Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006124.1 Hibiscus syriacus cultivar Beakdansim tig00014524_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: 97783
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:56 original size:35 final size:36
Alignment explanation
Indices: 4--73 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 36
1 TTT
4 CATTCTAAACCCTAAATTC-CAAAATAATTCAATTA
1 CATTCTAAACCCTAAATTCTCAAAATAATTCAATTA
* *
39 CATTCTAAA-ACTCAAATTCTCAAAATATTTCAATT
1 CATTCTAAACCCT-AAATTCTCAAAATAATTCAATT
74 TAAGGAGGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 2 0.06
35 15 0.48
36 14 0.45
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.34
Consensus pattern (36 bp):
CATTCTAAACCCTAAATTCTCAAAATAATTCAATTA
Found at i:1159 original size:35 final size:35
Alignment explanation
Indices: 1111--1210 Score: 130
Period size: 35 Copynumber: 2.9 Consensus size: 35
1101 AAAAAGACAG
* * *
1111 AAATTGAAGTATTTTAGAATTT-GGGTTTTAGAATG
1 AAATTGAATTATTTTGGAATTTAGGG-TTTAGAATA
*
1146 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATA
1 AAATTGAATTATTTTGGAATTTAGGGTTTAGAATA
* *
1181 AAATTGAATTACTTTGGAATTTATGGTTTA
1 AAATTGAATTATTTTGGAATTTAGGGTTTA
1211 TTTTGGATTG
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
35 54 0.95
36 3 0.05
ACGTcount: A:0.34, C:0.01, G:0.20, T:0.45
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTAGGGTTTAGAATA
Found at i:4391 original size:78 final size:79
Alignment explanation
Indices: 4230--4461 Score: 393
Period size: 79 Copynumber: 3.0 Consensus size: 79
4220 TTTGAGATCA
* *
4230 TTGAGACTCAAATAAGTCTAATAGTTTTC-AATAAAATGGTTTTGTTTTAGTAGGGGAAGAAGTG
1 TTGAGACTCAAATAAGTCTAATAG-TTTCAAATAAAATGGTTCTGTTTTAGTAGGGGAAGCAGTG
4294 GATCAAATGATAGAG
65 GATCAAATGATAGAG
4309 TTGAGACTCAAATAAGTCTAATAGTTTCAAATAAAATGGTTCTGTTTTAGTAGGGGAAGCA-TGG
1 TTGAGACTCAAATAAGTCTAATAGTTTCAAATAAAATGGTTCTGTTTTAGTAGGGGAAGCAGTGG
4373 ATCAAATGATAGAG
66 ATCAAATGATAGAG
*
4387 TTGAGACTCAAATAAG--T-ATAGTTTCAAATAAAATGGTTCTGTTTTAGTAGGGGAGGCAGTGG
1 TTGAGACTCAAATAAGTCTAATAGTTTCAAATAAAATGGTTCTGTTTTAGTAGGGGAAGCAGTGG
4449 ATCAAATGATAGA
66 ATCAAATGATAGA
4462 ACTTGTGTCA
Statistics
Matches: 148, Mismatches: 3, Indels: 7
0.94 0.02 0.04
Matches are distributed among these distances:
75 40 0.27
76 17 0.11
78 37 0.25
79 54 0.36
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.31
Consensus pattern (79 bp):
TTGAGACTCAAATAAGTCTAATAGTTTCAAATAAAATGGTTCTGTTTTAGTAGGGGAAGCAGTGG
ATCAAATGATAGAG
Found at i:12521 original size:14 final size:15
Alignment explanation
Indices: 12493--12522 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12483 ACTTGGCAAC
12493 AAGAGGGGTATAAAA
1 AAGAGGGGTATAAAA
12508 AAGAGGGG-ATAAAA
1 AAGAGGGGTATAAAA
12522 A
1 A
12523 TGCATTGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.57, C:0.00, G:0.33, T:0.10
Consensus pattern (15 bp):
AAGAGGGGTATAAAA
Found at i:14023 original size:4 final size:4
Alignment explanation
Indices: 14016--14041 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
14006 AAATAAACCC
14016 CTGG CTGG CTGG CTGG CTGG CTGG CT
1 CTGG CTGG CTGG CTGG CTGG CTGG CT
14042 AGACCTGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.27, G:0.46, T:0.27
Consensus pattern (4 bp):
CTGG
Found at i:20822 original size:213 final size:211
Alignment explanation
Indices: 20444--20852 Score: 588
Period size: 213 Copynumber: 1.9 Consensus size: 211
20434 AGTAAACAAG
*
20444 GTGAGATGAATTGTTGTAAAAGATAAAATAGAATATATTATTTTAATCAATATTTTTTAATTTAA
1 GTGAGATGAATTGTGGTAAAAGATAAAATAGAATATATTATTTTAATCAATATTTTTTAATTTAA
* * *
20509 AAATTTAGAATAAAAGGTTGACATTAGTTTCTTACCTACGTCAAAGAGCACAAAGCTCAAGAAAT
66 AAATTTAAAATAAAAGGTTGACATTAGCTTCTTACCTACGTCAAAGAGCACAAAGCTCAAAAAAT
* * * * *
20574 AGGTGTGCATAATTGTTAAGTCTTAACATAATATATTAAATATTGGTACTTTTTAAGGAAAATGG
131 AGGTGTACAGAATTGTTAACTCTTAACAAAATATATTAAATATTGATACTTTTTAAGGAAAATGG
20639 GAAAAAGTAAAAAAAT
196 GAAAAAGTAAAAAAAT
* * * *
20655 GTGAGATGAATTGTGGTAAAAGGTACACT-GATATATATTATTTTAATCAGTATTTTTTTTAATT
1 GTGAGATGAATTGTGGTAAAAGATAAAATAGA-ATATATTATTTTAATCA--ATATTTTTTAATT
* * *
20719 TAAAAATTTAAAATAAAAGGTTGACATTGGCTTCTTA-CTCATGTCAAAGAGGACAAAGCTCAAA
63 TAAAAATTTAAAATAAAAGGTTGACATTAGCTTCTTACCT-ACGTCAAAGAGCACAAAGCTCAAA
* * * *
20783 AAATAGGTGTACAGAATTTTTAACTCTTAATAAAATATATTAAATGTTGATATTTTTTAAGGAAA
127 AAATAGGTGTACAGAATTGTTAACTCTTAACAAAATATATTAAATATTGATACTTTTTAAGGAAA
20848 ATGGG
192 ATGGG
20853 TATGCATTTG
Statistics
Matches: 174, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
210 2 0.01
211 42 0.24
212 2 0.01
213 128 0.74
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.35
Consensus pattern (211 bp):
GTGAGATGAATTGTGGTAAAAGATAAAATAGAATATATTATTTTAATCAATATTTTTTAATTTAA
AAATTTAAAATAAAAGGTTGACATTAGCTTCTTACCTACGTCAAAGAGCACAAAGCTCAAAAAAT
AGGTGTACAGAATTGTTAACTCTTAACAAAATATATTAAATATTGATACTTTTTAAGGAAAATGG
GAAAAAGTAAAAAAAT
Found at i:22758 original size:2 final size:2
Alignment explanation
Indices: 22751--22792 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
22741 GGTTAATAGA
22751 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22793 GAAACAAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27470 original size:18 final size:17
Alignment explanation
Indices: 27432--27471 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
27422 AAAATTATAT
* *
27432 ATTTTTTAAATAATTAC
1 ATTTTTTAAATAATAAA
27449 ATTTTTTACAATAATAAA
1 ATTTTTTA-AATAATAAA
27467 ATTTT
1 ATTTT
27472 AATCTCATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTTTAAATAATAAA
Found at i:33746 original size:20 final size:20
Alignment explanation
Indices: 33700--33746 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
33690 CCATTTTTAT
* *
33700 TTTTAACTTTTCATATATAA
1 TTTTAACTTATCATACATAA
33720 TTGTTAA-TTATCATACATAA
1 TT-TTAACTTATCATACATAA
33740 CTTTTAA
1 -TTTTAA
33747 GTAAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.51
Consensus pattern (20 bp):
TTTTAACTTATCATACATAA
Found at i:33931 original size:3 final size:3
Alignment explanation
Indices: 33923--33953 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
33913 AGTCTTCATA
33923 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
33954 CCAGTTTACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:35923 original size:21 final size:18
Alignment explanation
Indices: 35879--35948 Score: 113
Period size: 18 Copynumber: 3.7 Consensus size: 18
35869 AGGGATTATC
35879 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
35897 AGTGGTCCTTCGGGACATAT
1 AGTGGTCCTTCGGGAC--AT
35917 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
35936 AGTGGTCCTTCGG
1 AGTGGTCCTTCGG
35949 AACAAATATT
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
18 29 0.59
19 2 0.04
20 2 0.04
21 16 0.33
ACGTcount: A:0.16, C:0.23, G:0.33, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:37651 original size:30 final size:30
Alignment explanation
Indices: 37617--37692 Score: 145
Period size: 30 Copynumber: 2.6 Consensus size: 30
37607 TCTTTAACCG
37617 TTAATCGAACCGAAATTTATTTGAAATTTA
1 TTAATCGAACCGAAATTTATTTGAAATTTA
37647 TTAATCGAACCGAAATTTATTTGAAATTTA
1 TTAATCGAACCGAAATTTATTTGAAATTTA
37677 TTAATCGAACC-AAATT
1 TTAATCGAACCGAAATT
37693 AACCGTTAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 5 0.11
30 41 0.89
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (30 bp):
TTAATCGAACCGAAATTTATTTGAAATTTA
Found at i:37805 original size:94 final size:95
Alignment explanation
Indices: 37702--37932 Score: 392
Period size: 95 Copynumber: 2.4 Consensus size: 95
37692 TAACCGTTAA
37702 TCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCAATTAAT
1 TCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCAATTAAT
*
37767 -GTTAAAGAAAAAAATTCGGTTAATTTGGT
66 GGTTAAAGAAAAAAATTCGGTTAATTTGAT
* * *
37796 TCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACAGTCAAATGATTTCGGTTCGATTAAT
1 TCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCAATTAAT
*
37861 GGTTAAAGAAAAAAATTTGGTTAATTTGAT
66 GGTTAAAGAAAAAAATTCGGTTAATTTGAT
