Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006970.1 Hibiscus syriacus cultivar Beakdansim tig00017948_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: 51511
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3975 original size:18 final size:19
Alignment explanation
Indices: 3935--3976 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
3925 AAAACTGGGT
* *
3935 GTTTTAATAAAACATTTTA
1 GTTTTAATAAAACATCTGA
3954 -TTTTAATAAAACA-CTGA
1 GTTTTAATAAAACATCTGA
3971 GTTTTA
1 GTTTTA
3977 GGGTCTGCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (19 bp):
GTTTTAATAAAACATCTGA
Found at i:5842 original size:30 final size:29
Alignment explanation
Indices: 5802--5896 Score: 136
Period size: 30 Copynumber: 3.2 Consensus size: 29
5792 ACGTGGGGGC
* *
5802 ATGGTGGTGGCATGGGATATTGAATATAAA
1 ATGGTAGTGGCATGGGATGTTGAATA-AAA
5832 ATGGTAGTGGCATGGGATGTTGAATAAAAA
1 ATGGTAGTGGCATGGGATGTTGAAT-AAAA
*
5862 ATGGTAGTGGAATGGGATGTTGAATAAAA
1 ATGGTAGTGGCATGGGATGTTGAATAAAA
5891 TATGGT
1 -ATGGT
5897 GGAATAAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
29 4 0.07
30 55 0.92
31 1 0.02
ACGTcount: A:0.35, C:0.02, G:0.34, T:0.29
Consensus pattern (29 bp):
ATGGTAGTGGCATGGGATGTTGAATAAAA
Found at i:6285 original size:89 final size:90
Alignment explanation
Indices: 6092--6348 Score: 354
Period size: 89 Copynumber: 2.8 Consensus size: 90
6082 ATATGTGATG
* * * *
6092 CAAGGTTGAATAAGTTCTTCTGATTATGAACTTCTTCTGCCTCTATCGGATGAGTTCTTCTCATT
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTC-GT-GGATGAGTTCTTCTCATT
* * **
6157 ATGAACTCTCCGCTGTAAATATTGATG
64 ATGAACTCTCCACTGGAAATATTGAAC
* *
6184 CAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTGGATAAGTT-TTCTCATTAT
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTGGATGAGTTCTTCTCATTAT
* *
6248 GAACTTTCCACTGGAAATCTTGAAC
66 GAACTCTCCACTGGAAATATTGAAC
* *
6273 CAAGGTTGAACAAGTTCTTCTCTTTATGAACTTCTTTTCCCTCGTTGGATGAGTTCTTCTCATTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCG-TGGATGAGTTCTTCTCATTA
6338 TGAACTCTCCA
65 TGAACTCTCCA
6349 TTTGAAATGT
Statistics
Matches: 146, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
89 70 0.48
90 17 0.12
91 20 0.14
92 39 0.27
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (90 bp):
CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTGGATGAGTTCTTCTCATTAT
GAACTCTCCACTGGAAATATTGAAC
Found at i:6904 original size:35 final size:36
Alignment explanation
Indices: 6865--7267 Score: 276
Period size: 39 Copynumber: 11.5 Consensus size: 36
6855 TGAGATAGAT
* *
6865 TTTGTTTCAA-GGTAACTGTCTCAAGAGAGAGAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
6900 TTTGTTTCAAGGGAAAC-GATCTCAA-AG-G-----T
1 TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAA
* * *
6929 TTGTGTTTCAAGAGAAACTGTCTAAAGGGAGACAAAA
1 TT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * *
6966 CTTATTTCAAGGAAAACTGTCTCAAGAGAGATAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
7002 TTTGTTTCCAGGGAAACAGAT-TC-A-A-AG----AT
1 TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAA
*
7031 TTTTTTTCAAGGGAAACTGTCTC-A-AGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
7065 TTTGTTTTAAGGGAAACTCTCTCAAGAGAGAC-AAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
7100 TTTGTTTCAACGGAAACTGTCTC-A-AGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
7134 -TTGTTTCAAGGGAAATTATCTCAAGAGAGATAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
** * *
7169 TCTTTTGTTTCAAGGGAAACTACCTCAAGCGAGATAAAA
1 ---TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
** * *
7208 TCTTATGTTTCAAGGGAAACTACCTCAAGCGAGATAAAA
1 --TT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
7247 TCTTCTGTTTCAAGTGAAACT
1 --TT-TGTTTCAAGGGAAACT
7268 ATCTGAAACG
Statistics
Matches: 300, Mismatches: 40, Indels: 52
0.77 0.10 0.13
Matches are distributed among these distances:
28 1 0.00
29 23 0.08
30 21 0.07
31 2 0.01
32 1 0.00
33 27 0.09
34 28 0.09
35 47 0.16
36 61 0.20
37 2 0.01
38 2 0.01
39 85 0.28
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:6974 original size:66 final size:65
Alignment explanation
Indices: 6867--6990 Score: 160
Period size: 66 Copynumber: 1.9 Consensus size: 65
6857 AGATAGATTT
* * * * * *
6867 TGTTTCAAGGTAACTGTCTCAAGAGAGAGAAAATTTGTTTCAAGGGAAAC-GATCTCAAAGGTTT
