Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008001.1 Hibiscus syriacus cultivar Beakdansim tig00110458_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: 3902382
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 18
Found at i:3868292 original size:21 final size:19
Alignment explanation
Indices: 3868263--3868301 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
3868253 AGGGAAAAAT
*
3868263 AAAATAAATAAGTAAGATAAG
1 AAAAAAAAT-AGTAA-ATAAG
3868284 AAAAAAAATAGTAAATAA
1 AAAAAAAATAGTAAATAA
3868302 TAATTATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 5 0.29
21 8 0.47
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.18
Consensus pattern (19 bp):
AAAAAAAATAGTAAATAAG
Found at i:3868349 original size:2 final size:2
Alignment explanation
Indices: 3868338--3868367 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3868328 AAAGGAAAAA
*
3868338 AT AT AA 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
3868368 CAAAGTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3868891 original size:18 final size:17
Alignment explanation
Indices: 3868870--3868912 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
3868860 ATATATACAT
3868870 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
3868888 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
3868905 ATAA-AATA
1 ATAATAATA
3868913 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:3868925 original size:65 final size:62
Alignment explanation
Indices: 3868800--3868927 Score: 152
Period size: 65 Copynumber: 2.0 Consensus size: 62
3868790 TATTAAAGAA
* * * *
3868800 ATATATATATAATAATAAAATATAGTAAAAAAATAAATGAAAATAATTTAATATATATATAT
1 ATATACATATAATAATAAAACATAATAAAAAAATAAATGAAAATAATTCAATATATATATAT
*
3868862 ATATACATATAATAATAATAACATGAATAATAAAAATAAATGAATAA-AATATCCATATA-ATAT
1 ATATACATATAATAATAA-AACAT-AATAA-AAAAATAAATGAA-AATAAT-TCAATATATATAT
3868925 AT
61 AT
3868927 A
1 A
3868928 AAGAGATTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
62 17 0.30
63 4 0.07
64 4 0.07
65 23 0.41
66 8 0.14
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (62 bp):
ATATACATATAATAATAAAACATAATAAAAAAATAAATGAAAATAATTCAATATATATATAT
Found at i:3869319 original size:37 final size:37
Alignment explanation
Indices: 3869269--3869370 Score: 125
Period size: 37 Copynumber: 2.8 Consensus size: 37
3869259 GTGCTTGTGG
* * * *
3869269 ATCCTATCTTTAGGAATTTAAATCTTA-CTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGC-AAAACTCT
* * *
3869306 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
3869343 ATCCTATTTTTAGGAGTTTAAATCCTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAG
3869371 TAGGACGAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
37 55 0.98
38 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
Found at i:3870264 original size:106 final size:103
Alignment explanation
Indices: 3870135--3870369 Score: 273
Period size: 98 Copynumber: 2.3 Consensus size: 103
3870125 TGTTCCGAGG
* **
3870135 CCAATATCCTTCGCCGTGAAGTTGAAATTGACTCTGGAACTGGGAAATTGTTTGTCGACAGTCAG
1 CCAATATCCTTCGCCGTGGAGTTGAAA-TGA-T-TGG--CTCCGAAATTGTTTGTCGACAGTCAG
*
3870200 CCACCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTG-G-GT
61 CCACCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTGT
* * **
3870241 CCAATATCCTTCGCCGTGGAGTTG--A-GATTGGCTCCGAAATTGTTTTTTGACAGTCAGCTGCC
1 CCAATATCCTTCGCCGTGGAGTTGAAATGATTGGCTCCGAAATTGTTTGTCGACAGTCAGCCACC
*
3870303 CCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTGT
66 CCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTGT
* * *
3870341 CACGATATCCTCCGTCGTGGAGTTGAAAT
1 C-CAATATCCTTCGCCGTGGAGTTGAAAT
3870370 CGCGGATGTT
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
98 56 0.50
99 1 0.01
100 6 0.05
101 21 0.19
102 2 0.02
103 1 0.01
104 1 0.01
106 23 0.21
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (103 bp):
CCAATATCCTTCGCCGTGGAGTTGAAATGATTGGCTCCGAAATTGTTTGTCGACAGTCAGCCACC
CCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTGT
Found at i:3870585 original size:36 final size:36
Alignment explanation
Indices: 3870538--3870613 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
3870528 TGTTTGGAGA
* * *
3870538 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
*