* *
37891 TCAGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACGGT
1 TCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGT
37933 TAAGGAAAAA
Statistics
Matches: 128, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
94 62 0.48
95 66 0.52
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.39
Consensus pattern (95 bp):
TCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCAATTAAT
GGTTAAAGAAAAAAATTCGGTTAATTTGAT
Found at i:37923 original size:69 final size:72
Alignment explanation
Indices: 37844--38006 Score: 197
Period size: 74 Copynumber: 2.3 Consensus size: 72
37834 CAGTCAAATG
* *
37844 ATTTCGGTTCGATTAATGGTTAAAGAAAAA-AATTT-GGTTAAT-TTGATTCAGTTAATAATTTT
1 ATTTCGGTTCGATTAACGGTTAAAGAAAAATAATTTAGGTTAATGTTAATTCAGTTAATAATTTT
37906 CAAATAA
66 CAAATAA
* * ** * *
37913 ATTTTGGTTCGATTAACGGTTAAGGAAAAATAATTTATTTTATTCGGTTAATTCGGTTAATAATT
1 ATTTCGGTTCGATTAACGGTTAAAGAAAAATAATTTAGGTTAAT--GTTAATTCAGTTAATAATT
37978 TTCAAATAA
64 TTCAAATAA
* *
37987 ATTTCGATTCTATTAACGGT
1 ATTTCGGTTCGATTAACGGT
38007 CAAATAATTT
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
69 27 0.35
70 5 0.06
71 4 0.05
74 42 0.54
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (72 bp):
ATTTCGGTTCGATTAACGGTTAAAGAAAAATAATTTAGGTTAATGTTAATTCAGTTAATAATTTT
CAAATAA
Found at i:38022 original size:100 final size:96
Alignment explanation
Indices: 37905--38101 Score: 234
Period size: 95 Copynumber: 2.0 Consensus size: 96
37895 TTAATAATTT
* * * * * * *
37905 TCAAATAAATTTTGGTTCGATTAACGGTTAAGGAAAAATAATTTATTTTATTCGGTTAATTCGGT
1 TCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAA-AAGTCAGTTGATTCGG----TTCAGT
*
37970 TAATAATTTTCAAATAAATTTCGATTCTATTAACGG
61 TAATAATTTTCAAATAAATTTCGATTCGATTAACGG
* * *
38006 TCAAAT-AATTTCGGTTCGATTAATGGTTAAAGAAAAAAAGTCGGTTGATTTGGTTCAGTTAATA
1 TCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAAAAGTCAGTTGATTCGGTTCAGTTAATA
*
38070 ATTTTCAAATAAATTTCGGTTCGATTAACGG
66 ATTTTCAAATAAATTTCGATTCGATTAACGG
38101 T
1 T
38102 TAAAGAAAAT
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
95 40 0.48
99 10 0.12
100 28 0.33
101 6 0.07
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (96 bp):
TCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAAAAGTCAGTTGATTCGGTTCAGTTAATA
ATTTTCAAATAAATTTCGATTCGATTAACGG
Found at i:38074 original size:169 final size:168
Alignment explanation
Indices: 37795--38223 Score: 696
Period size: 169 Copynumber: 2.5 Consensus size: 168
37785 GTTAATTTGG
* * *
37795 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACAGTCAAATGATTTCGGTTCGATTAA
1 TTCGGTTAATAATTTTCAAATAAATTTCGATTCGATTAACGGTCAAATAATTTCGGTTCGATTAA
* * *
37860 TGGTTAAAGAAAAAAATTTGGTTAATTTGATTCAGTTAATAATTTTCAAATAAATTTTGGTTCGA
66 TGGTTAAAGAAAAAAAGTCGGTTAATTTGATTCAGTTAATAATTTTCAAATAAATTTCGGTTCGA
* *
37925 TTAACGGTTAAGGAAAAATAATTTATTTTATTCGGTTAA
131 TTAACGGTTAAAG-AAAATAATTTATTTTATTCAGTTAA
*
37964 TTCGGTTAATAATTTTCAAATAAATTTCGATTCTATTAACGGTCAAATAATTTCGGTTCGATTAA
1 TTCGGTTAATAATTTTCAAATAAATTTCGATTCGATTAACGGTCAAATAATTTCGGTTCGATTAA
* *
38029 TGGTTAAAGAAAAAAAGTCGGTTGATTTGGTTCAGTTAATAATTTTCAAATAAATTTCGGTTCGA
66 TGGTTAAAGAAAAAAAGTCGGTTAATTTGATTCAGTTAATAATTTTCAAATAAATTTCGGTTCGA
38094 TTAACGGTTAAAGAAAATAATTTATTTTATTCAGTTAA
131 TTAACGGTTAAAGAAAATAATTTATTTTATTCAGTTAA
* * * *
38132 TTCGGTTAATACTTTTCAAATAAATTTGGTTTCGATTAACGGTCAAATAATTTTGGTTCGATTAA
1 TTCGGTTAATAATTTTCAAATAAATTTCGATTCGATTAACGGTCAAATAATTTCGGTTCGATTAA
*
38197 TGGTTAAAGAAAAAAAATTCGGTTAAT
66 TGGTTAAAG-AAAAAAAGTCGGTTAAT
38224 AATTTTCAAA
Statistics
Matches: 241, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
168 93 0.39
169 148 0.61
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.40
Consensus pattern (168 bp):
TTCGGTTAATAATTTTCAAATAAATTTCGATTCGATTAACGGTCAAATAATTTCGGTTCGATTAA
TGGTTAAAGAAAAAAAGTCGGTTAATTTGATTCAGTTAATAATTTTCAAATAAATTTCGGTTCGA
TTAACGGTTAAAGAAAATAATTTATTTTATTCAGTTAA
Found at i:38340 original size:63 final size:65
Alignment explanation
Indices: 38263--38416 Score: 240
Period size: 66 Copynumber: 2.4 Consensus size: 65
38253 TGGTCAAATA
*
38263 ATTCGATTAATGTTAAAGAAAAA-CGGTTAATTTGGTTCGGTTAATAATTTTCAAAT-AATTTCG
1 ATTCGATTAATGTTAAAGAAAAATCAGTTAATTTGGTTCGGTTAATAATTTTCAAATAAATTTCG
*
38326 GTTCGATTAATGTTAAAGAAAAATTTCAGTTAATTTGGTTCGGTTAATAATTTTCAAATAAATTT
1 ATTCGATTAATGTTAAAGAAAAA--TCAGTTAATTTGGTTCGGTTAATAATTTTCAAATAAATTT
38391 CG
64 CG
*
38393 ATTCGATTAACGGTTAAAGAAAAA
1 ATTCGATTAA-TGTTAAAGAAAAA
38417 ATAATTTATT
Statistics
Matches: 82, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
63 22 0.27
66 32 0.39
67 16 0.20
68 12 0.15
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (65 bp):
ATTCGATTAATGTTAAAGAAAAATCAGTTAATTTGGTTCGGTTAATAATTTTCAAATAAATTTCG
Found at i:43533 original size:16 final size:16
Alignment explanation
Indices: 43508--43541 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
43498 GGGAGATTAA
* *
43508 TTTTACTTTAATTTAT
1 TTTTAATTTAATATAT
43524 TTTTAATTTAATATAT
1 TTTTAATTTAATATAT
43540 TT
1 TT
43542 ATTTCTACCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTAATTTAATATAT
Found at i:43820 original size:29 final size:29
Alignment explanation
Indices: 43777--43846 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 29
43767 TAAATTTTAA
*
43777 AATTATCTCTTTATTTTTGTTTTAACTTATT
1 AATTAT-T-TTTATTTTTGTCTTAACTTATT
*
43808 AATTATTTTTATTTTTGTCTTAATTTATT
1 AATTATTTTTATTTTTGTCTTAACTTATT
*
43837 AAATATTTTT
1 AATTATTTTT
43847 TATCTTAATG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 29 0.81
30 1 0.03
31 6 0.17
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.66
Consensus pattern (29 bp):
AATTATTTTTATTTTTGTCTTAACTTATT
Found at i:43863 original size:23 final size:24
Alignment explanation
Indices: 43819--43865 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
43809 ATTATTTTTA
* * *
43819 TTTTTGTCTTAATTTATTAAATAT
1 TTTTTATCTTAATGTATAAAATAT
43843 TTTTTATCTTAATGTA-AAAATAT
1 TTTTTATCTTAATGTATAAAATAT
43866 ATATTCTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.57
Consensus pattern (24 bp):
TTTTTATCTTAATGTATAAAATAT
Found at i:43923 original size:15 final size:12
Alignment explanation
Indices: 43891--43937 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
43881 CATCACTTAA
43891 AAATATATTATT
1 AAATATATTATT
43903 AAATATATTAACTT
1 AAATATATT-A-TT
43917 GAAATATA-T-TT
1 -AAATATATTATT
43928 AAATATATTA
1 AAATATATTA
43938 CTATTAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
10 7 0.23
11 3 0.10
12 9 0.30
13 1 0.03
14 3 0.10
15 7 0.23
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (12 bp):
AAATATATTATT
Found at i:43999 original size:66 final size:65
Alignment explanation
Indices: 43918--44058 Score: 160
Period size: 66 Copynumber: 2.2 Consensus size: 65
43908 TATTAACTTG
* * * *
43918 AAATATATTTAAATATATTACTATTA-ATTTAGTATAAAAATATCTATTTTACTCTTATTTTTAT
1 AAATATATATAAATATATTACTATTATATTTACT-TAAAAATAT-TATTTTACTCTTATTTTAAA
43982 TT
64 TT
* * * * *
43984 AAA-ATATATATAATATTTTATTCTTATCTTTACTTAAAAATATTATTTTATTCTTATTTTAAAT
1 AAATATATATA-AATATATTACTATTATATTTACTTAAAAATATTATTTTACTCTTATTTTAAAT
44048 T
65 T
44049 AAATATATAT
1 AAATATATAT
44059 TTTAAATTAA
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
65 28 0.44
66 30 0.48
67 5 0.08
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.53
Consensus pattern (65 bp):
AAATATATATAAATATATTACTATTATATTTACTTAAAAATATTATTTTACTCTTATTTTAAATT
Found at i:44009 original size:35 final size:32
Alignment explanation
Indices: 43957--44059 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 32
43947 TAGTATAAAA
* *
43957 ATATCTATTTTACTCTTATTTTTATTTAAAATAT
1 ATAT-TATTTTATTCTTATTTTTAATT-AAATAT
* *
43991 ATATAATATTTTATTCTTATCTTTACTTAAA-A-
1 ATAT--TATTTTATTCTTATTTTTAATTAAATAT
*
44023 ATATTATTTTATTCTTATTTTAAATTAAATAT
1 ATATTATTTTATTCTTATTTTTAATTAAATAT
44055 ATATT
1 ATATT
44060 TTAAATTAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
30 22 0.37
31 1 0.02
32 9 0.15
33 1 0.02
34 7 0.12
35 19 0.32