1 TGTTTCAAGGAAACTGTCTAAAGAGAGACAAAACTTATTTCAAGGAAAACTG-TCTCAAAGGTTT
6931 G
65 G
*
6932 TGTTTCAAGAGAAACTGTCTAAAGGGAGACAAAACTTATTTCAAGGAAAACTGTCTCAA
1 TGTTTCAAG-GAAACTGTCTAAAGAGAGACAAAACTTATTTCAAGGAAAACTGTCTCAA
6991 GAGAGATAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
65 9 0.18
66 40 0.80
67 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (65 bp):
TGTTTCAAGGAAACTGTCTAAAGAGAGACAAAACTTATTTCAAGGAAAACTGTCTCAAAGGTTTG
Found at i:7002 original size:102 final size:98
Alignment explanation
Indices: 6869--7124 Score: 311
Period size: 102 Copynumber: 2.6 Consensus size: 98
6859 ATAGATTTTG
* *
6869 TTTCAAGGTAACTGTCTCAAGAGAGAGAAAATTTGTTTCAAGGGAAAC-GATCTCAAAGGTTTGT
1 TTTCAAGGAAACTGTCTCAAGAGAGA-AAAATTTGTTTCAAGGGAAACAGATCTCAAAGATTT-T
6933 GTTTCAAGAGAAACTGTCTAAAGGGAGACAAAACTTA
64 GTTTCAAGAGAAACTGTCTAAA--GAGACAAAACTTA
*
6970 TTTCAAGGAAAACTGTCTCAAGAGAGATAAAATTTGTTTCCAGGGAAACAGAT-TCAAAGATTTT
1 TTTCAAGG-AAACTGTCTCAAGAGAGA-AAAATTTGTTTCAAGGGAAACAGATCTCAAAGATTTT
* * * * *
7034 TTTTCAAGGGAAACTGTCTCAAGAGACAAAATTTG
64 GTTTCAAGAGAAACTGTCTAAAGAGACAAAACTTA
* * * * *
7069 TTTTAAGGGAAACTCTCTCAAGAGAGACAAATTTGTTTCAACGGAAACTG-TCTCAA
1 TTTCAA-GGAAACTGTCTCAAGAGAGAAAAATTTGTTTCAAGGGAAACAGATCTCAA
7125 GAGACAAAAT
Statistics
Matches: 136, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
97 1 0.01
98 23 0.17
99 33 0.24
100 2 0.01
101 28 0.21
102 46 0.34
103 3 0.02
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (98 bp):
TTTCAAGGAAACTGTCTCAAGAGAGAAAAATTTGTTTCAAGGGAAACAGATCTCAAAGATTTTGT
TTCAAGAGAAACTGTCTAAAGAGACAAAACTTA
Found at i:7123 original size:69 final size:68
Alignment explanation
Indices: 7035--7241 Score: 216
Period size: 69 Copynumber: 2.9 Consensus size: 68
7025 AAAGATTTTT
* * *
7035 TTTCAAGGGAAACTGTCTCAAGAGACAAAATTTGTTTTAAGGGAAACTCTCTCAAGAGAGACAAA
1 TTTCAACGGAAACTGTCTCAAGAGACAAAA-TTGTTTCAAGGGAAACTATCTCAAGAGAGACAAA
7100 TTTG
65 TTTG
* *
7104 TTTCAACGGAAACTGTCTCAAGAGACAAAATTGTTTCAAGGGAAATTATCTCAAGAGAGATAAAA
1 TTTCAACGGAAACTGTCTCAAGAGACAAAATTGTTTCAAGGGAAACTATCTCAAGAGAGA-CAAA
7169 TCTTTTG
65 ---TTTG
* ** * * *
7176 TTTCAAGGGAAACTACCTCAAGCGAGATAAAATCTTATGTTTCAAGGGAAACTACCTCAAGCGAG
1 TTTCAACGGAAACTGTCTCAA--GAGACAAAA---T-TGTTTCAAGGGAAACTATCTCAAGAGAG
7241 A
60 A
7242 TAAAATCTTC
Statistics
Matches: 116, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
68 27 0.23
69 32 0.28
72 22 0.19
74 8 0.07
77 1 0.01
78 26 0.22
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (68 bp):
TTTCAACGGAAACTGTCTCAAGAGACAAAATTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAT
TTG
Found at i:7132 original size:33 final size:33
Alignment explanation
Indices: 6932--7161 Score: 191
Period size: 36 Copynumber: 6.8 Consensus size: 33
6922 CAAAGGTTTG
* * *
6932 TGTTTCAAGAGAAACTGTCTAAAGGGAGACAAAACT
1 TGTTTCAAGGGAAACTGTCTCAA--GAGAC-AAATT
* * *
6968 TATTTCAAGGAAAACTGTCTCAAGAGAGATAAAATT
1 TGTTTCAAGGGAAACTGTCTC-A-AGAGA-CAAATT
* * *
7004 TGTTTCCAGGGAAACAGAT-TCAA-AG---ATTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGACAAATT
*
7033 TTTTTCAAGGGAAACTGTCTCAAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAC-AAATT
* *
7067 TGTTTTAAGGGAAACTCTCTCAAGAGAGACAAATT
1 TGTTTCAAGGGAAACTGTCTC-A-AGAGACAAATT
* *
7102 TGTTTCAACGGAAACTGTCTCAAGAGACAAAAT
1 TGTTTCAAGGGAAACTGTCTCAAGAGACAAATT
* *
7135 TGTTTCAAGGGAAATTATCTCAAGAGA
1 TGTTTCAAGGGAAACTGTCTCAAGAGA
7162 GATAAAATCT
Statistics
Matches: 157, Mismatches: 25, Indels: 27
0.75 0.12 0.13
Matches are distributed among these distances:
28 1 0.01
29 21 0.13
30 2 0.01
33 36 0.23
34 23 0.15
35 25 0.16
36 46 0.29
37 2 0.01
38 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (33 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGACAAATT
Found at i:7318 original size:38 final size:39
Alignment explanation
Indices: 7035--7329 Score: 298
Period size: 39 Copynumber: 8.0 Consensus size: 39
7025 AAAGATTTTT
* *
7035 TTTCAAGGGAAACTGTCTCAA--GAGACAAAA--TT-TG
1 TTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTCTG
* * * *
7069 TTTTAAGGGAAACTCTCTCAAGAGAGA-CAAA--TT-TG
1 TTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTCTG
* * *
7104 TTTCAACGGAAACTGTCTCAA--GAGACAAAA---T-TG
1 TTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTCTG
* * *