3870574 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
3870610 GAAA
1 GAAA
3870614 TGTTTTCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:3870683 original size:39 final size:39
Alignment explanation
Indices: 3870629--3870808 Score: 109
Period size: 39 Copynumber: 4.9 Consensus size: 39
3870619 TCAATGTTTA
* *
3870629 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTC
1 TGTTTCGAGGGAAACTGTCTCAAGGGAGACAAAATTTTC
* * * **
3870668 TGTTTCGAGGGAAACTATCTCAAGAGAGAGAAAA-AAT-
1 TGTTTCGAGGGAAACTGTCTCAAGGGAGACAAAATTTTC
* ** *
3870705 TATTTCGAGGGAAA-TGT-T-------TTC--AATGTTTA
1 TGTTTCGAGGGAAACTGTCTCAAGGGAGACAAAAT-TTTC
* *
3870734 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTC
1 TGTTTCGAGGGAAACTGTCTCAAGGGAGACAAAATTTTC
* *
3870773 TGTTTCGAGGGAAACTATCTC-AGGAGAGAAAAAATT
1 TGTTTCGAGGGAAACTGTCTCAAGG-GAGACAAAATT
3870809 AATTTCAAGG
Statistics
Matches: 102, Mismatches: 24, Indels: 30
0.65 0.15 0.19
Matches are distributed among these distances:
26 2 0.02
28 1 0.01
29 11 0.11
30 3 0.03
31 1 0.01
35 1 0.01
36 2 0.02
37 13 0.13
38 5 0.05
39 60 0.59
40 3 0.03
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (39 bp):
TGTTTCGAGGGAAACTGTCTCAAGGGAGACAAAATTTTC
Found at i:3870735 original size:105 final size:105
Alignment explanation
Indices: 3870513--3870831 Score: 515
Period size: 105 Copynumber: 3.1 Consensus size: 105
3870503 TTCGTTATAT
* ** *
3870513 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* * *
3870575 AAACTATCTCA-AGCGAGATAAAATTCATTTCAAGGGAAA
66 AAACTATCTCAGAGAGAGAAAAAATTAATTTCAAGGGAAA
3870614 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
3870679 AAACTATCTCAAGAGAGAGAAAAAATT-ATTTCGAGGGAAA
66 AAACTATCTC-AGAGAGAGAAAAAATTAATTTCAAGGGAAA
3870719 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
3870784 AAACTATCTCAG-GAGAGAAAAAATTAATTTCAAGGGAAA
66 AAACTATCTCAGAGAGAGAAAAAATTAATTTCAAGGGAAA
3870823 TGTTTTCAA
1 TGTTTTCAA
3870832 GAGAAACTGT
Statistics
Matches: 204, Mismatches: 8, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
101 46 0.23
103 16 0.08
104 42 0.21
105 88 0.43
106 12 0.06
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (105 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
AAACTATCTCAGAGAGAGAAAAAATTAATTTCAAGGGAAA
Found at i:3871035 original size:36 final size:36
Alignment explanation
Indices: 3870919--3871035 Score: 101
Period size: 36 Copynumber: 3.1 Consensus size: 36
3870909 AACAGCCTTG
* **
3870919 AGTGAAATGAAATGCCTTCTTTCGAGTGAAAATGGTCTCA
1 AGTGAAAT-AAAT--CTTCTTTCGAG-AAAAACAGTCTCA
* * * * **
3870959 AGCGAGACAAATCTTGCTTT-AAGAAAAACAGTCTTG
1 AGTGAAATAAATCTT-CTTTCGAGAAAAACAGTCTCA
3870995 AGTGAAATAAATCTTCTTTCGAGAAAAACAGTCTCA
1 AGTGAAATAAATCTTCTTTCGAGAAAAACAGTCTCA
3871031 AGTGA
1 AGTGA
3871036 GACAAAGTAT
Statistics
Matches: 60, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
35 4 0.07
36 38 0.63
37 5 0.08
38 4 0.07
39 4 0.07
40 5 0.08
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (36 bp):
AGTGAAATAAATCTTCTTTCGAGAAAAACAGTCTCA
Found at i:3871052 original size:72 final size:75
Alignment explanation
Indices: 3870902--3871060 Score: 202
Period size: 72 Copynumber: 2.2 Consensus size: 75
3870892 TAAAATCTTC
* **
3870902 TTAA-AAAAACAGCCTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAATGGTCTCAAGCGAGA
1 TTAAGAAAAACAGCCTTGAGTGAAATGAAAT-CCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGA
*
3870966 CAAATCTTGCT
65 CAAATCATGCT
* *
3870977 TTAAGAAAAACAGTCTTGAGTGAAAT-AAAT-CTTCTTTCGAG-AAAAACAGTCTCAAGTGAGAC
1 TTAAGAAAAACAGCCTTGAGTGAAATGAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGAC
*
3871039 AAAGT-ATGTT
66 AAA-TCATGCT
3871049 TTAAGAAAAACA
1 TTAAGAAAAACA
3871061 AATTTGAGTG
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
72 35 0.47
73 12 0.16
75 8 0.11
76 20 0.27
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.26
Consensus pattern (75 bp):
TTAAGAAAAACAGCCTTGAGTGAAATGAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGAC
AAATCATGCT
Found at i:3872469 original size:192 final size:191
Alignment explanation
Indices: 3872141--3872548 Score: 647
Period size: 192 Copynumber: 2.1 Consensus size: 191
3872131 CGGAGCGTTC
* * * * * * *
3872141 AACCAATTGCTTTAGAGGGACAGCTTAATATTATAATATTTTTATCAGGTTTAACTGAAGGGTTC
1 AACCAATTGCCTTAGTGGAATAGCTTAATATTATAATACTTTAATCAGGCTTAACTGAAGGGTTC