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (32 bp):
ATATTATTTTATTCTTATTTTTAATTAAATAT
Found at i:44074 original size:16 final size:18
Alignment explanation
Indices: 44038--44082 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
44028 ATTTTATTCT
44038 TATTTTAAATTAAATATA
1 TATTTTAAATTAAATATA
44056 TATTTTAAATTAAATATA
1 TATTTTAAATTAAATATA
44074 TATTTTAAA
1 TATTTTAAA
44083 AATATATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTTTAAATTAAATATA
Found at i:44092 original size:11 final size:11
Alignment explanation
Indices: 44073--44104 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
44063 AATTAAATAT
*
44073 ATATTTTAAAA
1 ATATATTAAAA
44084 ATATATTAAAA
1 ATATATTAAAA
44095 ATATATTAAA
1 ATATATTAAA
44105 TTAAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
ATATATTAAAA
Found at i:44109 original size:16 final size:16
Alignment explanation
Indices: 44088--44125 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
44078 TTAAAAATAT
*
44088 ATTAAAAATATATTAA
1 ATTAAAAATAAATTAA
44104 ATTAAAAATAAATTAA
1 ATTAAAAATAAATTAA
*
44120 AATAAA
1 ATTAAA
44126 TTTAGTCTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTAAAAATAAATTAA
Found at i:44118 original size:27 final size:24
Alignment explanation
Indices: 44061--44121 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 24
44051 ATATATATTT
*
44061 TAAATTAAATATATATTTTAAAAA
1 TAAATTAAAAATATATTTTAAAAA
*
44085 TATATTAAAAATATATTAAATTAAAAA
1 TAAATTAAAAATATATT---TTAAAAA
44112 TAAATTAAAA
1 TAAATTAAAA
44122 TAAATTTAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 15 0.48
27 16 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
TAAATTAAAAATATATTTTAAAAA
Found at i:54960 original size:165 final size:163
Alignment explanation
Indices: 54541--56235 Score: 1508
Period size: 165 Copynumber: 10.2 Consensus size: 163
54531 TAAAGAAACT
* *
54541 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGACTACGC
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTACGC
* * * * * *
54606 TCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGACAAGAAGGGCTATTTGCCAACAAACGA
66 TCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG-C--CAAA-GA
* * ** * *
54671 CCTTCGAGTTTGACTATGCTCAGCTCCAAGGCATATC
127 CCCTCGAGTTCGACTACACTCAGCTCGAAGGCACATC
** * * * **
54708 ATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TGACCAAAGACCTTCGAGTTCGACTACG
* *
54773 CTCAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
65 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCC
* * * *
54838 TCGAGTTTGATTACACTTAGCTTCGAGGGCACATC
130 TCGAGTTCGACTACACTCAGC-TCGAAGGCACATC
* *
54873 ATTTACAACATAACTCAAGGCTAGAATGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACG
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACC-AAAGACCTTCGAGTTCGACTACG
* * * * *
54938 CTCAGCTCCAAGGCATATCATTTGTAGCATAGTTTAAGTCAAGAAGGGTTATCTGCCAAAGACCT
65 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCC
* *
55003 TCGAGTTCGATTACACTCAGATTCG-AGGTCACATC
130 TCGAGTTCGACTACACTCAG-CTCGAAGG-CACATC
* * *
55038 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATTTGTGACCAAAAGACATTCGAGTTTGACTACG
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACC-AAAGACCTTCGAGTTCGACTACG
* * * ** * * *
55103 GTTAGCTCCAAGGCATATCATTTGCAATATAACTTAAGTCGAGGAGAGTTATCTGCCAAAGACCC
65 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCC
* *
55168 TCGAGTTCGATTACACTCAGCTTC-AAGGGTACATC
130 TCGAGTTCGACTACACTCAGC-TCGAA-GGCACATC
* * * * * * * *
55203 ATTTACAACATAACTTAAGGCTAAAAGGGTTACCGGTGATCAAAAGACCTTTGAGTTCGACTAGG
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGA-CCAAAGACCTTCGAGTTCGACTACG
* * *
55268 CTCAGCTTCAAGGCATATCATTTGCAGCATTA-CTTAAGTCGAGAAGGTTTATCTGCCAACCAAA
65 CTCAGCTCCAAGGCACATCATTTGCAGCA-TAGCTTAAGTCGAGAAGGGTTATCTG----CCAAA
* * *
55332 GA-CCTGCGAGTTCGACTACGCTCGGCTCTAAGGCACATC
125 GACCCT-CGAGTTCGACTACACTCAGCTCGAAGGCACATC
* * * * * * ** * * * *
55371 ATTTGCAGCATAGCTTAAGTCAAGAAAGGTTATC--TG-CCAAAGACCCGCAAGTTTGATTACAC
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTACGC
* * * * * * *
55433 TCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAG
66 TCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG---CC-AAAG
*** * ** *
55498 ATATTCGAGTTCAACTACGTTCAGCTCCAAGGCACATC
126 ACCCTCGAGTTCGACTACACTCAGCTCGAAGGCACATC
** * * * * * * * *
55536 ATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATC--TG-CCAAAGACCCTCAAGTTTGATCATA-
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGA-C-TAC
* * * * * * * *
55597 -CTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAATGGTTATCTGTCACCAAA
64 GCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG---CC-AA
* * * * *
55661 AGACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCATATC
124 AGACCCTCGAGTTCGACTACACTCAGCTCGAAGGCACATC
* * * * * ** * *
55701 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATATGCCAACCAAAGACCTGCGAGTTTGACTACG
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TGACCAAAGACCTTCGAGTTCGACTACG
* * * *
55766 CTCGGATCTAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGTTATCTGCCAAAGACCC
65 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCC
* * * * *
55831 ACAAGTTTGATTACACTCAGCTTCGAGGGCACATC
130 TCGAGTTCGACTACACTCAGC-TCGAAGGCACATC
* * * *
55866 ATTTATAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACATTCGAGTTCAACTACG
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACC-AAAGACCTTCGAGTTCGACTACG
* * * * *
55931 TTCAGCTCCAAGGCAAATTATTTACAACATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCC
65 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCC
* *
55996 TCGAGTTC-AATCACACTCAGCTTCGAGGGCACATC
130 TCGAGTTCGACT-ACACTCAGC-TCGAAGGCACATC
* * * * *
56031 ATTTACAGCATAACTCAAGGCTATAATGGTTATTTGTCACCAAAAGACCTTCGAGTTCAACTACG
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACC-AAAGACCTTCGAGTTCGACTACG
* * * * *
56096 CTCAGCTCCAAGGCATATCATTTACAGAATAACTTAAGTCGAGAAGGGTTATCTACCAACTAAAG
65 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCT-GC--C-AAAG
* * *
56161 ACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATC
126 ACCCTCGAGTTCGACTACACTCAGCTCGAAGGCACATC
* * * *
56199 ATTTATAGCATAGCTCAAGGCAAGAAGGGCTATCTGT
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGT
56236 CAATAAAATT
Statistics
Matches: 1288, Mismatches: 204, Indels: 71
0.82 0.13 0.05
Matches are distributed among these distances:
164 80 0.06
165 895 0.69
166 9 0.01
167 36 0.03
168 196 0.15
169 70 0.05
170 2 0.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.25
Consensus pattern (163 bp):
ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTACGC
TCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCT
CGAGTTCGACTACACTCAGCTCGAAGGCACATC
Found at i:55391 original size:414 final size:414
Alignment explanation
Indices: 54563--56234 Score: 2084
Period size: 414 Copynumber: 4.0 Consensus size: 414
54553 ACTCAAGGCT
* * * * * *
54563 AGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATT
1 AGAAGGGTTATCTG-C--CAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATT
* * * * * * * * * * * ** * *
54627 TGCAACATAGCTCAAGACAAGAAGGGCTATTTGCCAACAAACGACCTTCGAGTTTGACTATGCTC
63 TACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACATTCGAGTTCAACTACGTTC
* *
54692 AGCTCCAAGGCATATCATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
128 AGCTCCAAGGCATATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTG----CCAAAGACC
* * * ** * * * *
54757 TTCGAGTTCGA-CTACGCTCAGCTCCAA-GGCACATCATTTGTAGCATAGCTTAAGTCGAGAAGG
189 CTCGAGTTCGATC-ACACTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGG
* * ** * * * * * * *
54820 GCTATCTG---CC-AAAGACCCTCGAGTTTGATTACACTTAGCTTCGAGGGCACATCATTTACAA
253 GTTATCTGTCACCAAAAGACCTTCGAGTTCAACTACGCTCAGC-TCCAAGGCATATCATTTACAG
* * * * ** *
54881 CATAACTCAAGGCTAGAATGGTTATCTG-TGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCT
317 CATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTGCGAGTTCGACTACGCTCAGCT
* * * *
54945 CCAAGGCATATCATTTGTAGCATAGTTTAAGTCA
