Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007079.1 Hibiscus syriacus cultivar Beakdansim tig00018475_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: 62616
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Found at i:30883 original size:37 final size:37
Alignment explanation
Indices: 30830--30934 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
30820 CATTTTCGTC
30830 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * * *
30867 TTGCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
30904 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
30935 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:31317 original size:18 final size:17
Alignment explanation
Indices: 31276--31326 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 17
31266 TATTAGTCCC
31276 TTTATTTATTATATATTCA
1 TTTATTT-TTAT-TATTCA
31295 TTTATTTTTATTATTCA
1 TTTATTTTTATTATTCA
*
31312 TGTTATTATTATTAT
1 T-TTATTTTTATTAT
31327 ATGTATGTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.23
18 16 0.53
19 7 0.23
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTATTTTTATTATTCA
Found at i:31843 original size:2 final size:2
Alignment explanation
Indices: 31836--31865 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
31826 TAATACTTTG
*
31836 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31866 TTTTTCCCTT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:37472 original size:183 final size:183
Alignment explanation
Indices: 37164--37700 Score: 968
Period size: 183 Copynumber: 2.9 Consensus size: 183
37154 ATTAAATCCG
37164 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
37229 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGTTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
37294 TTGTCAGGCCAAAAACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
37347 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
37412 ATAGATTATGTTCAAACTATGACACTGCTTGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
37477 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
37530 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** * *
37595 ATAGATTACATTCAAA-TCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCATTGCT
66 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
**
37659 TTTGTCAGTTCAAAGACTTTGTGATGAGATGAACCCTTCAGT
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
37701 TAAACCTGAT
Statistics
Matches: 341, Mismatches: 12, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
182 1 0.00
183 340 1.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
Found at i:38897 original size:36 final size:34
Alignment explanation
Indices: 38857--38970 Score: 86
Period size: 36 Copynumber: 3.2 Consensus size: 34
38847 CACTCAAATT
38857 TGTTTTTCTTAAAACATACTTTGTCTCACTTGAGAC
1 TGTTTTTCTTAAAACA-A-TTTGTCTCACTTGAGAC
* * * ** *
38893 TGTTTTTCTCGAAAGA-AGATTTATTTCACTCAAGAT
1 TGTTTTTCT-TAAA-ACA-ATTTGTCTCACTTGAGAC
*