* * *
3872206 ATCTCATCACAAAGTCTTCAGCCTGACAAAAGTAGTGGAGCAAACACCGAATTGCCAAGTGTCCT
66 ATCTCATCACAAAGTCTTCAACCTGACAAAAGTAGTGGAGCAAACACCGAATCGCCAAGTGTCCG
*
3872271 AGCAATGTAATGGTTTGAATGCAATCTATTCATAAAGCCAGGGCTTTTGAGTTTCCTCTAT
131 AGCAATGTAATGGTTTGAATACAATCTATTCATAAAGCCAGGGCTTTTGAGTTTCCTCTAT
3872332 AACCAATTGCCTTAGTGGAATAGCTTAATATTATAATCACCTTTAAT-AGGCTTAACTGAAGGGT
1 AACCAATTGCCTTAGTGGAATAGCTTAATATTATAAT-A-CTTTAATCAGGCTTAACTGAAGGGT
** *
3872396 TCATCTCATCACAAAGTCTTCAACCTGACAAAAGTAGTGGAGCAAACATTGAATCGCCAAGTGTT
64 TCATCTCATCACAAAGTCTTCAACCTGACAAAAGTAGTGGAGCAAACACCGAATCGCCAAGTGTC
* *
3872461 CGAGCAATGTCATGGTTTGAATACGATCTATTCATAAAGCCAGGGCTTTTGAGTTTCCTCTAT
129 CGAGCAATGTAATGGTTTGAATACAATCTATTCATAAAGCCAGGGCTTTTGAGTTTCCTCTAT
3872524 AACCAATTGCCTTAGTGGAATAGCT
1 AACCAATTGCCTTAGTGGAATAGCT
3872549 CATCTTTACA
Statistics
Matches: 199, Mismatches: 16, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
191 33 0.17
192 161 0.81
193 5 0.03
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (191 bp):
AACCAATTGCCTTAGTGGAATAGCTTAATATTATAATACTTTAATCAGGCTTAACTGAAGGGTTC
ATCTCATCACAAAGTCTTCAACCTGACAAAAGTAGTGGAGCAAACACCGAATCGCCAAGTGTCCG
AGCAATGTAATGGTTTGAATACAATCTATTCATAAAGCCAGGGCTTTTGAGTTTCCTCTAT
Found at i:3881263 original size:456 final size:453
Alignment explanation
Indices: 3880401--3881996 Score: 1619
Period size: 456 Copynumber: 3.5 Consensus size: 453
3880391 CAAATCAGTA
* * * * * * *
3880401 ACCACCACGGAGGCGAAGGACAAGGTGCAGAGTGGACTCCTTCTGGATGTTATAATCAGCAAGAG
1 ACCACCACGCAGCCGAAGGACAAGGTGCAGGGTAGACTCTTTCTGAATGTTATAATCAGCAAGTG
* * *
3880466 TACGACCATCCTCCAGCTGCTTCCCTGCAAAGATCAA-CCTCTGCTGATCTGGGGGAATCCCCTC
66 TACGACCATCCTCAAGCTGCTTCCCAGCAAAGAT-AAGCCTCTGCTGATCTGGTGGAATCCCCTC
* * * * * *
3880530 CTTGTCCTGGATCTTTGCTTTCACATTGTCAATGGTGTCCGAGCTCTCAACCTCCAGGGTGATAG
130 CTTGTCCTGGATCTTGGCCTTCACATTATCAATTGTGTCAGAGCTCTCAACCTCCAAGGTGATAG
* * * * * * * * * * *
3880595 TTTTTCCAGTCAGGGTCTTGACAAATATCTGCATTCCTCCTCTAAGGCGCAAGACCAAATGCAGG
195 TCTTTCCAGTAAGAGTCTTCACAAAAATCTGCATACCACCTCTGAGACGCAAGACCAAGTGGAGG
* * * * * * * * *
3880660 GTTGACTCCTTCTGAATGTTATAGTCTGCGAGAGTCCTCCCATCCTCGAGCTGCTTCCCGGCGAA
260 GTAGACTCCTTCTGAATGTTGTAGTCTGCAAGGGTCCTGCCATCCTCAAGCTGTTTCCCAGCAAA
* * * * *
3880725 GATCAACCTCTGCTGAT-CAGGTGCGATTCCCTCCTTATCCTGGATCTTAGCCTTAACGTTATCA
325 AATTAACCTCTGCTGGTCCA-GTG-GA-TCCCTCCTTGTCCTGGATCTTAGCCTTAACATTATCA
* * * * * *
3880789 ATTGTGTCAGAACTCTCCACCTCCAA-TGTAATGGTCTTACCAGTCAAGGTTTTCACAAAAATCT
387 ATTGTGTCGGAGCTCTCCACCT-CAAGGGTGATCGTCTTACCAGT-AAGGTTTTCACAAAGATCT
3880853 GCAT
450 GCAT
* * * * *
3880857 TCCACCACGCAGACGAAGGACCAA-GTGGAGGGTCGACTCTTTCTGAATATTATAATCAGCAAGT
1 ACCACCACGCAGCCGAAGGA-CAAGGTGCAGGGTAGACTCTTTCTGAATGTTATAATCAGCAAGT
* ** * * * *
3880921 GTCCTCCCATCCTCCAA-CTGCTTGCCAGCGAAGATCAGCCTCTGTTGATCTGGTGGAATCCCCT
65 GTACGACCATCCT-CAAGCTGCTTCCCAGCAAAGATAAGCCTCTGCTGATCTGGTGGAATCCCCT
* * * * * * *
3880985 CCTTGTCCTGGATCTTAGCTTTCACATTGTCAATTGTATCAGAGCTCTCAACTTCCAAAGTAATA
129 CCTTGTCCTGGATCTTGGCCTTCACATTATCAATTGTGTCAGAGCTCTCAACCTCCAAGGTGATA
* * * * *
3881050 GTCTTTCCTGTAAGAGTCTTCACAAAAATTTGCATGCCACCTCGGAGACGCAACACCAAGTGGAG
194 GTCTTTCCAGTAAGAGTCTTCACAAAAATCTGCATACCACCTCTGAGACGCAAGACCAAGTGGAG
* * * * *
3881115 AGTAGACTCCTTCTGAATATTGTAATCTGCTAGGGTCCTGCCATCTTCAAGCTGTTTCCCAGCAA
259 GGTAGACTCCTTCTGAATGTTGTAGTCTGCAAGGGTCCTGCCATCCTCAAGCTGTTTCCCAGCAA
* * *
3881180 AAATTAACCTCTGCTGGTCCAGTGGTATGCCCTCCTTGTCCTGAATCTTAGCTTTCACATTATCA
324 AAATTAACCTCTGCTGGTCCAGTGG-AT-CCCTCCTTGTCCTGGATCTTAGCCTTAACATTATCA
* * * *
3881245 ATAGTGTCGGAGCTCTCCACCTCAAGGGTGATTGTCTTGCCTGTAAGGGTTTTCACAAAGATCTG
387 ATTGTGTCGGAGCTCTCCACCTCAAGGGTGATCGTCTTACCAGTAA-GGTTTTCACAAAGATCTG
3881310 CAT
451 CAT
* * ** *
3881313 GCCACCCCTG-AGCCGAAGGACAAGGTGCAACGTAGACTCTTTCTGAATGTTGTAATCAGCAAGT
1 ACCACCAC-GCAGCCGAAGGACAAGGTGCAGGGTAGACTCTTTCTGAATGTTATAATCAGCAAGT
* * * * *
3881377 GTACGACCATCCTCAAGTTGTTTCCCAGCAAAGATAAGCCTCTGCTGGTCTGGTGGTATGCCCTC
65 GTACGACCATCCTCAAGCTGCTTCCCAGCAAAGATAAGCCTCTGCTGATCTGGTGGAATCCCCTC
* * * * *
3881442 CTTGTCCTGGATCTTGGCCTTCACATTATCGATAGTGTCGGAGCTCTCCACCT-CAAGGGTGATT
130 CTTGTCCTGGATCTTGGCCTTCACATTATCAATTGTGTCAGAGCTCTCAACCTCCAA-GGTGATA
* * * * * * *
3881506 GTCTTGCCCGTAAGGGTTTTCACAAAGATCTGCATACCACCCCTGAGCCG-AAGGA-CAAGGTGG