381 CTAAGGCACATCATTTGCAGCATAGCTTAAGTCA
* * * *
54979 AGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGATTCGAGGTCACATCATTTAC
1 AGAAGGGTTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC
* * **
55044 AGCATAACTCAAGGCTAGAAGGGTTATTTGTGACCAAAAGACATTCGAGTTTGACTACGGTT-AG
66 AGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACATTCGAGTTCAACTAC-GTTCAG
* * *
55108 CTCCAAGGCATATCATTTGCAATATAACTTAAGTCGAGGAGAGTTATCTGCCAAAGACCCTCGAG
130 CTCCAAGGCATATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAG
* * * * * * *
55173 TTCGATTACACTCAGCTTCAAGGGTACATCATTTACAACATAACTTAAGGCTAAAAGGGTTACCG
195 TTCGATCACACTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCT
* * * * * * * *
55238 GTGATCAAAAGACCTTTGAGTTCGACTAGGCTCAGCTTCAAGGCATATCATTTGCAGCATTACTT
260 GTCACCAAAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAACTT
* *
55303 AAGTCGAGAAGGTTTATCTGCCAACCAAAGACCTGCGAGTTCGACTACGCTCGGCTCTAAGGCAC
325 AAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTGCGAGTTCGACTACGCTCAGCTCTAAGGCAC
55368 ATCATTTGCAGCATAGCTTAAGTCA
390 ATCATTTGCAGCATAGCTTAAGTCA
* * *
55393 AGAAAGGTTATCTGCCAAAGACCCGCAAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTAC
1 AGAAGGGTTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC
*
55458 AGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGATATTCGAGTTCAACTACGTTCAGC
66 AGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACATTCGAGTTCAACTACGTTCAGC
* * * * * *
55523 TCCAAGGCACATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGT
131 TCCAAGGCATATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAGT
* * * *
55588 TTGATCATACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAATGGTTATCTG
196 TCGATCACACTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG
*
55653 TCACCAAAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTA
261 TCACCAAAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAACTTA
* * * *
55718 AGTCGAGAAGGGTTATATGCCAACCAAAGACCTGCGAGTTTGACTACGCTCGGATCTAAGGCACA
326 AGTCGAGAAGGGTTATCTGCCAACCAAAGACCTGCGAGTTCGACTACGCTCAGCTCTAAGGCACA
55783 TCATTTGCAGCATAGCTTAAGTCA
391 TCATTTGCAGCATAGCTTAAGTCA
* * *
55807 AGAAGGGTTATCTGCCAAAGACCCACAAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTAT
1 AGAAGGGTTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC
55872 AGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACATTCGAGTTCAACTACGTTCAGC
66 AGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACATTCGAGTTCAACTACGTTCAGC
* * * *
55937 TCCAAGGCAAATTATTTACAACATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAGT
131 TCCAAGGCATATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAGT
* * * * *
56002 TCAATCACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTATAATGGTTATTTG
196 TCGATCACACTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG
*
56067 TCACCAAAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCATATCATTTACAGAATAACTTA
261 TCACCAAAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAACTTA
* * *
56132 AGTCGAGAAGGGTTATCTACCAACTAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACA
326 AGTCGAGAAGGGTTATCTGCCAACCAAAGACCTGCGAGTTCGACTACGCTCAGCTCTAAGGCACA
** * *
56197 TCATTTATAGCATAGCTCAAGGCA
391 TCATTTGCAGCATAGCTTAAGTCA
*
56221 AGAAGGGCTATCTG
1 AGAAGGGTTATCTG
56235 TCAATAAAAT
Statistics
Matches: 1106, Mismatches: 140, Indels: 22
0.87 0.11 0.02
Matches are distributed among these distances:
410 31 0.03
411 33 0.03
413 30 0.03
414 970 0.88
415 28 0.03
416 14 0.01
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.25
Consensus pattern (414 bp):
AGAAGGGTTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC
AGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACATTCGAGTTCAACTACGTTCAGC
TCCAAGGCATATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAGT
TCGATCACACTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG
TCACCAAAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAACTTA
AGTCGAGAAGGGTTATCTGCCAACCAAAGACCTGCGAGTTCGACTACGCTCAGCTCTAAGGCACA
TCATTTGCAGCATAGCTTAAGTCA
Found at i:55717 original size:579 final size:575
Alignment explanation
Indices: 54581--56237 Score: 2081
Period size: 579 Copynumber: 2.9 Consensus size: 575
54571 TATCTGTCAA
* * * * * * *
54581 CAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAACATAGCTCAAGAC
1 CAAAGACCTGCGAGTTCGACTACACTC-GCATCTAAGGCACATCATTTACAACATAACTTAAGGC
* ** * *
54645 AAGAAGGGCTATTTGCCAACAAACGACCTTCGAGTTTGACTATGCTCAGCTCCAAGGCATATCAT
65 AAGAAGGGTTACCTG-C-A-AAA-GACCTTCGAGTTTGACTACGCTCAGCTTCAAGGCATATCAT
54710 TTGTAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCT
126 TTGTAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCT
* *
54775 CAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTC
191 CAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTC
* *
54840 GAGTTTGATTACACTTAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAATGGTTA
256 GAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAATGGTTA
* *
54905 TCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGTAGCATAG
321 TCTGTCACCAAAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCATATCATTTGTAGCATAG
* * * * * *
54970 TTTAAGTCAAGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGATTCGAGGTCAC
386 CTTAAGTCGAGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATCATACTCAGCTTCGAGGGCAC
* * **
55035 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATTTGTGACCAAAAGACATTCGAGTTTGACT
451 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACATTCGAGTTCAACT
* * * * *
55100 ACGGTTAGCTCCAAGGCATATCATTTGCAATATAACTTAAGTCGAGGAGAGTTATCTG-C
516 ACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTTAAGTCGAGAAGAGTTATATGAC
* * *
55159 CAAAGACCCT-CGAGTTCGATTACACTCAGCTTC-AAGGGTACATCATTTACAACATAACTTAAG
1 CAAAGA-CCTGCGAGTTCGACTACACTC-GCATCTAA-GGCACATCATTTACAACATAACTTAAG
* * *
55222 GCTAA-AAGGGTTACCGGTGATCAAAAGACCTTTGAGTTCGACTAGGCTCAGCTTCAAGGCATAT
63 GC-AAGAAGGGTTACC--TG--CAAAAGACCTTCGAGTTTGACTACGCTCAGCTTCAAGGCATAT
* * * *
55286 CATTTGCAGCATTACTTAAGTCGAGAAGGTTTATCTGCCAACCAAAGACCTGCGAGTTCGACTAC
123 CATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * * *
55351 GCTCGGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAAGGTTATCTGCCAAAGACC
188 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACC
* * *
55416 CGCAAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGG
253 CTCGAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAATGG
** * *
55481 TTATCTGTCACCAAAAGATATTCGAGTTCAACTACGTTCAGCTCCAAGGCACATCATTTGTAGCA
318 TTATCTGTCACCAAAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCATATCATTTGTAGCA
* * * *
55546 TAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTTGATCATACTCAGCTTCGAGGG
383 TAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATCATACTCAGCTTCGAGGG
* *
55611 CACATCATTTACAGCATAACTCAAGGCTAGAATGGTTATCTGTCACCAAAAGACCTTCGAGTTCA
448 CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACATTCGAGTTCA
* *
55676 ACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATATGCCAA
513 ACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTTAAGTCGAGAAGAGTTATATG---A
55741 C
575 C
* * * * * * *
55742 CAAAGACCTGCGAGTTTGACTACGCTCGGATCTAAGGCACATCATTTGCAGCATAGCTTAAGTCA
1 CAAAGACCTGCGAGTTCGACTACACTCGCATCTAAGGCACATCATTTACAACATAACTTAAGGCA
* * ** * * * * * *
55807 AGAAGGGTTATCTGCCAAAGACCCACAAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTAT
66 AGAAGGGTTACCTGCAAAAGACCTTCGAGTTTGACTACGCTCAGCTTC-AAGGCATATCATTTGT
* * * * * * *
55872 AGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAAGACATTCGAGTTCAACTACGTTCAG
130 AGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCAG
* * * *
55936 CTCCAAGGCAAATTATTTACAACATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAG
194 CTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAG
** * * *
56001 TTCAATCACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTATAATGGTTATTT
259 TTTGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAATGGTTATCT
** * *
56066 GTCACCAAAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCATATCATTTACAGAATAACTT
324 GTCACCAAAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCATATCATTTGTAGCATAGCTT
* * *
56131 AAGTCGAGAAGGGTTATCTACCAACTAAAGACCTTCGAGTTCGA-C-TACGCTCAGC-TCTAAGG
389 AAGTCGAGAAGGGTTATCT-GC--C-AAAGACCTTCGAGTTCGATCATA--CTCAGCTTCGAGGG
* * * *
56193 CACATCATTTATAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCA
448 CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCA
56238 ATAAAATTGT
Statistics
Matches: 928, Mismatches: 129, Indels: 40
0.85 0.12 0.04
Matches are distributed among these distances:
578 54 0.06
579 728 0.78
580 8 0.01
581 7 0.01
582 87 0.09
583 44 0.05
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (575 bp):
CAAAGACCTGCGAGTTCGACTACACTCGCATCTAAGGCACATCATTTACAACATAACTTAAGGCA
AGAAGGGTTACCTGCAAAAGACCTTCGAGTTTGACTACGCTCAGCTTCAAGGCATATCATTTGTA
GCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCT
CCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAGTT
TGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAATGGTTATCTGT
CACCAAAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCATATCATTTGTAGCATAGCTTAA
GTCGAGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATCATACTCAGCTTCGAGGGCACATCAT
TTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACATTCGAGTTCAACTACGCT
CAGCTCCAAGGCATATCATTTGCAACATAACTTAAGTCGAGAAGAGTTATATGAC
Found at i:56874 original size:37 final size:35
Alignment explanation
Indices: 56822--56950 Score: 102
Period size: 37 Copynumber: 3.5 Consensus size: 35
56812 CATATATATA
*
56822 TATATATATATTATAGTTTGCAAACGGTTTGAAAATACG
1 TATATA-ATA-TATAGTTT-CAAACGATTTGAAAA-ACG
* *
56861 TATATAATATATAGTTTCTAAAAAC-ATTTTAAAAATG
1 TATATAATATATAGTTTC---AAACGATTTGAAAAACG
* *
56898 TATATAATATATAGTTTTAAAAACGCTTTTG-AAAAC-
1 TATATAATATATAG-TTT-CAAACG-ATTTGAAAAACG
56934 TATATAATATATAGTTT
1 TATATAATATATAGTTT
56951 TTAAAATGTT
Statistics
Matches: 76, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
35 3 0.04
36 19 0.25
37 28 0.37
38 16 0.21
39 10 0.13
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.41
Consensus pattern (35 bp):
TATATAATATATAGTTTCAAACGATTTGAAAAACG
Found at i:56938 original size:36 final size:35
Alignment explanation
Indices: 56861--57019 Score: 147
Period size: 36 Copynumber: 4.4 Consensus size: 35
56851 TGAAAATACG
* * *
56861 TATATAATATATAGTTTCTAAAAACATTTTAAAAATG
1 TATATAATATATAGTTT-TAAAAACCTTTTGAAAA-C
56898 TATATAATATATAGTTTTAAAAACGCTTTTGAAAAC
1 TATATAATATATAGTTTTAAAAAC-CTTTTGAAAAC
* ** *
56934 TATATAATATATAGTTTTTAAAATGTTTTTAGAAAC
1 TATATAATATATAGTTTTAAAAACCTTTTGA-AAAC
* * ** * *
56970 TATATATTATATACATATTTTCAAACCGTTTGCAAAC
1 TATATAATATATA-GT-TTTAAAAACCTTTTGAAAAC
57007 TATATAATATATA
1 TATATAATATATA
57020 TATATATATG
Statistics
Matches: 102, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
35 5 0.05
36 45 0.44
37 42 0.41
38 10 0.10
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (35 bp):
TATATAATATATAGTTTTAAAAACCTTTTGAAAAC
Found at i:56964 original size:73 final size:73
Alignment explanation
Indices: 56843--57019 Score: 180
Period size: 73 Copynumber: 2.4 Consensus size: 73
56833 TATAGTTTGC
* *
56843 AAACGGTTTGAAAATACGTATATAATATATAGTTTCTAAAAACATTTTA-AAAATGTATA-TA-A
1 AAACCGTTTG-AAA-AC-TATATAATATATAGTTTCTAAAAACATTTTAGAAAATATATATTATA
*
56905 TATATAGTTTTAA
63 TACATA-TTTT-A
* * *** *
56918 AAACGCTTTTGAAAACTATATAATATATAGTTTTTAAAATGTTTTTAGAAACTATATATTATATA
1 AAAC-CGTTTGAAAACTATATAATATATAGTTTCTAAAAACATTTTAGAAAATATATATTATATA
*
56983 CATATTTTC
65 CATATTTTA
*
56992 AAACCGTTTGCAAACTATATAATATATA
1 AAACCGTTTGAAAACTATATAATATATA
57020 TATATATATG
Statistics
Matches: 86, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
73 49 0.57
74 14 0.16
75 13 0.15
76 10 0.12
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (73 bp):
AAACCGTTTGAAAACTATATAATATATAGTTTCTAAAAACATTTTAGAAAATATATATTATATAC
ATATTTTA
Found at i:57590 original size:21 final size:21
Alignment explanation
Indices: 57475--57590 Score: 60
Period size: 21 Copynumber: 5.6 Consensus size: 21
57465 GCGAAATAAA
**
57475 AATCGCAACGCGA-TCCCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
57495 AATCGCAAATC-AGTTTCCAA
1 AATCGCAACGCGATTTTCCAG
* *
57515 AATCGCAACGCGATTCTT-GAC
1 AATCGCAACGCGATT-TTCCAG
* ** *
57536 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
57556 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
57578 AATCGCAACGCGA
1 AATCGCAACGCGA
57591 ATATGAAAAT
Statistics
Matches: 70, Mismatches: 20, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
19 1 0.01
20 25 0.36
21 40 0.57
22 4 0.06
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:57620 original size:20 final size:20
Alignment explanation
Indices: 57578--57770 Score: 237
Period size: 20 Copynumber: 9.6 Consensus size: 20
57568 GATTTTCCAG
* ** *
57578 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
57598 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
*
57618 AATTGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
57638 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
57658 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
57678 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
57698 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
57718 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
57739 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
57759 AATCGCAACGCG
1 AATCGCAACGCG
57771 ATTTTTAAAG
Statistics
Matches: 149, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
19 1 0.01
20 129 0.87
21 19 0.13
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:58192 original size:33 final size:33
Alignment explanation
Indices: 58148--58220 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
58138 ATTTCACTTA
58148 GATTTT-ATTTCGCGTTACGATTCTCTCGTTGC
1 GATTTTCATTTCGCGTTACGATTCTCTCGTTGC
* *
58180 GATTTTCATTTCGCGTTGCTATTCTCTCGTTGC
1 GATTTTCATTTCGCGTTACGATTCTCTCGTTGC
58213 GATTTTCA
1 GATTTTCA
58221 AGTTAGTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 6 0.16
33 32 0.84
ACGTcount: A:0.12, C:0.22, G:0.18, T:0.48
Consensus pattern (33 bp):
GATTTTCATTTCGCGTTACGATTCTCTCGTTGC
Found at i:58361 original size:41 final size:40
Alignment explanation
Indices: 58300--58391 Score: 132
Period size: 41 Copynumber: 2.3 Consensus size: 40
58290 TACAGAAGAG
* **
58300 TCGCAACGAGATAAATGAAAATCGCAACGTGAAAATGACTA
1 TCGCAACGAGATAAATGAAAATCGCAACGCG-AAATGAAAA
58341 TCTGCAACGAGA-AAATGAAAATCGCAACGCGAAATGAAAA
1 TC-GCAACGAGATAAATGAAAATCGCAACGCGAAATGAAAA
58381 TCGCAACGAGA
1 TCGCAACGAGA
58392 GAATCGCAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
39 9 0.19
40 9 0.19
41 20 0.43
42 9 0.19
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (40 bp):
TCGCAACGAGATAAATGAAAATCGCAACGCGAAATGAAAA
Found at i:58377 original size:19 final size:20
Alignment explanation
Indices: 58300--58391 Score: 123
Period size: 21 Copynumber: 4.5 Consensus size: 20
58290 TACAGAAGAG
58300 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
58321 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
58341 TCTGCAACGAGAAAATGAAAA
1 TC-GCAACGAGAAAATGAAAA
*
58362 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
58381 TCGCAACGAGA
1 TCGCAACGAGA
58392 GAATCGCAAC
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
19 18 0.30
20 16 0.26
21 27 0.44
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:58436 original size:19 final size:18
Alignment explanation
Indices: 58414--58500 Score: 82
Period size: 19 Copynumber: 5.1 Consensus size: 18
58404 GAAACCAAAA
58414 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGATTTTCATT
*
58433 TCGCGTTGCGA--TTC-TC
1 TCGC-TTGCGATTTTCATT
58449 TCG-TTGCGATTTTCATT
1 TCGCTTGCGATTTTCATT
58466 TCGCGTTGCGATTTTC---
1 TCGC-TTGCGATTTTCATT
58482 TCG-TTGCGATTTTCATT
1 TCGCTTGCGATTTTCATT
58499 TC
1 TC
58501 TCTCGTTGCG
Statistics
Matches: 57, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
14 17 0.30
16 10 0.18
17 9 0.16
19 21 0.37
ACGTcount: A:0.10, C:0.23, G:0.20, T:0.47
