i:57720 original size:20 final size:19
Alignment explanation
Indices: 57697--57741 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
57687 GCAGTTTCGA
57697 AAATCGCAACGCGATTTTCC
1 AAATCGCAACGCGATTTT-C
* *
57717 AAATTTGCGACGCGATTTTC
1 AAA-TCGCAACGCGATTTTC
57737 AAATC
1 AAATC
57742 CGTAACGCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 7 0.33
21 13 0.62
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (19 bp):
AAATCGCAACGCGATTTTC
Found at i:57803 original size:20 final size:20
Alignment explanation
Indices: 57778--57826 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
57768 AACAGTACTA
57778 TCGCAACGCGATTTTCAAAT
1 TCGCAACGCGATTTTCAAAT
*
57798 TCGCAACACGATTTTCAAAT
1 TCGCAACGCGATTTTCAAAT
*
57818 CCGCAACGC
1 TCGCAACGC
57827 TAATTACCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.31, C:0.31, G:0.14, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGATTTTCAAAT
Found at i:57827 original size:77 final size:77
Alignment explanation
Indices: 57699--57880 Score: 301
Period size: 77 Copynumber: 2.4 Consensus size: 77
57689 AGTTTCGAAA
* * * *
57699 ATCGCAACGCGATTTTCCAAATTTGCGACGCGATTTTCAAATCCGTAACGCTAATTACCGATATA
1 ATCGCAACGCGATTTT-CAAATTCGCAACACGATTTTCAAATCCGCAACGCTAATTACCGATATA
*
57764 GGTAAACAGTACT
65 GGTAAACAATACT
57777 ATCGCAACGCGATTTTCAAATTCGCAACACGATTTTCAAATCCGCAACGCTAATTACCGATATAG
1 ATCGCAACGCGATTTTCAAATTCGCAACACGATTTTCAAATCCGCAACGCTAATTACCGATATAG
57842 GTAAACAATACT
66 GTAAACAATACT
*
57854 ATCGCAACGCGATTTTCAAATCCGCAA
1 ATCGCAACGCGATTTTCAAATTCGCAA
57881 TGCTAATCAC
Statistics
Matches: 98, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
77 82 0.84
78 16 0.16
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (77 bp):
ATCGCAACGCGATTTTCAAATTCGCAACACGATTTTCAAATCCGCAACGCTAATTACCGATATAG
GTAAACAATACT
Found at i:57886 original size:57 final size:57
Alignment explanation
Indices: 57798--57940 Score: 232
Period size: 57 Copynumber: 2.5 Consensus size: 57
57788 ATTTTCAAAT
*
57798 TCGCAACACGATTTTCAAATCCGCAACGCTAATTACCGATATAGGTAAACAATACTA
1 TCGCAACACGATTTTCAAATCCGCAACGCTAATCACCGATATAGGTAAACAATACTA
* * * *
57855 TCGCAACGCGATTTTCAAATCCGCAATGCTAATCACTGATATAGGTAAACAGTACTA
1 TCGCAACACGATTTTCAAATCCGCAACGCTAATCACCGATATAGGTAAACAATACTA
*
57912 TCGCAACACGATTTTCAAATTCGCAACGC
1 TCGCAACACGATTTTCAAATCCGCAACGC
57941 GATTTTCAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 78 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (57 bp):
TCGCAACACGATTTTCAAATCCGCAACGCTAATCACCGATATAGGTAAACAATACTA
Found at i:57936 original size:77 final size:77
Alignment explanation
Indices: 57855--58102 Score: 370
Period size: 77 Copynumber: 3.2 Consensus size: 77
57845 AACAATACTA
* * * *
57855 TCGCAACGCGATTTTCAAATCCGCAATGCTAATCACTGATATAGGTAAACAGTACTATCGCAACA
1 TCGCAACGCGATTTTCAAATCCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACG
57920 CGATTTTCAAAT
66 CGATTTTCAAAT
*
57932 TCGCAACGCGATTTTCAAATCCGCAACGCTAATTACCGATATAGGTAAACAGTACTATAGCAACG
1 TCGCAACGCGATTTTCAAATCCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACG
*
57997 CGGTTTTCAAAT
66 CGATTTTCAAAT
* * * * *
58009 TCGTAATGCGATTTTCAAATCCGCAACGCTGATTACGGATATAGGTAAACAATACTATCGCAACG
1 TCGCAACGCGATTTTCAAATCCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACG
58074 CGATTTTCAAAT
66 CGATTTTCAAAT
* **
58086 TCGTAACGTTATTTTCA
1 TCGCAACGCGATTTTCA
58103 CAAATTGAAT
Statistics
Matches: 155, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 155 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (77 bp):
TCGCAACGCGATTTTCAAATCCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACG
CGATTTTCAAAT