38929 TGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGAC
1 TGTTTTTCTTAAAAC-A-ATTTGTCTCACTTGAGAC
*
38965 CGTTTT
1 TGTTTT
38971 CACTCGAAAG
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
34 1 0.02
35 3 0.05
36 49 0.83
37 5 0.08
38 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (34 bp):
TGTTTTTCTTAAAACAATTTGTCTCACTTGAGAC
Found at i:38933 original size:72 final size:75
Alignment explanation
Indices: 38841--39024 Score: 220
Period size: 72 Copynumber: 2.5 Consensus size: 75
38831 ATGCAGATGA
* * * *
38841 TTATCTCACTCAA-ATTTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTC
1 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACCGTTTTCACTC
38903 GAAAGAA-G-AT
64 GAAAGAAGGCAT
*
38913 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGA
1 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
38978 AAGAAGGCAT
66 AAGAAGGCAT
** *
38988 TTCATTTCACTCAAGGCTGTTTTT-TT-AAAGAAGATTT
1 TT-ATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTT
39025 TATCTTGCTT
Statistics
Matches: 98, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
71 1 0.01
72 50 0.51
73 11 0.11
74 11 0.11
75 6 0.06
76 19 0.19
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (75 bp):
TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
AAGAAGGCAT
Found at i:39117 original size:104 final size:99
Alignment explanation
Indices: 39018--39370 Score: 320
Period size: 104 Copynumber: 3.6 Consensus size: 99
39008 TTTTTTAAAG
*
39018 AAGATTTTATCTTGCTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGCCTCCCTTGAGACAGTT
1 AAGATTTTATCTT-CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTT
*** * *
39083 TCTCTTGAAAACATTTCCCTTG--AA-ATTATTT-
65 TCTCTTGAAAACATAAACATTGAAAACATTTTTTA
* * * *
39114 ----TTTTCTC-TCCTGAGATAGTTTCCCTCGAAACAGAAAATTTTATCTCCATTGAGACAGTTT
1 AAGATTTTATCTTCTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTT
*
39174 CTCTTG-AAACATAAACATTGAAAACATTTCCCTTGA
66 CTCTTGAAAACATAAACATTGAAAACATTT---TTTA
* * *
39210 AATGATTTTTTTTTCTCTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCGTGAGACAG
1 AA-GA-TTTTATCT-TCTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAG
*
39275 TTTCTCTTG-AAACATAAACATTGAAAACATTTCCCTTGA
63 TTTCTCTTGAAAACATAAACATTGAAAACATTT---TTTA
* * * *
39314 AATGAATTTTATCTCTCTTGAGACAGCTTCCCTTGAAA-TG--AATTTTGTCTCCCTTGA
1 AA-G-ATTTTATCT-TCTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGA
39371 AATGAATTTT
Statistics
Matches: 217, Mismatches: 24, Indels: 27
0.81 0.09 0.10
Matches are distributed among these distances:
89 10 0.05
90 54 0.25
91 3 0.01
92 9 0.04
95 2 0.01
101 16 0.07
102 5 0.02
103 1 0.00
104 116 0.53
105 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (99 bp):
AAGATTTTATCTTCTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTT
CTCTTGAAAACATAAACATTGAAAACATTTTTTA
Found at i:39368 original size:21 final size:21
Alignment explanation
Indices: 39342--39391 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