Consensus pattern (18 bp):
TCGCTTGCGATTTTCATT
Found at i:58461 original size:33 final size:33
Alignment explanation
Indices: 58419--58541 Score: 156
Period size: 33 Copynumber: 3.5 Consensus size: 33
58409 CAAAATCGCA
58419 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
58452 TTGCGATTTTCATTTCGCGTTGCGATTTTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
58485 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
58526 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
58542 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
33 44 0.56
34 2 0.03
35 6 0.08
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.03
41 20 0.25
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:58493 original size:14 final size:14
Alignment explanation
Indices: 58431--58495 Score: 67
Period size: 14 Copynumber: 4.3 Consensus size: 14
58421 GCGATTTTCA
*
58431 TTTCGCGTTGCGAT
1 TTTCTCGTTGCGAT
*
58445 TCTCTCGTTGCGAT
1 TTTCTCGTTGCGAT
58459 TTTCATTTCGCGTTGCGAT
1 TTTC---T--CGTTGCGAT
58478 TTTCTCGTTGCGAT
1 TTTCTCGTTGCGAT
58492 TTTC
1 TTTC
58496 ATTTCTCTCG
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
14 28 0.65
16 1 0.02
17 1 0.02
19 13 0.30
ACGTcount: A:0.08, C:0.23, G:0.22, T:0.48
Consensus pattern (14 bp):
TTTCTCGTTGCGAT
Found at i:58538 original size:20 final size:20
Alignment explanation
Indices: 58443--58539 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
58433 TCGCGTTGCG
58443 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
58463 ATT-TCGCGTTGCGA---T-
1 ATTCTCTCGTTGCGATTTTC
58478 -TT-TCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
58496 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
58517 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
58537 ATT
1 ATT
58540 TCAACCAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
14 12 0.19
16 1 0.02
17 1 0.02
19 10 0.16
20 24 0.39
21 14 0.23
ACGTcount: A:0.11, C:0.24, G:0.18, T:0.47
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:60385 original size:93 final size:93
Alignment explanation
Indices: 60226--60448 Score: 437
Period size: 93 Copynumber: 2.4 Consensus size: 93
60216 TGGATTGCTT
*
60226 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
60291 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
60319 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
60384 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
60412 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
60449 AATACCCTGA
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 129 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:60630 original size:14 final size:14
Alignment explanation
Indices: 60613--60639 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
60603 AACGCGAAAC
60613 CAAAATCGCAACGA
1 CAAAATCGCAACGA
60627 CAAAATCGCAACG
1 CAAAATCGCAACG
60640 CGAAACCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.30, G:0.15, T:0.07
Consensus pattern (14 bp):
CAAAATCGCAACGA
Found at i:60661 original size:19 final size:19
Alignment explanation
Indices: 60578--60655 Score: 103
Period size: 19 Copynumber: 4.4 Consensus size: 19
60568 GCAACGAGAG
**
60578 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
60597 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
60616 AATCGCAA--CG--A-CAA
1 AATCGCAACGCGAAACCAA
60630 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
60649 AATCGCA
1 AATCGCA
60656 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
14 11 0.21
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 35 0.67
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:60673 original size:19 final size:19
Alignment explanation
Indices: 60651--60785 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
60641 GAAACCAAAA
*
60651 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
60670 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
60684 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
60703 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
60719 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
60736 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
60755 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
60775 TCGTGTTGCGA
1 TCGCGTTGCGA
60786 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 12, Indels: 21
0.74 0.10 0.17
Matches are distributed among these distances:
14 17 0.18
16 8 0.09
17 8 0.09
19 48 0.52
20 12 0.13
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:60692 original size:14 final size:14
Alignment explanation
Indices: 60673--60729 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
60663 TTTCATTTCG
60673 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
60687 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
60704 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
60720 CGTTGCGATT
1 CGTTGCGATT
60730 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:60698 original size:33 final size:33
Alignment explanation
Indices: 60656--60748 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
60646 CAAAATCGCA
60656 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
60689 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
60722 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
60749 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:62730 original size:14 final size:14
Alignment explanation
Indices: 62711--62746 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
62701 ATTGTTTAAT
62711 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
62725 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
62739 TGATTTGT
1 TGATTTGT
62747 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:62869 original size:19 final size:19
Alignment explanation
Indices: 62853--62931 Score: 114
Period size: 19 Copynumber: 4.4 Consensus size: 19
62843 AAAAATGACT
62853 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
62872 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
62891 ATCGCAA--CG--A-GAAA
1 ATCGCAATGCGAAATGAAA
62905 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
62925 ATCGCAA
1 ATCGCAA
62932 CGAGAGAATC
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 11 0.20
15 1 0.02
16 1 0.02
17 3 0.06
19 27 0.50
20 11 0.20
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:62904 original size:14 final size:14
Alignment explanation
Indices: 62887--62945 Score: 55
Period size: 14 Copynumber: 3.8 Consensus size: 14
62877 AATGCGAAAT
62887 GAAAATCGCAACGA
1 GAAAATCGCAACGA
62901 GAAAATCGCAATGCGGAAA
1 GAAAATCGCAA--C-G--A
62920 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
*
62935 GAGAATCGCAA
1 GAAAATCGCAA
62946 TGCGATTTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
14 21 0.55
15 1 0.03
16 1 0.03
17 2 0.05
18 1 0.03
19 1 0.03
20 11 0.29
ACGTcount: A:0.47, C:0.19, G:0.24, T:0.10
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:62925 original size:34 final size:34
Alignment explanation
Indices: 62868--62949 Score: 148
Period size: 34 Copynumber: 2.4 Consensus size: 34
62858 AATGCGAAAT
62868 GAAAATCGCAATGC-GAAATGAAAATCGCAACGA
1 GAAAATCGCAATGCGGAAATGAAAATCGCAACGA
62901 GAAAATCGCAATGCGGAAATGAAAATCGCAACGA
1 GAAAATCGCAATGCGGAAATGAAAATCGCAACGA
*
62935 GAGAATCGCAATGCG
1 GAAAATCGCAATGCG
62950 ATTTTCATTT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 14 0.30
34 33 0.70
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.12
Consensus pattern (34 bp):
GAAAATCGCAATGCGGAAATGAAAATCGCAACGA
Found at i:63035 original size:33 final size:33
Alignment explanation
Indices: 62998--63090 Score: 186
Period size: 33 Copynumber: 2.8 Consensus size: 33
62988 TCATTTCGCA
62998 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
63031 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
63064 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
63091 TTCATTTCCG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:63036 original size:14 final size:14
Alignment explanation