194 GTCTTTCCAGTAAGAGTCTTCACAAAAATCTGCATACCACCTCTGAGACGCAA-GACCAA-GTGG
* * * * * *
3881569 AGGGTAGACTCCTTTTGGATGTTGTAGTCAGCAAGGGTGCGGCCATCCTCAAGCTGTTTTCCAGC
257 AGGGTAGACTCCTTCTGAATGTTGTAGTCTGCAAGGGTCCTGCCATCCTCAAGCTGTTTCCCAGC
* ** * * * *
3881634 AAAAA-TAAGCCTCTGTTGGTCTGGAGGAATCCCTTCCTTGTCTTGGATCTTGGCCTTGACATTA
322 AAAAATTAA-CCTCTGCTGGTCCAGTGG-ATCCC-TCCTTGTCCTGGATCTTAGCCTTAACATTA
* * * *
3881698 TCGATTGTGTCGGAGCTTTCCACCTCAAGGGTGATCGTCTTTCCAGTAAGTGTTTTTACAAAGAT
384 TCAATTGTGTCGGAGCTCTCCACCTCAAGGGTGATCGTCTTACCAGTAAG-GTTTTCACAAAGAT
3881763 CTGCAT
448 CTGCAT
* * * * *
3881769 ACCACCCCTCAGCCGAAGGACAAGGTGAAGGGTAGACTCTTTCTGGATGTTGTAATCAGCAAGTG
1 ACCACCACGCAGCCGAAGGACAAGGTGCAGGGTAGACTCTTTCTGAATGTTATAATCAGCAAGTG
* * * * * * * * * *
3881834 TACGGCCATCCTCAAGCTGTTTTCCAGCAAAGATAAGCCTCTGTTGGTCGGGAGGGATCCCTTCT
66 TACGACCATCCTCAAGCTGCTTCCCAGCAAAGATAAGCCTCTGCTGATCTGGTGGAATCCCCTCC
* * * * * *
3881899 TTATCCTGGATCTTGGCCTTGACATTATCAATTGTGTCTGAGCTTTCCACCTCCAAGGTGATGGT
131 TTGTCCTGGATCTTGGCCTTCACATTATCAATTGTGTCAGAGCTCTCAACCTCCAAGGTGATAGT
* * * * *
3881964 CTTCCCGGTAAGAGTTTTCACGAAGATCTGCAT
196 CTTTCCAGTAAGAGTCTTCACAAAAATCTGCAT
3881997 CTGTTATGCA
Statistics
Matches: 949, Mismatches: 172, Indels: 38
0.82 0.15 0.03
Matches are distributed among these distances:
455 29 0.03
456 909 0.96
457 11 0.01
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (453 bp):
ACCACCACGCAGCCGAAGGACAAGGTGCAGGGTAGACTCTTTCTGAATGTTATAATCAGCAAGTG
TACGACCATCCTCAAGCTGCTTCCCAGCAAAGATAAGCCTCTGCTGATCTGGTGGAATCCCCTCC
TTGTCCTGGATCTTGGCCTTCACATTATCAATTGTGTCAGAGCTCTCAACCTCCAAGGTGATAGT
CTTTCCAGTAAGAGTCTTCACAAAAATCTGCATACCACCTCTGAGACGCAAGACCAAGTGGAGGG
TAGACTCCTTCTGAATGTTGTAGTCTGCAAGGGTCCTGCCATCCTCAAGCTGTTTCCCAGCAAAA
ATTAACCTCTGCTGGTCCAGTGGATCCCTCCTTGTCCTGGATCTTAGCCTTAACATTATCAATTG
TGTCGGAGCTCTCCACCTCAAGGGTGATCGTCTTACCAGTAAGGTTTTCACAAAGATCTGCAT
Found at i:3881992 original size:228 final size:227
Alignment explanation
Indices: 3880414--3881996 Score: 1432
Period size: 228 Copynumber: 6.9 Consensus size: 227
3880404 ACCACGGAGG
* * * * * * * *
3880414 CGAAGGACAAGGTGCAGAGTGGACTCCTTCTGGATGTTATAATCAGCAAGAGTACGACCATCCTC
1 CGAAGGACAAGGTGGAGGGTAGACTCTTTCTGAATGTTGTAATCAGCAAGTGTACGGCCATCCTC
* * * * *
3880479 CAGCTGCTTCCCTGCAAAGATCAA-CCTCTGCTGATCTGGGGGAATCCCCTCCTTGTCCTGGATC
66 AAGCTGTTTCCCAGCAAAGAT-AAGCCTCTGCTGGTCTGGTGGAAT-CCCTCCTTGTCCTGGATC
* * * * * * * * *
3880543 TTTGCTTTCACATTGTCAATGGTGTCCGAGCTCTCAACCTCCAGGGTGATAGTTTTTCCAGTCAG
129 TTAGCCTTCACATTATCAATTGTGTCGGAGCTCTCCACCTCCAAGGTGATAGTCTTTCCAGTAAG
* * * * * * * *
3880608 GGTCTTGACAAATATCTGCATTCCTCCTCTAAGG
194 GGTTTTCACAAAGATCTGCATACCACCCCTGAGC
* * * * * * * * * * **
3880642 CGCAA-GACCAA-ATGCAGGGTTGACTCCTTCTGAATGTTATAGTCTGCGAGAGTCCTCCCATCC
1 CG-AAGGA-CAAGGTGGAGGGTAGACTCTTTCTGAATGTTGTAATCAGCAAGTGTACGGCCATCC
* * * * * * * *
3880705 TCGAGCTGCTTCCCGGCGAAGATCAA-CCTCTGCTGATCAGGTGCGATTCCCTCCTTATCCTGGA
64 TCAAGCTGTTTCCCAGCAAAGAT-AAGCCTCTGCTGGTCTGGTG-GAATCCCTCCTTGTCCTGGA
* * * * * * * *
3880769 TCTTAGCCTTAACGTTATCAATTGTGTCAGAACTCTCCACCTCCAATGTAATGGTCTTACCAGTC
127 TCTTAGCCTTCACATTATCAATTGTGTCGGAGCTCTCCACCTCCAAGGTGATAGTCTTTCCAGT-
* * * *
3880834 AA-GGTTTTCACAAAAATCTGCATTCCACCAC-GCAGA
191 AAGGGTTTTCACAAAGATCTGCATACCACCCCTG-AGC
* * * * **
3880870 CGAAGGACCAA-GTGGAGGGTCGACTCTTTCTGAATATTATAATCAGCAAGTGTCCTCCCATCCT
1 CGAAGGA-CAAGGTGGAGGGTAGACTCTTTCTGAATGTTGTAATCAGCAAGTGTACGGCCATCCT
* * * * * *
3880934 CCAA-CTGCTTGCCAGCGAAGATCAGCCTCTGTTGATCTGGTGGAATCCCCTCCTTGTCCTGGAT
65 -CAAGCTGTTTCCCAGCAAAGATAAGCCTCTGCTGGTCTGGTGGAAT-CCCTCCTTGTCCTGGAT
* * * * * * * * *
3880998 CTTAGCTTTCACATTGTCAATTGTATCAGAGCTCTCAACTTCCAAAGTAATAGTCTTTCCTGTAA
128 CTTAGCCTTCACATTATCAATTGTGTCGGAGCTCTCCACCTCCAAGGTGATAGTCTTTCCAGTAA
* * * * * * * *
3881063 GAGTCTTCACAAAAATTTGCATGCCACCTCGGAGA
193 GGGTTTTCACAAAGATCTGCATACCACCCCTGAGC
* * * * * * * * * *
3881098 CGCAA-CACCAA-GTGGAGAGTAGACTCCTTCTGAATATTGTAATCTGCTAGGGTCCTGCCATCT
1 CG-AAGGA-CAAGGTGGAGGGTAGACTCTTTCTGAATGTTGTAATCAGCAAGTGTACGGCCATCC
* ** * *
3881161 TCAAGCTGTTTCCCAGCAAAAATTAA-CCTCTGCTGGTCCAGTGGTATGCCCTCCTTGTCCTGAA
64 TCAAGCTGTTTCCCAGCAAAGA-TAAGCCTCTGCTGGTCTGGTGGAAT-CCCTCCTTGTCCTGGA
* * * * *
3881225 TCTTAGCTTTCACATTATCAATAGTGTCGGAGCTCTCCACCT-CAAGGGTGATTGTCTTGCCTGT