39332 TGAGACAGCT
39342 TCCCTTGAAATGAATTTTGTC
1 TCCCTTGAAATGAATTTTGTC
39363 TCCCTTGAAATGAATTTTGTC
1 TCCCTTGAAATGAATTTTGTC
39384 TCCCTTGA
1 TCCCTTGA
39392 GACAGTTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (21 bp):
TCCCTTGAAATGAATTTTGTC
Found at i:39782 original size:105 final size:105
Alignment explanation
Indices: 39591--40221 Score: 907
Period size: 105 Copynumber: 6.0 Consensus size: 105
39581 ATATAGTGAC
* * * * * *
39591 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACAGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
*
39656 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
39697 ACTCCAGACAACGCAAGTTCAACTTCACGAC-AAGGGGACCGCTGCTTGTCAACAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAA-GGGACCGCTGCTTGTCAACAACAACTTCCC
39761 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
39802 ACTTCAGACAAGGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAATAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
39867 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
39907 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTTCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
39972 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
40012 ACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
* *
40073 A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
40112 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTCC
** * * * *
40176 CGGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTAG
64 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
40218 ACTC
1 ACTC
40222 GGAACAATGC
Statistics
Matches: 480, Mismatches: 36, Indels: 18
0.90 0.07 0.03
Matches are distributed among these distances:
99 2 0.00
100 80 0.17
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 302 0.63
106 83 0.17
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:40822 original size:37 final size:37
Alignment explanation
Indices: 40764--40868 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
40754 CATTTTCGTC
*
40764 CTACTAGGATTCAAACCCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
40801 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
40838 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
40869 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:41250 original size:18 final size:17
Alignment explanation
Indices: 41209--41259 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 17
41199 TATTAGTCCC
41209 TTTATTTATTATATATTCA
1 TTTATTT-TTAT-TATTCA
41228 TTTATTTTTATTATTCA
1 TTTATTTTTATTATTCA
*
41245 TGTTATTATTATTAT
1 T-TTATTTTTATTAT
41260 ATGTATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.23
18 16 0.53
19 7 0.23
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTATTTTTATTATTCA
Found at i:41762 original size:2 final size:2
Alignment explanation
Indices: 41755--41790 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
41745 TAATACTTTG