Indices: 63017--63071 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
63007 TCATTTCGCA
63017 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
63031 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
63048 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
63064 TTGCGATT
1 TTGCGATT
63072 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:63036 original size:52 final size:52
Alignment explanation
Indices: 62940--63115 Score: 223
Period size: 52 Copynumber: 3.3 Consensus size: 52
62930 AACGAGAGAA
* *
62940 TCGCAATGCGATTTTCATTTCCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCATT
62993 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
* * * * *
63045 TCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTCATT
1 TCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTCATT
63097 TCCGCATTGCGATTTTCAT
1 T-CGCATTGCGATTTTCAT
63116 GTTGGGATTT
Statistics
Matches: 111, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
51 3 0.03
52 63 0.57
53 36 0.32
54 9 0.08
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:63125 original size:53 final size:52
Alignment explanation
Indices: 62979--63143 Score: 210
Period size: 52 Copynumber: 3.2 Consensus size: 52
62969 GATTCTCTCG
* * * * *
62979 TTGCGATTTTCATTTCGCATTGCGATTTTCAT-TTCGCA-TTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATGTTGGGATTTTC-ATT-TCGCA
* *
63031 TTGCGATTTTCATTTCGCATTGCGATTCTC-TCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCA
63083 TTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTT-CGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCA
63136 TTGCGATT
1 TTGCGATT
63144 CTCTCGTTGC
Statistics
Matches: 99, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
51 1 0.01
52 47 0.47
53 47 0.47
54 4 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCA
Found at i:63165 original size:33 final size:33
Alignment explanation
Indices: 62946--63157 Score: 125
Period size: 33 Copynumber: 6.2 Consensus size: 33
62936 AGAATCGCAA
*
62946 TGCGATTTTCATTTCCGCGTTGCGATTCTC-TCGT
1 TGCGATTTTCATTT-CGCATTGCGATTCTCAT-GT
*
62980 TGCGATTTTCATTTCGCATTGCGATTTTCAT-T
1 TGCGATTTTCATTTCGCATTGCGATTCTCATGT
* * * *
63012 T-CGCA-TTGCGATTCTCTCGTTGCGATTTTCAT-T
1 TGCG-ATTTTC-ATT-TCGCATTGCGATTCTCATGT
* * * *
63045 T-CGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCG-ATTTTC-ATT-TCGCATTGCGATTCTCA--T-G--T
*
63084 TGCGATTTTCATTTCCGCATTGCGATTTTCATGT
1 TGCGATTTTCATTT-CGCATTGCGATTCTCATGT
*
63118 TGGGATTTTCATTTCGCATTGCGATTCTC-TCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCAT-GT
63151 TGCGATT
1 TGCGATT
63158 GTAATTTCCG
Statistics
Matches: 153, Mismatches: 11, Indels: 29
0.79 0.06 0.15
Matches are distributed among these distances:
31 5 0.03
32 7 0.05
33 83 0.54
34 29 0.19
35 1 0.01
36 1 0.01
37 1 0.01
38 1 0.01
39 20 0.13
40 5 0.03
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCATGT
Found at i:63165 original size:86 final size:85
Alignment explanation
Indices: 62946--63157 Score: 363
Period size: 86 Copynumber: 2.5 Consensus size: 85
62936 AGAATCGCAA
*
62946 TGCGATTTTCATTTCCGCGTTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
1 TGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
63011 TTCGCATTGCGATTCTCTCGT
65 TTCGCATTGCGATTCTCTCGT
63032 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
*
63097 TCCGCATTGCGATTTTCAT-GT
66 T-CGCATTGCGATTCTC-TCGT
*
63118 TGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
63158 GTAATTTCCG
Statistics
Matches: 121, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
85 51 0.42
86 69 0.57
87 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.46
Consensus pattern (85 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
TCGCATTGCGATTCTCTCGT
Found at i:63172 original size:53 final size:53
Alignment explanation
Indices: 63031--63176 Score: 140
Period size: 53 Copynumber: 2.8 Consensus size: 53
63021 GATTCTCTCG
* *
63031 TTGCGATTTTCA-TTTCGCATTGCGA-TTCTC-TCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCAGTTCCGCATTGCAATTTC-CAT-GTTGCGATTTTCATTTCGCA
* * * *
63083 TTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCA
1 TTGCGATTTTCAGTTCCGCATTGCAATTTCCATGTTGCGATTTTCATTTCGCA
* * *
63136 TTGCGATTCTCTC-GTTGCG-ATTGTAATTTCCGTGTTGCGAT
1 TTGCGATT-T-TCAGTTCCGCATTGCAATTTCCATGTTGCGAT
63177 AGTCAAATGC
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
52 12 0.15
53 57 0.72
54 8 0.10
55 2 0.03
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.46
Consensus pattern (53 bp):
TTGCGATTTTCAGTTCCGCATTGCAATTTCCATGTTGCGATTTTCATTTCGCA
Found at i:63793 original size:12 final size:12
Alignment explanation
Indices: 63776--63800 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
63766 TCTTCGGGGA
63776 CTTTTTCTTCTT
1 CTTTTTCTTCTT
63788 CTTTTTCTTCTT
1 CTTTTTCTTCTT
63800 C
1 C
63801 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:64009 original size:24 final size:24
Alignment explanation
Indices: 63975--64021 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
63965 CTGAAACATC
63975 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
63999 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
64022 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:64776 original size:40 final size:39
Alignment explanation
Indices: 64733--64904 Score: 220
Period size: 40 Copynumber: 4.3 Consensus size: 39
64723 TACAGATTAT
* * * *
64733 CGTTGCGATTTACAGATTATCGTTGCGATTTACAGATTCT
1 CGTTGCGATTTACGGA-TATCGTTGCGATTTACGGATACG
64773 CGTTGCGATTTACGGATTATCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGA-TATCGTTGCGATTTACGGATACG
*
64813 CGTTGCGATATACGGATA-CGCATTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATATCG--TTGCGATTTACGGATACG
* * *
64853 CGTTGCTATTTACGGATACACGTTGCGGTTTACGGATACG
1 CGTTGCGATTTACGGATA-TCGTTGCGATTTACGGATACG
64893 CGTTGCGATTTA
1 CGTTGCGATTTA
64905 TGTGTTCGCG
Statistics
Matches: 119, Mismatches: 9, Indels: 8
0.88 0.07 0.06
Matches are distributed among these distances:
38 2 0.02
39 2 0.02
40 113 0.95
42 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (39 bp):
CGTTGCGATTTACGGATATCGTTGCGATTTACGGATACG
Found at i:64806 original size:20 final size:19
Alignment explanation
Indices: 64714--64904 Score: 177
Period size: 20 Copynumber: 9.6 Consensus size: 19
64704 AAATTTCAAT
* *
64714 GTTGTGATTTACAGATTATC
1 GTTGCGATTTACGGA-TATC
*
64734 GTTGCGATTTACAGATTATC
1 GTTGCGATTTACGGA-TATC
* *
64754 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGA-TATC
64774 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGA-TATC
*
64794 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATA-TC
*
64814 GTTGCGATATACGGATA-C
1 GTTGCGATTTACGGATATC
*
64832 GCATTGCGATTTACGGATACGC
1 G--TTGCGATTTACGGATA-TC
* *
64854 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATA-TC
* *
64874 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATA-TC
64894 GTTGCGATTTA
1 GTTGCGATTTA
64905 TGTGTTCGCG
Statistics
Matches: 153, Mismatches: 13, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
18 2 0.01
19 2 0.01
20 147 0.96
22 2 0.01
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (19 bp):
GTTGCGATTTACGGATATC
Found at i:64817 original size:60 final size:60
Alignment explanation
Indices: 64714--64904 Score: 233
Period size: 60 Copynumber: 3.2 Consensus size: 60
64704 AAATTTCAAT
* * * * * * *
64714 GTTGTGATTTACAGATTATCGTTGCGATTTACAGATTA-TCGTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTATCGTTGCGATTTACGGA-TACACGTTGCGATTTACGGATACGC
* *
64774 GTTGCGATTTACGGATTATCGTTGCGATTTACGGATACGCGTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTATCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGC
* * * *
64834 ATTGCGATTTACGGA-TACGCGTTGCTATTTACGGATACACGTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTA-TCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGC
64894 GTTGCGATTTA
1 GTTGCGATTTA
64905 TGTGTTCGCG
Statistics
Matches: 114, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
59 4 0.04
60 110 0.96