Found at i:57959 original size:20 final size:20
Alignment explanation
Indices: 57913--57960 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
57903 ACAGTACTAT
* *
57913 CGCAACACGATTTTCAAATT
1 CGCAACGCGATTTTCAAATC
57933 CGCAACGCGATTTTCAAATC
1 CGCAACGCGATTTTCAAATC
57953 CGCAACGC
1 CGCAACGC
57961 TAATTACCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.23
Consensus pattern (20 bp):
CGCAACGCGATTTTCAAATC
Found at i:57966 original size:134 final size:134
Alignment explanation
Indices: 57726--58017 Score: 494
Period size: 134 Copynumber: 2.2 Consensus size: 134
57716 CAAATTTGCG
* * *
57726 ACGCGATTTTCAAATCCGTAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCGATT
1 ACGCGATTTTCAAATCCGTAATGCTAATCACCGATATAGGTAAACAGTACTATCGCAACACGATT
57791 TTCAAATTCGCAACACGATTTTCAAATCCGCAACGCTAATTACCGATATAGGTAAACAATACTAT
66 TTCAAATTCGCAACACGATTTTCAAATCCGCAACGCTAATTACCGATATAGGTAAACAATACTAT
*
57856 CGCA
131 AGCA
* *
57860 ACGCGATTTTCAAATCCGCAATGCTAATCACTGATATAGGTAAACAGTACTATCGCAACACGATT
1 ACGCGATTTTCAAATCCGTAATGCTAATCACCGATATAGGTAAACAGTACTATCGCAACACGATT
* *
57925 TTCAAATTCGCAACGCGATTTTCAAATCCGCAACGCTAATTACCGATATAGGTAAACAGTACTAT
66 TTCAAATTCGCAACACGATTTTCAAATCCGCAACGCTAATTACCGATATAGGTAAACAATACTAT
57990 AGCA
131 AGCA
* *
57994 ACGCGGTTTTCAAATTCGTAATGC
1 ACGCGATTTTCAAATCCGTAATGC
58018 GATTTTCAAA
Statistics
Matches: 147, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
134 147 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (134 bp):
ACGCGATTTTCAAATCCGTAATGCTAATCACCGATATAGGTAAACAGTACTATCGCAACACGATT
TTCAAATTCGCAACACGATTTTCAAATCCGCAACGCTAATTACCGATATAGGTAAACAATACTAT
AGCA
Found at i:58244 original size:57 final size:57
Alignment explanation
Indices: 58156--58280 Score: 214
Period size: 57 Copynumber: 2.2 Consensus size: 57
58146 TTTGCGAAAT
** *
58156 TCGCGTTGCGATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTAAAAA
1 TCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCATTGCGAATTTAAAAA
*
58213 TCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCATTGCGAATTTGAAAA
1 TCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCATTGCGAATTTAAAAA
58270 TCGCGTTGCGA
1 TCGCGTTGCGA
58281 AATTAGAGTT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 64 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (57 bp):
TCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCATTGCGAATTTAAAAA
Found at i:59171 original size:13 final size:13
Alignment explanation
Indices: 59153--59178 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59143 ATTTTTATGA
59153 AAACCAGTTTCAT
1 AAACCAGTTTCAT
59166 AAACCAGTTTCAT
1 AAACCAGTTTCAT
59179 GATAAAGTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
AAACCAGTTTCAT
Found at i:60855 original size:6 final size:6
Alignment explanation
Indices: 60846--60891 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
60836 TTACATTTAT
* * *
60846 TTAGAA TTAGAC TTAGAA TTAGAA TTAGGA TTTGAA TTAGAA TTAG
1 TTAGAA TTAGAA TTAGAA TTAGAA TTAGAA TTAGAA TTAGAA TTAG
60892 GATTTATTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (6 bp):
TTAGAA
Found at i:60892 original size:18 final size:18
Alignment explanation
Indices: 60846--60896 Score: 77
Period size: 18 Copynumber: 2.8 Consensus size: 18
60836 TTACATTTAT
*
60846 TTAGAATTA-GACTTAGAA
1 TTAGAATTAGGA-TTTGAA
60864 TTAGAATTAGGATTTGAA
1 TTAGAATTAGGATTTGAA
60882 TTAGAATTAGGATTT
1 TTAGAATTAGGATTT
60897 ATTTACGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 29 0.94
19 2 0.06
ACGTcount: A:0.39, C:0.02, G:0.20, T:0.39
Consensus pattern (18 bp):
TTAGAATTAGGATTTGAA
Found at i:61443 original size:12 final size:12
Alignment explanation