41755 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
41791 TTATTTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41859 original size:20 final size:22
Alignment explanation
Indices: 41831--41870 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
41821 TATATAATTA
*
41831 TTATTTTAC-TATTT-TTTTTC
1 TTATCTTACTTATTTATTTTTC
41851 TTATCTTACTTATTTATTTT
1 TTATCTTACTTATTTATTTT
41871 ATTTTTCCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 5 0.29
22 4 0.24
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.72
Consensus pattern (22 bp):
TTATCTTACTTATTTATTTTTC
Found at i:45028 original size:45 final size:45
Alignment explanation
Indices: 44941--45151 Score: 277
Period size: 45 Copynumber: 4.8 Consensus size: 45
44931 ATTAGTATGC
* * * *
44941 AAATAAGCTTAC-AACTTATGGAAT-AGTGGCAA--ATATTGGTA
1 AAATAAGCTTACGAGCTTATAGAATAAATGGTAAGTATATTGGTA
* *
44982 AAATAAGCTTATGAGCTTATAGAATAAACGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATAGAATAAATGGTAAGTATATTGGTA
* *
45027 AAATAAGCGTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATAGAATAAATGGTAAGTATATTGGTA
* *
45072 GAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATAGAATAAATGGTAAGTATATTGGTA
* * *
45117 GAATAAGCTTACGAGCTTATAGGATAAATGATAAG
1 AAATAAGCTTACGAGCTTATAGAATAAATGGTAAG
45152 AAATTTTATA
Statistics
Matches: 151, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
41 11 0.07
42 10 0.07
43 5 0.03
45 125 0.83
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.29
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATAGAATAAATGGTAAGTATATTGGTA
Found at i:49208 original size:101 final size:101
Alignment explanation
Indices: 49085--49295 Score: 289
Period size: 101 Copynumber: 2.1 Consensus size: 101
49075 GTATACCCAT
* * *
49085 ATTATAATATTATATACAATAAAGCTTGAGATGTCAGTCTAAAACAATTGGTTAAATGCCTTGGC
1 ATTATAATATTATATACAATAAAGCTTGAAATGTCACTCTAAAACAATTGGTTAAATGCCCTGGC
*
49150 TTTATGGAT-AAGATTCAGCTAGCCTGATAAAGGTG
66 TTTATGGATAAAGATTCAGCTAGCCTAATAAAGGTG
* * * * *
49185 ATTATATTATATATATACAATAAAGCTTGAAATGTCCCTTTAGAGCAATTGGTTAAATGCCCTGG
1 ATTATAATAT-TATATACAATAAAGCTTGAAATGTCACTCTAAAACAATTGGTTAAATGCCCTGG
* * *
49250 CTTTATTGATAAAGATTTAGCTAGCCTAATAAATGTG
65 CTTTATGGATAAAGATTCAGCTAGCCTAATAAAGGTG
*
49287 ATTACAATA
1 ATTATAATA
49296 AAATTGAATT
Statistics
Matches: 95, Mismatches: 14, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
100 9 0.09
101 56 0.59
102 30 0.32
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (101 bp):
ATTATAATATTATATACAATAAAGCTTGAAATGTCACTCTAAAACAATTGGTTAAATGCCCTGGC
TTTATGGATAAAGATTCAGCTAGCCTAATAAAGGTG
Found at i:51935 original size:47 final size:45
Alignment explanation
Indices: 51812--51936 Score: 117
Period size: 44 Copynumber: 2.8 Consensus size: 45
51802 GTGTTTTTTC
* * * *
51812 CTTGACTTTCTCGAGTAGAAGAGTCGATCTTTTAGTGTTGTCCTA
1 CTTGACTTTCTCGTGAAGAAGAGTCGATCTTTTAGTGGTGTCATA
* * * * * * * *
51857 CTTGGCTCTCTTGTGAAG-AGAATCAACCTTTTAGTGGTGTTATT