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (60 bp):
GTTGCGATTTACGGATTATCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGC
Found at i:64914 original size:20 final size:20
Alignment explanation
Indices: 64891--64942 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
64881 TTTACGGATA
* *
64891 CGCGTTGCGATTTAT-GTGTT
1 CGCGTTGCGATTT-TCATATT
64911 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTTCATATT
64931 CGCGTTGCGATT
1 CGCGTTGCGATT
64943 CTTGAAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.12, C:0.19, G:0.27, T:0.42
Consensus pattern (20 bp):
CGCGTTGCGATTTTCATATT
Found at i:64917 original size:40 final size:40
Alignment explanation
Indices: 64733--64942 Score: 219
Period size: 40 Copynumber: 5.2 Consensus size: 40
64723 TACAGATTAT
* * * * *
64733 CGTTGCGATTTACAGATTA-TCGTTGCGATTTACAGATTCT
1 CGTTGCGATTTACGGA-TACGCGTTGCGATTTACGGATACG
*
64773 CGTTGCGATTTACGGATTA-TCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGA-TACGCGTTGCGATTTACGGATACG
* *
64813 CGTTGCGATATACGGATACGCATTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACG
* * *
64853 CGTTGCTATTTACGGATACACGTTGCGGTTTACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACG
* * * ** *
64893 CGTTGCGATTTATGTG-TTCGCGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACG-GATACGCGTTGCGATTTACGGATACG
64933 CGTTGCGATT
1 CGTTGCGATT
64943 CTTGAAAATC
Statistics
Matches: 147, Mismatches: 21, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
39 2 0.01
40 144 0.98
41 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.36
Consensus pattern (40 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACG
Found at i:64937 original size:60 final size:60
Alignment explanation
Indices: 64714--64942 Score: 228
Period size: 60 Copynumber: 3.8 Consensus size: 60
64704 AAATTTCAAT
* * ** * * * *
64714 GTTGTGATTTACAGATTATCGTTGCGATTTACAGATTA-TCGTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGCGTTGCGATTTACAGA-TACGCGTTGCGATTTACGGATACGC
** * *
64774 GTTGCGATTTACGGATTATCGTTGCGATTTACGGATACGCGTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGCGTTGCGATTTACAGATACGCGTTGCGATTTACGGATACGC
* * * * * *
64834 ATTGCGATTTACGGATACGCGTTGCTATTTACGGATACACGTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGCGTTGCGATTTACAGATACGCGTTGCGATTTACGGATACGC
* * * *
64894 GTTGCGATTTATGTG-TTCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 GTTGCGATTTACG-GATTCGCGTTGCGATTTACAGATACGCGTTGCGATT
64943 CTTGAAAATC
Statistics
Matches: 141, Mismatches: 26, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
59 2 0.01
60 138 0.98
61 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.37
Consensus pattern (60 bp):
GTTGCGATTTACGGATTCGCGTTGCGATTTACAGATACGCGTTGCGATTTACGGATACGC
Found at i:64995 original size:21 final size:20
Alignment explanation
Indices: 64910--65007 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
64900 ATTTATGTGT
* *
64910 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
64930 TCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGATT-TTCAAAA
** **
64951 TCGCAATGCGAATTTGT-ACTA
1 TCGCGTTGCG-ATTT-TCAAAA
*
64972 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
64993 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
65008 GGAAATTGAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.29
21 39 0.63
22 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:65003 original size:42 final size:43
Alignment explanation
Indices: 64910--65008 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
64900 ATTTATGTGT
* *
64910 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
**
64951 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTTCAA-AA
*
64993 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
65009 GAAATTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 12 0.26
42 32 0.68
43 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
Found at i:72928 original size:21 final size:21
Alignment explanation
Indices: 72884--72949 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
72874 TAGAGGCTTT
* * *
72884 GTATCAATACCCGATG-ATTG
1 GTATTAATACCAGATGAACTG
72904 GTATTAATACCAGATGAACTG
1 GTATTAATACCAGATGAACTG
* * * *
72925 GTATTCATATCAGATTAACTA
1 GTATTAATACCAGATGAACTG
72946 GTAT
1 GTAT
72950 CCATATTGAA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 14 0.37
21 24 0.63
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (21 bp):
GTATTAATACCAGATGAACTG
Found at i:72954 original size:21 final size:21
Alignment explanation
Indices: 72914--72955 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
72904 GTATTAATAC
* *
72914 CAGATGAACTGGTATTCATAT
1 CAGATGAACTAGTATCCATAT
*
72935 CAGATTAACTAGTATCCATAT
1 CAGATGAACTAGTATCCATAT
72956 TGAATGAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (21 bp):
CAGATGAACTAGTATCCATAT
Found at i:75360 original size:23 final size:22
Alignment explanation
Indices: 75329--75372 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
75319 GGAGAAATAT
* *
75329 TTTTGAAATATAAATTTTAAAAA
1 TTTTAAAATA-AAAATTTAAAAA
75352 TTTTAAAATAAAAATTTAAAA
1 TTTTAAAATAAAAATTTAAAA
75373 TATTCTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
TTTTAAAATAAAAATTTAAAAA
Found at i:75369 original size:13 final size:14
Alignment explanation
Indices: 75346--75374 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
75336 ATATAAATTT
75346 TAAAAATTTTAAAA
1 TAAAAATTTTAAAA
75360 TAAAAA-TTTAAAA
1 TAAAAATTTTAAAA
75373 TA
1 TA
75375 TTCTTATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TAAAAATTTTAAAA
Found at i:78693 original size:30 final size:30
Alignment explanation
Indices: 78621--78693 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
78611 TCTCTTCATA
*
78621 AAAAATATCAATATGTAGATATACATTAGCG
1 AAAAA-ATCAATATGTAGATATACAATAGCG
78652 AAAAAAGTCAATATGTAG-TAATACAATAGC-
1 AAAAAA-TCAATATGTAGAT-ATACAATAGCG
78682 AAAAAGATCAAT
1 AAAAA-ATCAAT
78694 CCCTTCAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
30 12 0.32
31 26 0.68
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.25
Consensus pattern (30 bp):
AAAAAATCAATATGTAGATATACAATAGCG
Found at i:79330 original size:41 final size:41
Alignment explanation
Indices: 79285--79365 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
79275 GAGAAAGTAT
79285 AAAAACAACCTCAAAACAACTTAATAACTATGAGTAATTAA
1 AAAAACAACCTCAAAACAACTTAATAACTATGAGTAATTAA
* * *
79326 AAAAACAAGCTTAAAACAACTTAATGACTATGAGTAATTA
1 AAAAACAACCTCAAAACAACTTAATAACTATGAGTAATTA
79366 CTAATTATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.54, C:0.15, G:0.07, T:0.23
Consensus pattern (41 bp):
AAAAACAACCTCAAAACAACTTAATAACTATGAGTAATTAA
Found at i:79742 original size:15 final size:16
Alignment explanation
Indices: 79722--79752 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
79712 AATGATTATA
79722 TTTT-AAAAAGATATT
1 TTTTAAAAAAGATATT
79737 TTTTAAAAAAGATATT
1 TTTTAAAAAAGATATT
79753 AGTCTATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
TTTTAAAAAAGATATT
Found at i:84509 original size:14 final size:13
Alignment explanation
Indices: 84490--84520 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
84480 GATCGAACGC
84490 AACAAAACTACCA
1 AACAAAACTACCA
84503 TAACAAAACTACCA
1 -AACAAAACTACCA
84517 AACA
1 AACA
84521 TGTTGACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.61, C:0.29, G:0.00, T:0.10
Consensus pattern (13 bp):
AACAAAACTACCA
Found at i:90742 original size:4 final size:4
Alignment explanation
Indices: 90733--90762 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
90723 TTCTGCTTTC
90733 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
90763 CAATCTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:96541 original size:2 final size:2
Alignment explanation
Indices: 96534--96570 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
96524 ATGAGGTTAA
96534 AT AT AT AT 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 AT AT AT AT A
96571 ACTCTCGTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.