Indices: 61426--61450 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
61416 TTTTAATAAA
61426 AAATATTATTTT
1 AAATATTATTTT
61438 AAATATTATTTT
1 AAATATTATTTT
61450 A
1 A
61451 TTAAAAATAT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AAATATTATTTT
Found at i:62993 original size:23 final size:23
Alignment explanation
Indices: 62966--63010 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
62956 TATTTAAAAT
*
62966 ATTAAGACTTAATAA-ATTTTAAC
1 ATTAA-ACCTAATAATATTTTAAC
*
62989 ATTAAACCTATTAATATTTTAA
1 ATTAAACCTAATAATATTTTAA
63011 AACCCAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (23 bp):
ATTAAACCTAATAATATTTTAAC
Found at i:65800 original size:18 final size:18
Alignment explanation
Indices: 65777--65811 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
65767 AATTATAAGG
*
65777 ATTTATTTAAATTTAATC
1 ATTTATTAAAATTTAATC
65795 ATTTATTAAAATTTAAT
1 ATTTATTAAAATTTAAT
65812 TATAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTATTAAAATTTAATC
Found at i:65846 original size:17 final size:18
Alignment explanation
Indices: 65804--65846 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
65794 CATTTATTAA
65804 AATT-TAATTATAATTTT
1 AATTATAATTATAATTTT
*
65821 AA-TAGAATTATAA-TTT
1 AATTATAATTATAATTTT
65837 AATTATAATT
1 AATTATAATT
65847 TTTATTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
AATTATAATTATAATTTT
Found at i:65946 original size:17 final size:17
Alignment explanation
Indices: 65924--65958 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
65914 AGTTAAAATT
*
65924 ATAATTAATTTTAATAA
1 ATAATTAAATTTAATAA
*
65941 ATAATTAAATTTATTAA
1 ATAATTAAATTTAATAA
65958 A
1 A
65959 ATGAATAGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATAATTAAATTTAATAA
Found at i:67439 original size:12 final size:11
Alignment explanation
Indices: 67406--67440 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
67396 ATTAGGTTAT
67406 AAACAATTCAA
1 AAACAATTCAA
*
67417 AAACAACTCAA
1 AAACAATTCAA
67428 AAACCAATTCAA
1 AAA-CAATTCAA
67440 A
1 A
67441 TGAATTCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.63, C:0.23, G:0.00, T:0.14
Consensus pattern (11 bp):
AAACAATTCAA
Found at i:72520 original size:6 final size:6
Alignment explanation
Indices: 72509--72541 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
72499 TAAAGAGAAG
72509 GCCTAA GCCTAA GCCTAA GCCTAA GCCTAA GCC
1 GCCTAA GCCTAA GCCTAA GCCTAA GCCTAA GCC
72542 AGTCCTGGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.30, C:0.36, G:0.18, T:0.15
Consensus pattern (6 bp):
GCCTAA
Found at i:74408 original size:24 final size:24
Alignment explanation
Indices: 74368--74417 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
74358 ACTCTTAACC
*
74368 TTTTAACCTTTTTGATATTAATCT
1 TTTTAACCTTTTCGATATTAATCT
*
74392 TTTTAAACC-TTTCGATATTGATCT
1 TTTT-AACCTTTTCGATATTAATCT
74416 TT
1 TT
74418 CAAAAATTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.14, G:0.06, T:0.56
Consensus pattern (24 bp):
TTTTAACCTTTTCGATATTAATCT
Found at i:74807 original size:15 final size:15
Alignment explanation
Indices: 74787--74817 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
74777 ACATAAAATA
74787 CCCTCTCCCCACCTC
1 CCCTCTCCCCACCTC
74802 CCCTCTCCCCACCTC
1 CCCTCTCCCCACCTC
74817 C
1 C
74818 ACCGTAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.74, G:0.00, T:0.19
Consensus pattern (15 bp):
CCCTCTCCCCACCTC
Found at i:75219 original size:27 final size:28
Alignment explanation
Indices: 75183--75237 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
75173 GTCGAATTTA
*
75183 AACTCGAGTCAAGTATTTATCAAACTTT