7137 TTTCAAGGGAAATTATCTCAAGAGAGATAAAATCTTTTG
1 TTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTCTG
* *
7176 TTTCAAGGGAAACTACCTCAAGCGAGATAAAATCTTATG
1 TTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTCTG
*
7215 TTTCAAGGGAAACTACCTCAAGCGAGATAAAATCTTCTG
1 TTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTCTG
* * *
7254 TTTCAAGTGAAACTATCTGAAACGAGATAAAATCTTCTG
1 TTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTCTG
* *
7293 -TTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCT
1 TTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTCT
7330 TAAAAACAAT
Statistics
Matches: 229, Mismatches: 23, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
33 25 0.11
34 22 0.10
35 33 0.14
36 4 0.02
38 35 0.15
39 110 0.48
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (39 bp):
TTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTCTG
Found at i:7422 original size:75 final size:77
Alignment explanation
Indices: 7331--7474 Score: 199
Period size: 76 Copynumber: 1.9 Consensus size: 77
7321 AAATCTTCTT
7331 AAAAACAATATTGAGTGAAATGAAAT-GT-TTCTTTCGAGTAAAAA-TCGTCTCAA-CGAGACA-
1 AAAAACAATATTGAGTGAAAT-AAATCGTCTTCTTTCGAGTAAAAACT-GTCTCAAGCGAGACAG
7391 AATCTTGTTTTAAG
64 AATCTTGTTTTAAG
* * *
7405 AAAAACCAATCTTGAGTGAAATAAATCTTCTTGTTTCGAGTAAAAACTGTCTCAAGCGAGACAGA
1 AAAAA-CAATATTGAGTGAAATAAATCGTCTTCTTTCGAGTAAAAACTGTCTCAAGCGAGACAGA
7470 ATCTT
65 ATCTT
7475 CTGTTTCAAG
Statistics
Matches: 61, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
74 9 0.15
75 16 0.26
76 22 0.36
77 8 0.13
78 6 0.10
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.30
Consensus pattern (77 bp):
AAAAACAATATTGAGTGAAATAAATCGTCTTCTTTCGAGTAAAAACTGTCTCAAGCGAGACAGAA
TCTTGTTTTAAG
Found at i:7504 original size:39 final size:39
Alignment explanation
Indices: 7448--7529 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
7438 TTTCGAGTAA
* *
7448 AAACTGTCTCAAGCGAGACAGAATCTTCTGTTTCAAGGG
1 AAACTATCTCAAGCGAGACAAAATCTTCTGTTTCAAGGG
* *
7487 AAACTATCTCTAA-CGAGACAAAATTTTCTGTTTCAAGTG
1 AAACTATCTC-AAGCGAGACAAAATCTTCTGTTTCAAGGG
7526 AAAC
1 AAAC
7530 AACTCTTGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 36 0.95
40 2 0.05
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (39 bp):
AAACTATCTCAAGCGAGACAAAATCTTCTGTTTCAAGGG
Found at i:11590 original size:29 final size:29
Alignment explanation
Indices: 11542--11597 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
11532 TAATAAGAGC
11542 AGACAAAAAGATCAATGTTAGTAGAAACA
1 AGACAAAAAGATCAATGTTAGTAGAAACA
* *
11571 AGACAACAAGAATCAA-GTTAGTTGAAA
1 AGACAAAAAG-ATCAATGTTAGTAGAAA
11598 AGATTAGTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.54, C:0.11, G:0.18, T:0.18
Consensus pattern (29 bp):
AGACAAAAAGATCAATGTTAGTAGAAACA
Found at i:14245 original size:30 final size:30
Alignment explanation
Indices: 14211--14294 Score: 123
Period size: 30 Copynumber: 2.8 Consensus size: 30
14201 ACATGGGGGC
* * *
14211 ATGGTGGTGGCATGGGATATTGAATATAAA
1 ATGGTAGTGGCATGGGATGTTGAATAAAAA
*
14241 ATGGTAGTGACATGGGATGTTGAATAAAAA
1 ATGGTAGTGGCATGGGATGTTGAATAAAAA
*
14271 ATGGTAGTGGAATGGGATGTTGAA
1 ATGGTAGTGGCATGGGATGTTGAA
14295 GAAACTATGG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.35, C:0.02, G:0.35, T:0.29
Consensus pattern (30 bp):
ATGGTAGTGGCATGGGATGTTGAATAAAAA
Found at i:14696 original size:91 final size:91
Alignment explanation
Indices: 14507--14769 Score: 337
Period size: 91 Copynumber: 2.9 Consensus size: 91
14497 GTGATGCAAT
* * * * *
14507 GTTGAATAAGTTCTTCTGATTATGAACTTCTTCTGCCTCTATCGGATGAGTTCTTCTCATTATGT
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCT-TATTGGATGAGTTCTTCTCATTATGA
* * * * **
14572 ACTCTCCACTGTAAATGTTGATGCAAG
65 ACTCTCCATTGGAAATCTTAAACCAAG
* * *
14599 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTTTTGGATAAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATTGGATGAGTTCTTCTCATTATGAA
*
14664 CTCTCCATTGGAAATCTTAAACCCAG
66 CTCTCCATTGGAAATCTTAAACCAAG
* **
14690 GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATTGGATGAGTTCTTCTCATTATGAA
* *
14755 CACTCCATTTGAAAT
66 CTCTCCATTGGAAAT
14770 GTCAATCCCT
Statistics
Matches: 149, Mismatches: 22, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
91 115 0.77
92 34 0.23
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.40