127 TCTTAGCCTTCACATTATCAATTGTGTCGGAGCTCTCCACCTCCAA-GGTGATAGTCTTTCCAGT
*
3881289 AAGGGTTTTCACAAAGATCTGCATGCCACCCCTGAGC
191 AAGGGTTTTCACAAAGATCTGCATACCACCCCTGAGC
* ** *
3881326 CGAAGGACAAGGTGCAACGTAGACTCTTTCTGAATGTTGTAATCAGCAAGTGTACGACCATCCTC
1 CGAAGGACAAGGTGGAGGGTAGACTCTTTCTGAATGTTGTAATCAGCAAGTGTACGGCCATCCTC
* *
3881391 AAGTTGTTTCCCAGCAAAGATAAGCCTCTGCTGGTCTGGTGGTATGCCCTCCTTGTCCTGGATCT
66 AAGCTGTTTCCCAGCAAAGATAAGCCTCTGCTGGTCTGGTGGAAT-CCCTCCTTGTCCTGGATCT
* * * * * *
3881456 TGGCCTTCACATTATCGATAGTGTCGGAGCTCTCCACCT-CAAGGGTGATTGTCTTGCCCGTAAG
130 TAGCCTTCACATTATCAATTGTGTCGGAGCTCTCCACCTCCAA-GGTGATAGTCTTTCCAGTAAG
3881520 GGTTTTCACAAAGATCTGCATACCACCCCTGAGC
194 GGTTTTCACAAAGATCTGCATACCACCCCTGAGC
* * * *
3881554 CGAAGGACAAGGTGGAGGGTAGACTCCTTT-TGGATGTTGTAGTCAGCAAGGGTGCGGCCATCCT
1 CGAAGGACAAGGTGGAGGGTAGACT-CTTTCTGAATGTTGTAATCAGCAAGTGTACGGCCATCCT
* * * * *
3881618 CAAGCTGTTTTCCAGCAAAAATAAGCCTCTGTTGGTCTGGAGGAATCCCTTCCTTGTCTTGGATC
65 CAAGCTGTTTCCCAGCAAAGATAAGCCTCTGCTGGTCTGGTGGAATCCC-TCCTTGTCCTGGATC
* * * * *
3881683 TTGGCCTTGACATTATCGATTGTGTCGGAGCTTTCCACCT-CAAGGGTGATCGTCTTTCCAGTAA
129 TTAGCCTTCACATTATCAATTGTGTCGGAGCTCTCCACCTCCAA-GGTGATAGTCTTTCCAGTAA
* * *
3881747 GTGTTTTTACAAAGATCTGCATACCACCCCTCAGC
193 GGGTTTTCACAAAGATCTGCATACCACCCCTGAGC
* *
3881782 CGAAGGACAAGGTGAAGGGTAGACTCTTTCTGGATGTTGTAATCAGCAAGTGTACGGCCATCCTC
1 CGAAGGACAAGGTGGAGGGTAGACTCTTTCTGAATGTTGTAATCAGCAAGTGTACGGCCATCCTC
* * * * * * *
3881847 AAGCTGTTTTCCAGCAAAGATAAGCCTCTGTTGGTCGGGAGGGATCCCTTCTTTATCCTGGATCT
66 AAGCTGTTTCCCAGCAAAGATAAGCCTCTGCTGGTCTGGTGGAATCCC-TCCTTGTCCTGGATCT
* * * * * * * *
3881912 TGGCCTTGACATTATCAATTGTGTCTGAGCTTTCCACCTCCAAGGTGATGGTCTTCCCGGTAAGA
130 TAGCCTTCACATTATCAATTGTGTCGGAGCTCTCCACCTCCAAGGTGATAGTCTTTCCAGTAAGG
*
3881977 GTTTTCACGAAGATCTGCAT
195 GTTTTCACAAAGATCTGCAT
3881997 CTGTTATGCA
Statistics
Matches: 1155, Mismatches: 178, Indels: 44
0.84 0.13 0.03
Matches are distributed among these distances:
227 29 0.03
228 1103 0.95
229 23 0.02
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (227 bp):
CGAAGGACAAGGTGGAGGGTAGACTCTTTCTGAATGTTGTAATCAGCAAGTGTACGGCCATCCTC
AAGCTGTTTCCCAGCAAAGATAAGCCTCTGCTGGTCTGGTGGAATCCCTCCTTGTCCTGGATCTT
AGCCTTCACATTATCAATTGTGTCGGAGCTCTCCACCTCCAAGGTGATAGTCTTTCCAGTAAGGG
TTTTCACAAAGATCTGCATACCACCCCTGAGC
Found at i:3882999 original size:16 final size:16
Alignment explanation
Indices: 3882978--3883024 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
3882968 AAATATTAAA
3882978 TAAATTTATTTATAAT
1 TAAATTTATTTATAAT
* *
3882994 TAAATTTATATAAAAT
1 TAAATTTATTTATAAT
3883010 T-AATTTATATTATAA
1 TAAATTTAT-TTATAA
3883025 ATATTTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 7 0.27
16 19 0.73
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAAATTTATTTATAAT
Found at i:3885034 original size:32 final size:31
Alignment explanation
Indices: 3884998--3885074 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
3884988 CGGGGCCGTG
*
3884998 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
3885030 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
3885061 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
3885075 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:3885057 original size:63 final size:63
Alignment explanation
Indices: 3884951--3885074 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
3884941 CCCTAAGGGA
* * ** *
3884951 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
3885014 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
3885075 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:3885954 original size:7 final size:7
Alignment explanation
Indices: 3885942--3885972 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
3885932 GTCAAAGAAA
3885942 GTCAACG
1 GTCAACG
3885949 GTCAACG
1 GTCAACG
3885956 GTCAACG
1 GTCAACG
3885963 GTCAACG
1 GTCAACG
3885970 GTC
1 GTC
3885973 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:3885990 original size:22 final size:22
Alignment explanation
Indices: 3885962--3886004 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
3885952 AACGGTCAAC
3885962 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
3885984 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
3886005 AGACCGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:3886025 original size:19 final size:19