1 CTTGACTTTCTCGTGAAGAAGAGTCGATCTTTTAGTGGTGTCATA
51901 CTTGACTTTCTCGTGGAAAGAAGAGTCGATCTTTTA
1 CTTGACTTTCTCGT-G-AAGAAGAGTCGATCTTTTA
51937 TTGTTGCCAT
Statistics
Matches: 59, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
44 30 0.51
45 14 0.24
46 3 0.05
47 12 0.20
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (45 bp):
CTTGACTTTCTCGTGAAGAAGAGTCGATCTTTTAGTGGTGTCATA
Found at i:52105 original size:51 final size:51
Alignment explanation
Indices: 52009--52149 Score: 164
Period size: 51 Copynumber: 2.8 Consensus size: 51
51999 ATCATAAAGG
* * *
52009 GAAGTCAAAC-TTTTAG-AGATGTCA-TTCTCAACTTC-ACTTTCTCGTGGAGT
1 GAAGTC-AACTTTTTAGTAG-TATCATTTCTCAAC-TCAACTTACTCGTGGAGA
* * *
52059 GTAGTCAACTTTTTAGTAGTATCCTTTTTCAACTCAACTTACTCGTGGAGA
1 GAAGTCAACTTTTTAGTAGTATCATTTCTCAACTCAACTTACTCGTGGAGA
*
52110 GAAGTCAACTTTTTAGTAGTATCATTTCTCAACTTAACTT
1 GAAGTCAACTTTTTAGTAGTATCATTTCTCAACTCAACTT
52150 TATAGTATAA
Statistics
Matches: 77, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
49 3 0.04
50 16 0.21
51 58 0.75
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (51 bp):
GAAGTCAACTTTTTAGTAGTATCATTTCTCAACTCAACTTACTCGTGGAGA
Found at i:52978 original size:82 final size:82
Alignment explanation
Indices: 52830--53024 Score: 243
Period size: 82 Copynumber: 2.4 Consensus size: 82
52820 AGATTTTGTG
* * * * *
52830 GTCTTATCTCCCTTGAAAGAAAAGTGGAGCAGACCTGTCCTCTGAAATTGATCTGATTACCTGAA
1 GTCTGATCTCCCCTGAAAGAAAAGTGGAGCAGACCTGTCCTCTAAAATTGATATGACTACCTGAA
52895 AAAGAGGAACAAG-TCAA
66 AAAGAGGAA-AAGATCAA
* * *
52912 GTCTGATCTCCCCTGAAAGAAAAGCGGAGCAGCCCCT-TCTTCTAAAATTGATATGACTACAC-G
1 GTCTGATCTCCCCTGAAAGAAAAGTGGAGCAG-ACCTGTCCTCTAAAATTGATATGACTAC-CTG
52975 AAAAAGAGGAAAAGATCAA
64 AAAAAGAGGAAAAGATCAA
* * *
52994 GTTTGATTTACCCTGAAAGAAAAGTGGAGCA
1 GTCTGATCTCCCCTGAAAGAAAAGTGGAGCA
53025 AACCACATCT
Statistics
Matches: 98, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
81 3 0.03
82 91 0.93
83 4 0.04
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (82 bp):
GTCTGATCTCCCCTGAAAGAAAAGTGGAGCAGACCTGTCCTCTAAAATTGATATGACTACCTGAA
AAAGAGGAAAAGATCAA
Found at i:53061 original size:82 final size:81
Alignment explanation
Indices: 52893--53046 Score: 193
Period size: 82 Copynumber: 1.9 Consensus size: 81
52883 TGATTACCTG
* * * * * *
52893 AAAAAGAGGAACAAG-TCAAGTCTGATCTCCCCTGAAAGAAAAGCGGAGCAGCCCCTTCTTCTAA
1 AAAAAGAGGAA-AAGATCAAGTCTGATTTACCCTGAAAGAAAAGCGGAGCAACCACATCTTCAAA
*
52957 AATTGATATGACTACAC
65 AATAGATATGACTACAC
* *
52974 GAAAAAGAGGAAAAGATCAAGTTTGATTTACCCTGAAAGAAAAGTGGAGCAAACCACATCTTCAA
1 -AAAAAGAGGAAAAGATCAAGTCTGATTTACCCTGAAAGAAAAGCGGAGC-AACCACATCTTCAA
53039 AAATAGAT
64 AAATAGAT
53047 CTGTCTTCTA
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
81 3 0.05
82 41 0.67
83 17 0.28
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (81 bp):
AAAAAGAGGAAAAGATCAAGTCTGATTTACCCTGAAAGAAAAGCGGAGCAACCACATCTTCAAAA
ATAGATATGACTACAC
Found at i:53146 original size:164 final size:163