Consensus pattern (91 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATTGGATGAGTTCTTCTCATTATGAA
CTCTCCATTGGAAATCTTAAACCAAG
Found at i:15362 original size:65 final size:66
Alignment explanation
Indices: 15277--15400 Score: 180
Period size: 65 Copynumber: 1.9 Consensus size: 66
15267 GAGATAGATT
* * *
15277 TGTTTCTAGGGAAACTGTCTAAAGAGAGAC-AAA-TTCGTTTCAAGGGAAACCATCTCAAAGGTG
1 TGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAACTT-ATTTCAAGGGAAACCATCTCAAAGGTG
15340 TG
65 TG
* *
15342 TGTTTCAAGAGAAACTGTCTAAAGGGAGACAAAACTTATTTCAAGGGAAACTATCTCAA
1 TGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAACTTATTTCAAGGGAAACCATCTCAA
15401 GAGAGATAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
65 27 0.52
66 23 0.44
67 2 0.04
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAACTTATTTCAAGGGAAACCATCTCAAAGGTGT
G
Found at i:15392 original size:36 final size:36
Alignment explanation
Indices: 15342--15702 Score: 324
Period size: 36 Copynumber: 10.0 Consensus size: 36
15332 CAAAGGTGTG
* * * *
15342 TGTTTCAAGAGAAACTGTCTAAAGGGAGACAAAACT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * *
15378 TATTTCAAGGGAAACTATCTCAAGAGAGATAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* *
15414 TGTTTCAAGGGAAACAGAT-TC-A-A-AG----ATTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT
15443 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
*
15479 TGTTTCAAGGGAAACTGCCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
*
15515 TGTTTCAAGGGAAACGGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * * * *
15551 TGTTTAAAGGGAAATTATCTAAAGAGAGATAAAATCTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA---TT
** * *
15590 TGTTTCAAGGGAAACTACCTCAAGCGAGATAAAATCTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--TT
* ** *
15628 ATGTGTCAAGGGAAACTACCTCAAGCGAGACAAAATCTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--TT
* * * *
15667 CTGTTTCAAGTGAAACTATCTCAAGCGAGATAAAAT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
15703 CTTCTGTTTA
Statistics
Matches: 276, Mismatches: 36, Indels: 25
0.82 0.11 0.07
Matches are distributed among these distances:
28 1 0.00
29 21 0.08
30 1 0.00
31 1 0.00
32 2 0.01
33 2 0.01
34 1 0.00
35 1 0.00
36 145 0.53
37 2 0.01
38 2 0.01
39 97 0.35
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:15459 original size:101 final size:101
Alignment explanation
Indices: 15279--15529 Score: 335
Period size: 101 Copynumber: 2.5 Consensus size: 101
15269 GATAGATTTG
* * * * *
15279 TTTCTAGGGAAACTGTCTAAAGAGAGACAAATTCGTTTCAAGGGAAACCATCTCAAAGGTGTGTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGAAAAATTTGTTTCAAGGGAAACCATCTCAAAGATGTGTG
*
15344 TTTCAAGAGAAACTGTCTAAAGGGAGACAAAACTTA
66 TTTCAAGAGAAACTGTCTAAAGAGAGACAAAACTTA
* * *
15380 TTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACAGAT-TCAAAGAT-TT
1 TTTCAAGGGAAACTGTCTCAAGAGAGA-AAAATTTGTTTCAAGGGAAAC-CATCTCAAAGATGTG
* * * *
15443 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
64 TGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAACTTA
*
15481 TTTCAAGGGAAACTGCCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC
1 TTTCAAGGGAAACTGTCTCAAGAGAGA-AAAATTTGTTTCAAGGGAAAC
15530 GGTCTCAAGA
Statistics
Matches: 132, Mismatches: 16, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
101 104 0.79
102 26 0.20
103 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (101 bp):
TTTCAAGGGAAACTGTCTCAAGAGAGAAAAATTTGTTTCAAGGGAAACCATCTCAAAGATGTGTG
TTTCAAGAGAAACTGTCTAAAGAGAGACAAAACTTA
Found at i:15601 original size:39 final size:39
Alignment explanation
Indices: 15440--16007 Score: 357
Period size: 39 Copynumber: 15.0 Consensus size: 39
15430 GATTCAAAGA
* * *
15440 TTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--
1 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
** * *
15477 -TTTGTTTCAAGGGAAACTGCCTCAAGAGAGACAAAA--
1 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
** * *
15513 -TTTGTTTCAAGGGAAACGGTCTCAAGAGAGACAAAA--
1 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
* * * *
15549 -TTTGTTTAAAGGGAAATTATCTAAAGAGAGATAAAATC
1 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
*
15587 TTTTGTTTCAAGGGAAACTACCTCAAGCGAGATAAAATC
1 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