Alignment explanation
Indices: 3886003--3886116 Score: 106
Period size: 19 Copynumber: 5.9 Consensus size: 19
3885993 TCGGGTCGGG
3886003 TCAGACCGGTCAAACCGAT
1 TCAGACCGGTCAAACCGAT
*
3886022 TCAGACCGATCAAACCGAT
1 TCAGACCGGTCAAACCGAT
*
3886041 TCAGACCGGTCAAACCGTT
1 TCAGACCGGTCAAACCGAT
* *
3886060 TC-GAACCGGTTGAAACCG-G
1 TCAG-ACCGG-TCAAACCGAT
* *
3886079 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGAT
* *
3886099 TGAAAACCGGTCAAACCG
1 T-CAGACCGGTCAAACCG
3886117 GTTTCCAGCA
Statistics
Matches: 80, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
18 3 0.04
19 54 0.68
20 13 0.16
21 10 0.12
ACGTcount: A:0.32, C:0.30, G:0.23, T:0.16
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGAT
Found at i:3886066 original size:29 final size:30
Alignment explanation
Indices: 3886045--3886121 Score: 104
Period size: 29 Copynumber: 2.6 Consensus size: 30
3886035 ACCGATTCAG
*
3886045 ACCGGTCAAACCGTTTC-GAACCGGTTGAA
1 ACCGGTCAAACCGTTTCAGAACCGGTTAAA
*
3886074 ACCGGTCAAACCG-GTCAGAACCGGTTGAAA
1 ACCGGTCAAACCGTTTCAGAACCGGTT-AAA
3886104 ACCGGTCAAACCGGTTTC
1 ACCGGTCAAACC-GTTTC
3886122 CAGCAGCCAC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 2 0.05
29 22 0.54
30 14 0.34
31 1 0.02
32 2 0.05
ACGTcount: A:0.29, C:0.29, G:0.25, T:0.18
Consensus pattern (30 bp):
ACCGGTCAAACCGTTTCAGAACCGGTTAAA
Found at i:3886076 original size:10 final size:9
Alignment explanation
Indices: 3886001--3886118 Score: 83
Period size: 9 Copynumber: 12.3 Consensus size: 9
3885991 GGTCGGGTCG
*
3886001 GGTCAGACC
1 GGTCAAACC
3886010 GGTCAAACC
1 GGTCAAACC
* *
3886019 GATTCAGACC
1 G-GTCAAACC
*
3886029 GATCAAACC
1 GGTCAAACC
* *
3886038 GATTCAGACC
1 G-GTCAAACC
3886048 GGTCAAACC
1 GGTCAAACC
* *
3886057 GTTTCGAACC
1 G-GTCAAACC
*
3886067 GGTTGAAACC
1 GG-TCAAACC
3886077 GGTCAAACC
1 GGTCAAACC
3886086 GGTCAGAACC
1 GGTCA-AACC
*
3886096 GGTTGAAAACC
1 GG-T-CAAACC
3886107 GGTCAAACC
1 GGTCAAACC
3886116 GGT
1 GGT
3886119 TTCCAGCAGC
Statistics
Matches: 85, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
9 42 0.49
10 35 0.41
11 7 0.08
12 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.25, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:3886117 original size:20 final size:21
Alignment explanation
Indices: 3886081--3886119 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3886071 GAAACCGGTC
3886081 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
3886102 AAACCGGTCA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
3886120 TCCAGCAGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.15
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:3892410 original size:63 final size:63
Alignment explanation
Indices: 3892304--3892427 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
3892294 CCCTAAGGGA
* * ** *
3892304 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAT
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAT
* *
3892367 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
3892428 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAT
Found at i:3892412 original size:31 final size:32
Alignment explanation
Indices: 3892304--3892427 Score: 101
Period size: 31 Copynumber: 3.9 Consensus size: 32
3892294 CCCTAAGGGA
* *
3892304 ACATCTTAGGGCCTG-AGAGCCTACCCAAG-AT
1 ACATCTCAGGGCC-GCAGGGCCTACCCAAGAAT
* * * ** *
3892335 AGATTTCGGGGCCGTGGGGCCTACCTAAGAAT
1 ACATCTCAGGGCCGCAGGGCCTACCCAAGAAT
* *
3892367 ACATCTTAGGGCCGCAGGGCCTACCCGAGAAT
1 ACATCTCAGGGCCGCAGGGCCTACCCAAGAAT
* * *
3892399 -GATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTCAGGGCCGCAGGGCCTACCCAAGA
3892428 GTCACATTAG
Statistics
Matches: 71, Mismatches: 20, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
30 1 0.01
31 44 0.62
32 26 0.37
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (32 bp):
ACATCTCAGGGCCGCAGGGCCTACCCAAGAAT
Found at i:3893323 original size:5 final size:5
Alignment explanation
Indices: 3893313--3893370 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
3893303 AACGGTCAAC
* *
3893313 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
3893362 GGTCG GGTC
1 GGTCG GGTC
3893371 AGACCGGTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.07, C:0.22, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:3893334 original size:22 final size:22