1 AACTCGAGTCAACTATTTATCAAACTTT
* *
75211 AACT-GAGTCGACTATTTATCAAGCTTT
1 AACTCGAGTCAACTATTTATCAAACTTT
75238 TTGAGTAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (28 bp):
AACTCGAGTCAACTATTTATCAAACTTT
Found at i:76488 original size:53 final size:52
Alignment explanation
Indices: 76430--76587 Score: 235
Period size: 53 Copynumber: 3.0 Consensus size: 52
76420 ACAGAAGATC
* * *
76430 GTGTTGATTGTAAGAGATGCAAATCTGCTTTAAAGAACAATTTGATAAAAAAT
1 GTGTTGATTGTAAGAGATGCGAATCCG-TTTAAAGAACAATTCGATAAAAAAT
*
76483 GTGTTGATTGTAAGAGATGCGAATCCGTTTTAAGAAACAATTCGATAAAAAAT
1 GTGTTGATTGTAAGAGATGCGAATCCGTTTAAAG-AACAATTCGATAAAAAAT
* *
76536 ATGTTGATTGTAAGAGATGCGAATCCGTTTTAAGGAACAATTCGATAAAAAA
1 GTGTTGATTGTAAGAGATGCGAATCCG-TTTAAAGAACAATTCGATAAAAAA
76588 AAAGATATAG
Statistics
Matches: 96, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
52 6 0.06
53 85 0.89
54 5 0.05
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (52 bp):
GTGTTGATTGTAAGAGATGCGAATCCGTTTAAAGAACAATTCGATAAAAAAT
Found at i:80458 original size:34 final size:31
Alignment explanation
Indices: 80388--80476 Score: 97
Period size: 34 Copynumber: 2.7 Consensus size: 31
80378 TTAGTATTTT
* * *
80388 TTTAAATAGTTATTATATTTTATATTAATATA
1 TTTATATAATTATTAT-TTTTTTATTAATATA
*
80420 TTTATGTAATTATTATTTTTTTATTAAAATAATA
1 TTTATATAATTATTATTTTTTTATT--AAT-ATA
*
80454 TTTATATAATTATTATTTATTTA
1 TTTATATAATTATTATTTTTTTA
80477 GAATTATTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
31 8 0.17
32 13 0.27
33 3 0.06
34 24 0.50
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (31 bp):
TTTATATAATTATTATTTTTTTATTAATATA
Found at i:83455 original size:16 final size:16
Alignment explanation
Indices: 83420--83462 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
83410 AATTTTTTCA
* *
83420 AAAATATATGAAATTTT
1 AAAATAT-TTAAATTAT
*
83437 AAAATTTTTAAATTAT
1 AAAATATTTAAATTAT
83453 AAAATATTTA
1 AAAATATTTA
83463 TCATCATCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
AAAATATTTAAATTAT
Found at i:84000 original size:10 final size:11
Alignment explanation
Indices: 83977--84003 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
83967 AAAATTAAAA
83977 TTTAATATTTT
1 TTTAATATTTT
83988 TTTAATATTTT
1 TTTAATATTTT
83999 TTTAA
1 TTTAA
84004 AATTAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTAATATTTT
Found at i:84116 original size:10 final size:10
Alignment explanation
Indices: 84062--84118 Score: 69
Period size: 10 Copynumber: 5.6 Consensus size: 10
84052 TTTACATTAT
84062 ATTTTTATTG
1 ATTTTTATTG
*
84072 AATTTTATTG
1 ATTTTTATTG
* *
84082 AATTTTATTC
1 ATTTTTATTG
84092 ATTTTTATTGG
1 ATTTTTATT-G
*
84103 ATTTTTATTT
1 ATTTTTATTG
84113 ATTTTT
1 ATTTTT
84119 TAAAAAAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
10 32 0.78
11 9 0.22
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.68
Consensus pattern (10 bp):
ATTTTTATTG
Found at i:88539 original size:66 final size:67
Alignment explanation
Indices: 88462--88595 Score: 243
Period size: 66 Copynumber: 2.0 Consensus size: 67
88452 CATCTTTTAC
* *
88462 GAGAATGATGGGTTTAAATGAGTTGTATTTGTATTG-TTTTGTTTTTGAAATTAGGTTTCATCTC
1 GAGAATGATGGGTTTAAATGAGTTATATTTGTATTGTTTTTGTTTTTGAAATTAGGGTTCATCTC
88526 AA
66 AA
88528 GAGAATGATGGGTTTAAATGAGTTATATTTGTATTGTTTTTGTTTTTGAAATTAGGGTTCATCTC
1 GAGAATGATGGGTTTAAATGAGTTATATTTGTATTGTTTTTGTTTTTGAAATTAGGGTTCATCTC
88593 AA
66 AA
88595 G
1 G
88596 TCATACGTTT
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
66 35 0.54
67 30 0.46
ACGTcount: A:0.26, C:0.04, G:0.23, T:0.46
Consensus pattern (67 bp):
GAGAATGATGGGTTTAAATGAGTTATATTTGTATTGTTTTTGTTTTTGAAATTAGGGTTCATCTC
AA
Done.