* * * *
15626 TTATGTGTCAAGGGAAACTACCTCAAGCGAGACAAAATC
1 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
* *
15665 TTCTGTTTCAAGTGAAACTATCTCAAGCGAGATAAAATC
1 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
* * *
15704 TTCTGTTT-AGAGTGAAACTATCTGAAGCGAGATAAAATC
1 TTTTGTTTCA-AGGGAAACTATCTCAAGCGAGATAAAATC
* * * *
15743 TTCTATTTCGAGTGAAACTATCTCAAGCGAGATAAAATC
1 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
* ** * * * *
15782 -TTT-TTT-AA---AAACAATCTTGAGTGAAATGAAATG
1 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
* * ** * * * *
15815 TTTTCTTTCGAGTAAAAATCGTCTCAAGCAAGA-CAAATC
1 TTTTGTTTCAAGGGAAACT-ATCTCAAGCGAGATAAAATC
* ** * ** * *
15854 --TTGTTTTAAGAAAAACAATCTTGAGTGAAAT-AAATC
1 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
* ** * ***
15890 TTCTTGTTTCGAGTAAAAACTGTCTCAAGCGAGACGGAATC
1 TT-TTGTTTCAAG-GGAAACTATCTCAAGCGAGATAAAATC
* *
15931 TTCTGTTTCAAGGAAAACTATCTCAAGCGAGATAAAATC
1 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
* * ** * *
15970 TTCTGTTTCGAGATAAACCATCTCAAGTGAGATAAAAT
1 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
16008 ATTCTTTAAA
Statistics
Matches: 433, Mismatches: 80, Indels: 34
0.79 0.15 0.06
Matches are distributed among these distances:
33 18 0.04
34 3 0.01
35 3 0.01
36 113 0.26
37 14 0.03
38 3 0.01
39 244 0.56
40 29 0.07
41 6 0.01
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (39 bp):
TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
Found at i:19581 original size:15 final size:16
Alignment explanation
Indices: 19555--19584 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
19545 GATGAATGCA
19555 AATGTCATGCAAAATG
1 AATGTCATGCAAAATG
19571 AATGT-ATGCAAAAT
1 AATGTCATGCAAAAT
19585 ACATTGATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.27
Consensus pattern (16 bp):
AATGTCATGCAAAATG
Found at i:20073 original size:31 final size:29
Alignment explanation
Indices: 20031--20088 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
20021 CAATAAAAGC
20031 AGATAAAAAGAAATCAATGTTAGTAGAAACA
1 AGATAAAAAG-AATCAA-GTTAGTAGAAACA
* *
20062 AGATAACAAGAATCAAGTTAGTTGAAA
1 AGATAAAAAGAATCAAGTTAGTAGAAA
20089 AGATTAGTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.40
30 6 0.24
31 9 0.36
ACGTcount: A:0.55, C:0.07, G:0.17, T:0.21
Consensus pattern (29 bp):
AGATAAAAAGAATCAAGTTAGTAGAAACA
Found at i:20880 original size:18 final size:18
Alignment explanation
Indices: 20857--20893 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
20847 AAATTGGATG
*
20857 ATTTTAATAAAACATTTT
1 ATTTTAATAAAACACTTT
20875 ATTTTAATAAAACACTTT
1 ATTTTAATAAAACACTTT
20893 A
1 A
20894 GGATCTACGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTTTAATAAAACACTTT
Found at i:22790 original size:29 final size:29
Alignment explanation
Indices: 22732--22814 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
22722 ACGTGGGGGT
*
22732 ATGGGATATTGAATATAAAATGGTAGTGGC
1 ATGGGATGTTGAATA-AAAATGGTAGTGGC
22762 ATGGGATGTTGAATAAAAATGGTAGTGGC
1 ATGGGATGTTGAATAAAAATGGTAGTGGC
*
22791 ATGGGATGTTTAATAAAATATGGT
1 ATGGGATGTTGAATAAAA-ATGGT
22815 GGAATAAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
29 31 0.62
30 19 0.38
ACGTcount: A:0.36, C:0.02, G:0.30, T:0.31
Consensus pattern (29 bp):
ATGGGATGTTGAATAAAAATGGTAGTGGC
Found at i:23213 original size:91 final size:91
Alignment explanation
Indices: 23013--23271 Score: 367
Period size: 91 Copynumber: 2.8 Consensus size: 91
23003 ATATGTGATG
* * * *
23013 CAAGGTTGAATAAGTTCTTCTGATTATGAACTTCTTCTGCCTC-TATCGGATGAGCTCTTCTCAT
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGT-T-GGATGAGTTCTTCTCAT
* ** * * **
23077 TATGAAATCTCTGCTGTAAATGTTGATG
64 TATGAACTCTCCACTGGAAATCTTGAAC
* * *
23105 CAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATAAGTTATTCTCATTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTA
23170 TGAACTCTCCACTGGAAATCTTGAAC
66 TGAACTCTCCACTGGAAATCTTGAAC
23196 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTA
23261 TGAACTCTCCA
66 TGAACTCTCCA
23272 TTTGAAATGT
Statistics
Matches: 149, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
91 108 0.72
92 40 0.27
93 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (91 bp):
CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTA
TGAACTCTCCACTGGAAATCTTGAAC
Found at i:23813 original size:36 final size:36
Alignment explanation
Indices: 23767--24281 Score: 320
Period size: 36 Copynumber: 14.6 Consensus size: 36
23757 TTTTTTTTTA
* * * *
23767 AAACCATCTCAAGTGAGATAGATTTTGTTTCAAGTG
1 AAACTATCTCAAGAGAGATAAATTTTGTTTCAAGGG
* *
23803 AAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGG
1 AAACTATCTCAAGAGAGATAAATTTTGTTTCAAGGG
* * *
23839 AAACGATCTCAA-AG-G-T---TTGTGTTTCAAGAG
1 AAACTATCTCAAGAGAGATAAATTTTGTTTCAAGGG
* * * * ** *
23869 AAACTGTCTAAAGGGAGACAAAACTTATTTCAAGGG
1 AAACTATCTCAAGAGAGATAAATTTTGTTTCAAGGG
* *
23905 AAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGG
1 AAACTATCTCAAGAGAGATAAATTTTGTTTCAAGGG
*
23941 AAACAGAT-TC-A-A-AG----ATTTTGTTTCAAGGG
1 AAAC-TATCTCAAGAGAGATAAATTTTGTTTCAAGGG
**
23970 AAAAAGAT-TC-----A-A-AAATTTTGTTTCAAGGG
1 -AAACTATCTCAAGAGAGATAAATTTTGTTTCAAGGG
* * * *
23999 AAACTGTCTTAAGAGAGACAAAATTTGTTTCAAGGG
1 AAACTATCTCAAGAGAGATAAATTTTGTTTCAAGGG
** * * *
24035 AAACGGTCTCAAGAGAGACAAAATTTATTTCAAGGG
1 AAACTATCTCAAGAGAGATAAATTTTGTTTCAAGGG
* * * * *
24071 AAGCTGTCTCAAGAGAGACAAAATTTGTTTCAACGG
1 AAACTATCTCAAGAGAGATAAATTTTGTTTCAAGGG
* * * **
24107 AAACTGTCTCAAGAGAGACAAAATTTGTTTCAACAG
1 AAACTATCTCAAGAGAGATAAATTTTGTTTCAAGGG
* * *
24143 AAATTATCTCGAGAGAGATAAAATCTTTTTTTTCAAGGG
1 AAACTATCTCAAGAGAGAT-AAA--TTTTGTTTCAAGGG
* *
24182 AAACTACCTCAA-ACGAGATAAAATCGTCTGTTTCAAGGG
1 AAACTATCTCAAGA-GAGAT-AAAT--TTTGTTTCAAGGG
* * *
24221 AAACTACCTCAAGCGAGATAAAATCTTCTGTTTCAAGTG
1 AAACTATCTCAAGAGAGAT-AAAT-TT-TGTTTCAAGGG
*
24260 AAACTATCTCAAGCGAGATAAA
1 AAACTATCTCAAGAGAGATAAA
24282 ATCTTCTGTT
Statistics
Matches: 390, Mismatches: 62, Indels: 52
0.77 0.12 0.10
Matches are distributed among these distances:
27 1 0.00
28 4 0.01
29 35 0.09
30 23 0.06
31 1 0.00
32 1 0.00
33 2 0.01
34 3 0.01
35 4 0.01
36 217 0.56
37 5 0.01
38 5 0.01
39 89 0.23
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (36 bp):
AAACTATCTCAAGAGAGATAAATTTTGTTTCAAGGG
Found at i:23900 original size:66 final size:66
Alignment explanation
Indices: 23792--23916 Score: 180
Period size: 66 Copynumber: 1.9 Consensus size: 66
23782 AGATAGATTT
* * * *
23792 TGTTTCAAGTGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC-GATCTCAAAGGTT
1 TGTTTCAAGAGAAACTATCTAAAGAGAGACAAAACTTATTTCAAGGGAAACTG-TCTCAAAGGTT
23856 TG
65 TG
* *
23858 TGTTTCAAGAGAAACTGTCTAAAGGGAGACAAAACTTATTTCAAGGGAAACTGTCTCAA
1 TGTTTCAAGAGAAACTATCTAAAGAGAGACAAAACTTATTTCAAGGGAAACTGTCTCAA
23917 GAGAGATAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
66 51 0.98
67 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTATCTAAAGAGAGACAAAACTTATTTCAAGGGAAACTGTCTCAAAGGTTT
G
Found at i:23968 original size:29 final size:29
Alignment explanation
Indices: 23924--24002 Score: 133
Period size: 29 Copynumber: 2.8 Consensus size: 29
23914 CAAGAGAGAT
23924 AAAA-TTTGTTTCAAGGGAAACAGATTCA
1 AAAATTTTGTTTCAAGGGAAACAGATTCA
* *
23952 AAGATTTTGTTTCAAGGGAAAAAGATTCA
1 AAAATTTTGTTTCAAGGGAAACAGATTCA
23981 AAAATTTTGTTTCAAGGGAAAC
1 AAAATTTTGTTTCAAGGGAAAC
24003 TGTCTTAAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 3 0.07
29 43 0.93
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (29 bp):
AAAATTTTGTTTCAAGGGAAACAGATTCA
Found at i:24030 original size:130 final size:131
Alignment explanation
Indices: 23826--24072 Score: 372
Period size: 130 Copynumber: 1.9 Consensus size: 131
23816 AGAGACAAAA
* ** *
23826 TTTGTTTCAAGGGAAACGATCTCAAAGGTTTGTGTTTCAAGAGAAACTGTCTAAAGGGAGACAAA
1 TTTGTTTCAAGGGAAAAGATCTCAAAAATTTGTGTTTCAAGAGAAACTGTCTAAAGAGAGACAAA
* * *
23891 ACTTATTTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACAGATTCAAAGA
66 ACTTATTTCAAGGGAAACGGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACAGATTCAAAGA
23956 T
131 T
* *
23957 TTTGTTTCAAGGGAAAAAGAT-TCAAAAATTT-TGTTTCAAGGGAAACTGTCTTAAGAGAGACAA
1 TTTGTTTCAAGGG-AAAAGATCTCAAAAATTTGTGTTTCAAGAGAAACTGTCTAAAGAGAGACAA
* *
24020 AATTTGTTTCAAGGGAAACGGTCTCAAGAGAGACAAAATTTATTTCAAGGGAA
65 AACTTATTTCAAGGGAAACGGTCTCAAGAGAGACAAAATTTATTTCAAGGGAA
24073 GCTGTCTCAA
Statistics
Matches: 104, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
130 77 0.74
131 21 0.20
132 6 0.06
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (131 bp):