Alignment explanation
Indices: 3893306--3893370 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
3893296 AACGGTCAAC
3893306 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
3893328 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
3893350 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
3893371 AGACCGGTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:3893385 original size:9 final size:9
Alignment explanation
Indices: 3893367--3893416 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
3893357 GGTCGGGTCG
*
3893367 GGTCAGACC
1 GGTCAAACC
3893376 GGTCAAACC
1 GGTCAAACC
* *
3893385 GATTCAGACC
1 G-GTCAAACC
3893395 GGTCAGAACC
1 GGTCA-AACC
3893405 GGTCAAACC
1 GGTCAAACC
3893414 GGT
1 GGT
3893417 TTCCAGCAGC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
9 19 0.56
10 15 0.44
ACGTcount: A:0.28, C:0.30, G:0.28, T:0.14
Consensus pattern (9 bp):
GGTCAAACC
Found at i:3893414 original size:19 final size:18
Alignment explanation
Indices: 3893367--3893416 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
3893357 GGTCGGGTCG
3893367 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
*
3893385 GATTCAGACCGGTCAGAACC
1 G-GTCAGACCGGTCA-AACC
*
3893405 GGTCAAACCGGT
1 GGTCAGACCGGT
3893417 TTCCAGCAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 1 0.04
19 21 0.78
20 5 0.19
ACGTcount: A:0.28, C:0.30, G:0.28, T:0.14
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:3894622 original size:21 final size:21
Alignment explanation
Indices: 3894596--3894638 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3894586 GATCATTGTT
3894596 ATAATTTACCCTTTATTTTAA
1 ATAATTTACCCTTTATTTTAA
3894617 ATAATTTACCCTTTATTTTAA
1 ATAATTTACCCTTTATTTTAA
3894638 A
1 A
3894639 ATGAATGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.14, G:0.00, T:0.51
Consensus pattern (21 bp):
ATAATTTACCCTTTATTTTAA
Found at i:3895628 original size:15 final size:15
Alignment explanation
Indices: 3895608--3895689 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
3895598 TTTCAGAAAA
3895608 TGAATTACTGGAATT
1 TGAATTACTGGAATT
3895623 TGAATTACTGGAATT
1 TGAATTACTGGAATT
* **
3895638 TGAATTACTGAAAAA
1 TGAATTACTGGAATT
3895653 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
3895668 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
3895682 TGAATTAC
1 TGAATTAC
3895690 ATTTCTGTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 12 0.21
15 46 0.79
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:3895642 original size:30 final size:30
Alignment explanation
Indices: 3895608--3895689 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
3895598 TTTCAGAAAA
**
3895608 TGAATTACTGGAATTTGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
*
3895638 TGAATTACTGAAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
3895668 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
3895690 ATTTCTGTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 15 0.31
30 33 0.69
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.35
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGGAATT
Found at i:3895666 original size:45 final size:44
Alignment explanation
Indices: 3895604--3895689 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 44
3895594 GGTTTTTCAG
**
3895604 AAAATGAATTACTGGAATTTGAATTACTGGAATTTGAATTACTGA
1 AAAATGAATTACTGGAATTTGAATT-CTGGAAAATGAATTACTGA
3895649 AAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
1 AAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
3895690 ATTTCTGTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.36
45 25 0.64
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.34
Consensus pattern (44 bp):
AAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACTGA
Found at i:3895695 original size:20 final size:20
Alignment explanation
Indices: 3895672--3895740 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
3895662 GGAATTTGAA
3895672 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
3895692 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
3895712 TTCTGG-AAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
3895731 TTCTGGAAAA
1 TTCTGGAAAA
3895741 CATCTGAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 19 0.41