Alignment explanation
Indices: 52949--54099 Score: 561
Period size: 164 Copynumber: 7.0 Consensus size: 163
52939 AGCAGCCCCT
* * * * *
52949 TCTTCTAAAATTGATATGACTAC-ACGAAAAAGAGGAAAAGATCAAGTTTGATTTACCCTGAAAG
1 TCTTCCAAAATAGATATGTCTACTA-AAAAAAGAGGAAAAGATCAAGTCTGATTT-CCCTGAAAG
* * * *
53013 -AAAAGTGGAGCAAACCACATCTTCAAAAATAGATCTGTCT-TCTAAAAAA-AAGAACATATCAA
64 CAAAA-TGAAGCAAA-CACATCTTCAAAAATAGATCTGTCTACCCAAAAAAGAAGAACACATCAA
* * * * * *
53075 GTCTGATTTTCCCTAAATGCGTTATGGAGTAGGCACG
127 GTCTGATTTCCCCTAAATGCATGATGGAGCAGACACA
* * *
53112 TCTTCCAAAATAGATATGTCTACCTAAAAAAAGAGGCACAGATCAAGTCTGATTTCCCCTGAATG
1 TCTTCCAAAATAGATATGTCTA-CTAAAAAAAGAGGAAAAGATCAAGTCTGATTT-CCCTGAAAG
* * * * * * * *
53177 CATAATGAAGCAGACACGTCTTCCAAAATATATTTGTCTACCCAAAAAAGAGGCACACATCAAGT
64 CAAAATGAAGCAAACACATCTTCAAAAATAGATCTGTCTACCCAAAAAAGAAGAACACATCAAGT
*
53242 CTGATTTCCCCTGAATGCATGATGGAGCAGACACA
129 CTGATTTCCCCTAAATGCATGATGGAGCAGACACA
* * * ** * *
53277 TCTTCCAACATTGATTTGTCTACTCGAAAAAGAGGCATAA-ATCAAGTCTGATTTCCCTTAAATG
1 TCTTCCAAAATAGATATGTCTACTAAAAAAAGAGG-AAAAGATCAAGTCTGATTTCCCTGAAA-G
** * * * * * * * * * * *
53341 CATTATGGAA-TAGACACGTCTTCCAACATTGATTTGTCTACCC-AAAATGAGGCACAGATCAAG
64 CAAAAT-GAAGCAAACACATCTTCAAAAATAGATCTGTCTACCCAAAAAAGAAGAACACATCAAG
* * * * * * *
53404 TTTGATTTCCTCTGATTGCTTGATGGAGCAAACACG
128 TCTGATTTCCCCTAAATGCATGATGGAGCAGACACA
* *** * ** *
53440 TCTTCCAAAATAGATTTGTCTAC-CCGAAAA-AGGCACTGATCAAGTCTGATTTCCCCTCAATA-
1 TCTTCCAAAATAGATATGTCTACTAAAAAAAGAGGAAAAGATCAAGTCTGATTT-CCCTGAA-AG
** * * * * * * *
53502 CATGAT-AGAG-AAGACACGTCTTCCAACATTGATTTGTCTACCCAAAAAAG-AGTCACAAATCA
64 CAAAATGA-AGCAA-ACACATCTTCAAAAATAGATCTGTCTACCCAAAAAAGAAG-AACACATCA
* ** *
53564 AGTCTGATTT-CCCTAAATGCATGATGAAAAAGACACG
126 AGTCTGATTTCCCCTAAATGCATGATGGAGCAGACACA
* * ** * * * * *
53601 TCTTCCAACATTGAT-TGTTTCTACCCAAAAAAGAGGCACATATCAAGTCCGATTTCCCCTGAAT
1 TCTTCCAAAATAGATATG--TCTACTAAAAAAAGAGGAAAAGATCAAGTCTGATTT-CCCTGAAA
** * * * * * * * * * * * * *
53665 GCATGATGGAGAAAATACGTCTTCCAACATTGATTTGTCTACTCAAAAAAGAGGCACAGATCAAT
63 GCAAAATGAAGCAAACACATCTTCAAAAATAGATCTGTCTACCCAAAAAAGAAGAACACATCAAG
* * * *
53730 TTTGATTTCTCCTGAATGCATGATGGAGAAGACACA
128 TCTGATTTCCCCTAAATGCATGATGGAGCAGACACA
* * *** *
53766 TCTTCCAACATTA-ATTTGTCTACCCGAAAAAGAGGCACAA-ATCAAGTCTGATTTTCCCT-AAA
1 TCTTCCAA-AATAGATATGTCTACTAAAAAAAGAGG-AAAAGATCAAGTCTGA-TTTCCCTGAAA
** * * * * * * ** * * *
53828 CGCATGATGGAGCAGACACATCTTCCAACATTGATTTGTCTACCTGAAAAAGAGGCACAAATCAA
63 -GCAAAATGAAGCAAACACATCTTCAAAAATAGATCTGTCTACCCAAAAAAGAAGAACACATCAA
* *
53893 GTCTGATTTCCCCTGAAA-GCATGATGAAGCAGATACA
127 GTCTGATTTCCCCT-AAATGCATGATGGAGCAGACACA
* * * * ** *
53930 TCTTCTAACATTGATTTGTCTAC-CCAAAAAGAGGCACAA-ATCAAGTCTGATTTCCCCTGAATA
1 TCTTCCAAAATAGATATGTCTACTAAAAAAAGAGG-AAAAGATCAAGTCTGATTT-CCCTGAA-A
*** * * * * * * * * *
53993 -CATGCTGGAA--AAGACACGTCTTCCAATATTGATTTGTCTA-CCTAAAAAGAGGCACAAATCA
63 GCAAAAT-GAAGCAA-ACACATCTTCAAAAATAGATCTGTCTACCCAAAAAAGAAGAACACATCA