TTTGTTTCAAGGGAAAAGATCTCAAAAATTTGTGTTTCAAGAGAAACTGTCTAAAGAGAGACAAA
ACTTATTTCAAGGGAAACGGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACAGATTCAAAGA
T
Found at i:24177 original size:39 final size:39
Alignment explanation
Indices: 23981--24366 Score: 275
Period size: 39 Copynumber: 10.3 Consensus size: 39
23971 AAAAGATTCA
** * *
23981 AAAAT-TT-TGTTTCAAGGGAAACTGTCTTAAGAGAGAC
1 AAAATCTTCTGTTTCAAGGGAAACTACCTCAAGAGAGAT
*** *
24018 AAAA--TT-TGTTTCAAGGGAAACGGTCTCAAGAGAGAC
1 AAAATCTTCTGTTTCAAGGGAAACTACCTCAAGAGAGAT
* * ** *
24054 AAAA--TT-TATTTCAAGGGAAGCTGTCTCAAGAGAGAC
1 AAAATCTTCTGTTTCAAGGGAAACTACCTCAAGAGAGAT
* ** *
24090 AAAA--TT-TGTTTCAACGGAAACTGTCTCAAGAGAGAC
1 AAAATCTTCTGTTTCAAGGGAAACTACCTCAAGAGAGAT
** * * *
24126 AAAA--TT-TGTTTCAACAGAAATTATCTCGAGAGAGAT
1 AAAATCTTCTGTTTCAAGGGAAACTACCTCAAGAGAGAT
* *
24162 AAAATCTTTTTTTTCAAGGGAAACTACCTCAA-ACGAGAT
1 AAAATCTTCTGTTTCAAGGGAAACTACCTCAAGA-GAGAT
* *
24201 AAAATCGTCTGTTTCAAGGGAAACTACCTCAAGCGAGAT
1 AAAATCTTCTGTTTCAAGGGAAACTACCTCAAGAGAGAT
* * *
24240 AAAATCTTCTGTTTCAAGTGAAACTATCTCAAGCGAGAT
1 AAAATCTTCTGTTTCAAGGGAAACTACCTCAAGAGAGAT
** * * *
24279 AAAATCTTCTGTTT-AGAGTAAAACTATCTCAAGTGATAT
1 AAAATCTTCTGTTTCA-AGGGAAACTACCTCAAGAGAGAT
* * ** *
24318 AAAATCTTCTATTTCGAGTAAAACTATCTCAA-ATGAGAT
1 AAAATCTTCTGTTTCAAGGGAAACTACCTCAAGA-GAGAT
24357 AAAATCTTCT
1 AAAATCTTCT
24367 TTAAAAATAA
Statistics
Matches: 308, Mismatches: 33, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
36 131 0.43
37 4 0.01
38 4 0.01
39 169 0.55
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (39 bp):
AAAATCTTCTGTTTCAAGGGAAACTACCTCAAGAGAGAT
Found at i:24468 original size:77 final size:77
Alignment explanation
Indices: 24369--24514 Score: 215
Period size: 76 Copynumber: 1.9 Consensus size: 77
24359 AATCTTCTTT
* *
24369 AAAAATAATCTTGAGTGAAATAAAAATATT-TTCTTTCGAGTAAAAACCGTCTCAATCGAGACA-
1 AAAAACAATCTTGAGTGAAAT--AAATATTCTTCTTTCGAGTAAAAACCGTCTCAAGCGAGACAG
24432 AATCTTGTTTTAAG
64 AATCTTGTTTTAAG
* * *
24446 AAAAACAATCTTGAGTGAAATAAATCTTCTTGTTTCGAGTAAAAACTGTCTCAAGCGAGACAGAA
1 AAAAACAATCTTGAGTGAAATAAATATTCTTCTTTCGAGTAAAAACCGTCTCAAGCGAGACAGAA
24511 TCTT
66 TCTT
24515 CTGTTTCAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
75 6 0.10
76 30 0.48
77 26 0.42
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (77 bp):
AAAAACAATCTTGAGTGAAATAAATATTCTTCTTTCGAGTAAAAACCGTCTCAAGCGAGACAGAA
TCTTGTTTTAAG
Found at i:24544 original size:39 final size:39
Alignment explanation
Indices: 24488--24569 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
24478 TTTCGAGTAA
* * *
24488 AAACTGTCTCAAGCGAGACAGAATCTTCTGTTTCAAGGG
1 AAACTATCTCAAGCGAGACAAAATCTTCTGTTTCAAGCG
*
24527 AAACTATCTCCAA-CGAGACAAAATTTTCTGTTTCAAGCG
1 AAACTATCT-CAAGCGAGACAAAATCTTCTGTTTCAAGCG
24566 AAAC
1 AAAC
24570 AACTTTTGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 35 0.92
40 3 0.08
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (39 bp):
AAACTATCTCAAGCGAGACAAAATCTTCTGTTTCAAGCG
Found at i:24592 original size:60 final size:60
Alignment explanation
Indices: 24516--24629 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
24506 CAGAATCTTC
* *
24516 TGTTTCAAGGGAAACTATCTCCAA-CGAGACAAAATTTTCTGTTTCAAGCGAAACAACTTT
1 TGTTTCAAGGGAAACTATCT-CAAGCGAGACAAAATCTTCTGTTTCAAGAGAAACAACTTT
* * * *
24576 TGTTTTAAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGAGAAAC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATCTTCTGTTTCAAGAGAAAC
24630 CATCTCATGT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 3 0.06
60 44 0.94
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (60 bp):
TGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATCTTCTGTTTCAAGAGAAACAACTTT
Found at i:28520 original size:28 final size:31
Alignment explanation
Indices: 28464--28520 Score: 84
Period size: 28 Copynumber: 1.9 Consensus size: 31
28454 CAATAAGAGT
28464 AGACAATAAGAAATCAATGTTAGTAGAAACA
1 AGACAATAAGAAATCAATGTTAGTAGAAACA
*
28495 AGACAA-AA-AAATCAA-GTTAGTTGAAA
1 AGACAATAAGAAATCAATGTTAGTAGAAA
28521 AGATTAGTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 10 0.40
29 7 0.28
30 2 0.08
31 6 0.24
ACGTcount: A:0.56, C:0.09, G:0.16, T:0.19
Consensus pattern (31 bp):
AGACAATAAGAAATCAATGTTAGTAGAAACA
Found at i:29332 original size:18 final size:18
Alignment explanation