20 27 0.59
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:3895939 original size:26 final size:24
Alignment explanation
Indices: 3895889--3895948 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 24
3895879 TTTACTAAAA
* *
3895889 TATTATTGAAATATAAATATATTAT
1 TATTATT-AAATATAAAAAAATTAT
3895914 TCATTATTAAATATAAAAAAATTTAT
1 T-ATTATTAAATATAAAAAAA-TTAT
3895940 TATATATTA
1 TAT-TATTA
3895949 TTAAAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 14 0.47
26 16 0.53
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (24 bp):
TATTATTAAATATAAAAAAATTAT
Found at i:3895959 original size:26 final size:26
Alignment explanation
Indices: 3895888--3895964 Score: 84
Period size: 29 Copynumber: 2.8 Consensus size: 26
3895878 CTTTACTAAA
* *
3895888 ATATTATTGAAATATAAATATATTAT
1 ATATTATTAAAATAAAAATATATTAT
*
3895914 -TCATTATTAAATATAAAAAAATTTATTAT
1 AT-ATTATTAAA-AT--AAAAATATATTAT
3895943 ATATTATTAAAATAAAAATATA
1 ATATTATTAAAATAAAAATATA
3895965 ATATCTTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
25 1 0.02
26 16 0.38
27 2 0.05
28 2 0.05
29 20 0.48
30 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (26 bp):
ATATTATTAAAATAAAAATATATTAT
Found at i:3896035 original size:29 final size:28
Alignment explanation
Indices: 3895905--3896058 Score: 101
Period size: 29 Copynumber: 5.5 Consensus size: 28
3895895 TGAAATATAA
*
3895905 ATATATTAT-TCATTATTAAATATAAAAAA
1 ATATATTATAT-ATTA-TAAATATAAAAAT
*
3895934 ATTTATTATATATTATTAAA-ATAAAAAT
1 ATATATTATATATTA-TAAATATAAAAAT
* *
3895962 ATAATATCT-TATATTAT-TATAT-ATAAT
1 AT-ATAT-TATATATTATAAATATAAAAAT
*
3895989 -T-GATTAT-T-TTATATAATATTAAAAAT
1 ATATATTATATATTATA-AATA-TAAAAAT
3896015 ATATATTATATATTATAAATATTAATAAAT
1 ATATATTATATATTATAAATA-TAA-AAAT
* *
3896045 ATATTTTAAATATT
1 ATATATTATATATT
3896059 TTAATAATTA
Statistics
Matches: 100, Mismatches: 11, Indels: 27
0.72 0.08 0.20
Matches are distributed among these distances:
22 4 0.04
23 2 0.02
24 6 0.06
25 1 0.01
26 5 0.05
27 6 0.06
28 17 0.17
29 36 0.36
30 23 0.23
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
ATATATTATATATTATAAATATAAAAAT
Found at i:3896045 original size:30 final size:30
Alignment explanation
Indices: 3895997--3896071 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
3895987 ATTGATTATT
*
3895997 TTATATAATATTAA-AAATATATATTATATA
1 TTATA-AATATTAATAAATATATATTAAATA
*
3896027 TTATAAATATTAATAAATATATTTTAAATA
1 TTATAAATATTAATAAATATATATTAAATA
*
3896057 TT-TTAATAATTAATA
1 TTATAAAT-ATTAATA
3896072 TTTTGATGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
29 12 0.30
30 28 0.70
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
TTATAAATATTAATAAATATATATTAAATA
Found at i:3896054 original size:11 final size:11
Alignment explanation
Indices: 3896004--3896057 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
3895994 ATTTTATATA
*
3896004 ATATTAAAAAT
1 ATATTATAAAT
*
3896015 ATA-TAT-TAT
1 ATATTATAAAT
3896024 ATATTATAAAT
1 ATATTATAAAT
*
3896035 AT-TAATAAAT
1 ATATTATAAAT
*
3896045 ATATTTTAAAT
1 ATATTATAAAT
3896056 AT
1 AT
3896058 TTTAATAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
9 5 0.15
10 14 0.41
11 15 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATATTATAAAT
Found at i:3896301 original size:41 final size:41
Alignment explanation
Indices: 3896244--3896357 Score: 192
Period size: 41 Copynumber: 2.8 Consensus size: 41
3896234 ATGAATTATA
* *
3896244 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAACGTT
1 TTCCGAAAAACGAATTACGTGAAACAAACACGGAAAACATT
*
3896285 TTCCGAAAAACGAATTACGTGAAACAAACACGGAAAATATT
1 TTCCGAAAAACGAATTACGTGAAACAAACACGGAAAACATT
*
3896326 TTCCAAAAAACGAATTACGTGAAACAAACACG
1 TTCCGAAAAACGAATTACGTGAAACAAACACG
3896358 AGAATTCGGA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.47, C:0.19, G:0.16, T:0.18
Consensus pattern (41 bp):
TTCCGAAAAACGAATTACGTGAAACAAACACGGAAAACATT
Found at i:3897588 original size:13 final size:14
Alignment explanation
Indices: 3897570--3897599 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
3897560 AGCAAAGCAT
3897570 AGAAGAAGAAA-AA
1 AGAAGAAGAAAGAA
3897583 AGAAGAAGAAAGAA
1 AGAAGAAGAAAGAA
3897597 AGA
1 AGA
3897600 CAGCTTCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (14 bp):
AGAAGAAGAAAGAA
Done.