Indices: 29290--29333 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
29280 AAAAACTGGG
*
29290 TGATTTTAATAAAACATT
1 TGATTTTAATAAAACATC
*
29308 TTATTTTAATAAAACA-C
1 TGATTTTAATAAAACATC
29325 TGAGTTTTA
1 TGA-TTTTA
29334 GGGTCTGCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (18 bp):
TGATTTTAATAAAACATC
Found at i:31203 original size:30 final size:29
Alignment explanation
Indices: 31163--31257 Score: 145
Period size: 30 Copynumber: 3.2 Consensus size: 29
31153 ACGTGGGGGC
* *
31163 ATGGTGGTGGCATGGGATATTGAATATAAA
1 ATGGTAGTGGCATGGGATGTTGAATA-AAA
31193 ATGGTAGTGGCATGGGATGTTGAATAAAAA
1 ATGGTAGTGGCATGGGATGTTGAAT-AAAA
31223 ATGGTAGTGGCATGGGATGTTGAATAAAA
1 ATGGTAGTGGCATGGGATGTTGAATAAAA
31252 TATGGT
1 -ATGGT
31258 GGAATAAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
29 4 0.07
30 56 0.92
31 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.34, T:0.29
Consensus pattern (29 bp):
ATGGTAGTGGCATGGGATGTTGAATAAAA
Found at i:39034 original size:22 final size:21
Alignment explanation
Indices: 39006--39086 Score: 76
Period size: 23 Copynumber: 3.7 Consensus size: 21
38996 TTTTAGTGCA
*
39006 AAGGGAATCGATACCCCCTTG
1 AAGGGAACCGATACCCCCTTG
39027 AAGGGGAACCGACT-CCCCCTTTG
1 AA-GGGAACCGA-TACCCCC-TTG
*
39050 AATGGGAACCGATTCCCTCCTTG
1 AA-GGGAACCGATACCC-CCTTG
*
39073 -AGGGAATCGATACC
1 AAGGGAACCGATACC
39087 TCCCACGGGT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
21 13 0.25
22 15 0.29
23 21 0.41
24 2 0.04
ACGTcount: A:0.26, C:0.30, G:0.25, T:0.20
Consensus pattern (21 bp):
AAGGGAACCGATACCCCCTTG
Found at i:39083 original size:21 final size:22
Alignment explanation
Indices: 39008--39073 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 22
38998 TTAGTGCAAA
* *
39008 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTTGAAG
* *
39030 GGGAACCGACTCCCCCTTTGAAT
1 GGGAACCGATTCCCCC-TTGAAG
39053 GGGAACCGATTCCCTCCTTGA
1 GGGAACCGATTCCC-CCTTGA
39074 GGGAATCGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 13 0.35
23 22 0.59
24 2 0.05
ACGTcount: A:0.23, C:0.32, G:0.24, T:0.21
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:44617 original size:22 final size:22
Alignment explanation
Indices: 44592--44646 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
44582 ATACTTTTAT
44592 TTATTTTTAAATA-TTTTAATGA
1 TTATTTTTAAATATTTTTAAT-A
* *
44614 TTATTTATATATATTTTTAATA
1 TTATTTTTAAATATTTTTAATA
44636 TT-TTTGTTAAA
1 TTATTT-TTAAA
44647 GATTAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 3 0.11
22 17 0.63
23 7 0.26
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (22 bp):
TTATTTTTAAATATTTTTAATA
Found at i:44727 original size:13 final size:14
Alignment explanation
Indices: 44704--44732 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
44694 CTTTCTAAAC
44704 TAATCAATTAACGA
1 TAATCAATTAACGA
44718 TAAT-AATTAACGA
1 TAATCAATTAACGA
44731 TA
1 TA
44733 TTTGGTTCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.31
Consensus pattern (14 bp):
TAATCAATTAACGA
Found at i:49730 original size:20 final size:20
Alignment explanation
Indices: 49705--49837 Score: 185
Period size: 20 Copynumber: 6.7 Consensus size: 20
49695 TTTTCCTAAT
49705 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
49725 TCGCAATGAGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
49745 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
49765 TCGCATTGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
49785 TCGCATTGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
49805 TCTCAATGCGAGTATGTAAA
1 TCGCAATGCGAATACGTAAA
*
49825 TCGCAACGCGAAT
1 TCGCAATGCGAAT
49838 CTGACTATCG
Statistics
Matches: 99, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 99 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:49847 original size:20 final size:20
Alignment explanation
Indices: 49824--49889 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
49814 GAGTATGTAA
49824 ATCGCAACGCGAATCTGACT
1 ATCGCAACGCGAATCTGACT
* *
49844 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGAATCTGACT
*
49864 ATCGCAACACG-ATCTGACT
1 ATCGCAACGCGAATCTGACT
49883 ATCGCAA
1 ATCGCAA
49890 TATTGAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 14 0.34
20 27 0.66
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAATCTGACT
Done.