* * * *
54054 AGTTTGATTTCCCCTAAATGCATGATAGAGAAGATACA
126 AGTCTGATTTCCCCTAAATGCATGATGGAGCAGACACA
54092 TCTTCCAA
1 TCTTCCAA
54100 CTTTGATTTG
Statistics
Matches: 814, Mismatches: 136, Indels: 77
0.79 0.13 0.07
Matches are distributed among these distances:
159 1 0.00
160 4 0.00
161 88 0.11
162 98 0.12
163 184 0.23
164 327 0.40
165 109 0.13
166 3 0.00
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (163 bp):
TCTTCCAAAATAGATATGTCTACTAAAAAAAGAGGAAAAGATCAAGTCTGATTTCCCTGAAAGCA
AAATGAAGCAAACACATCTTCAAAAATAGATCTGTCTACCCAAAAAAGAAGAACACATCAAGTCT
GATTTCCCCTAAATGCATGATGGAGCAGACACA
Found at i:53244 original size:82 final size:82
Alignment explanation
Indices: 53070--54153 Score: 1213
Period size: 82 Copynumber: 13.3 Consensus size: 82
53060 AAAAGAACAT
* * * * * * * * * *
53070 ATCAAGTCTGATTTTCCCTAAATGCGTTATGGAGTAGGCACGTCTTCCAAAATAGATATGTCTAC
1 ATCAAGTCTGATTTCCCCTGAATGCATGATGAAGAAGACACGTCTTCCAACATTGATTTGTCTAC
* *
53135 CTAAAAAAAGAGGCACAG
66 C-CAAAAAAGAGGCACAA
* * *
53153 ATCAAGTCTGATTTCCCCTGAATGCATAATGAAGCAGACACGTCTTCCAAAATAT-ATTTGTCTA
1 ATCAAGTCTGATTTCCCCTGAATGCATGATGAAGAAGACACGTCTTCCAACAT-TGATTTGTCTA
*
53217 CCCAAAAAAGAGGCACAC
65 CCCAAAAAAGAGGCACAA
* * *
53235 ATCAAGTCTGATTTCCCCTGAATGCATGATGGAGCAGACACATCTTCCAACATTGATTTGTCTAC
1 ATCAAGTCTGATTTCCCCTGAATGCATGATGAAGAAGACACGTCTTCCAACATTGATTTGTCTAC
* * *
53300 TCGAAAAAGAGGCATAA
66 CCAAAAAAGAGGCACAA
* * * *
53317 ATCAAGTCTGATTTCCCTTAAATGCATTATGGAA-TAGACACGTCTTCCAACATTGATTTGTCTA
1 ATCAAGTCTGATTTCCCCTGAATGCATGAT-GAAGAAGACACGTCTTCCAACATTGATTTGTCTA
* *
53381 CCC-AAAATGAGGCACAG
65 CCCAAAAAAGAGGCACAA
* * * * * * *
53398 ATCAAGTTTGATTTCCTCTGATTGCTTGATGGAGCAA-ACACGTCTTCCAAAATAGATTTGTCTA
1 ATCAAGTCTGATTTCCCCTGAATGCATGATGAAG-AAGACACGTCTTCCAACATTGATTTGTCTA
* **
53462 CCC-GAAAA-AGGCACTG
65 CCCAAAAAAGAGGCACAA
* *
53478 ATCAAGTCTGATTTCCCCTCAATACATGAT-AGAGAAGACACGTCTTCCAACATTGATTTGTCTA
1 ATCAAGTCTGATTTCCCCTGAATGCATGATGA-AGAAGACACGTCTTCCAACATTGATTTGTCTA
*
53542 CCCAAAAAAGAGTCACAA
65 CCCAAAAAAGAGGCACAA
* * *
53560 ATCAAGTCTGATTT-CCCTAAATGCATGATGAAAAAGACACGTCTTCCAACATTGATTGTTTCTA
1 ATCAAGTCTGATTTCCCCTGAATGCATGATGAAGAAGACACGTCTTCCAACATTGATT-TGTCTA
*
53624 CCCAAAAAAGAGGCACAT
65 CCCAAAAAAGAGGCACAA
* * * *
53642 ATCAAGTCCGATTTCCCCTGAATGCATGATGGAGAAAATACGTCTTCCAACATTGATTTGTCTAC
1 ATCAAGTCTGATTTCCCCTGAATGCATGATGAAGAAGACACGTCTTCCAACATTGATTTGTCTAC
* *
53707 TCAAAAAAGAGGCACAG
66 CCAAAAAAGAGGCACAA
* * * * * *
53724 ATCAATTTTGATTTCTCCTGAATGCATGATGGAGAAGACACATCTTCCAACATTAATTTGTCTAC
1 ATCAAGTCTGATTTCCCCTGAATGCATGATGAAGAAGACACGTCTTCCAACATTGATTTGTCTAC
*
53789 CCGAAAAAGAGGCACAA
66 CCAAAAAAGAGGCACAA
* * * * * *
53806 ATCAAGTCTGATTTTCCCTAAACGCATGATGGAGCAGACACATCTTCCAACATTGATTTGTCTAC
1 ATCAAGTCTGATTTCCCCTGAATGCATGATGAAGAAGACACGTCTTCCAACATTGATTTGTCTAC
**
53871 CTGAAAAAGAGGCACAA
66 CCAAAAAAGAGGCACAA
* * * * *
53888 ATCAAGTCTGATTTCCCCTGAAAGCATGATGAAGCAGATACATCTTCTAACATTGATTTGTCTAC
1 ATCAAGTCTGATTTCCCCTGAATGCATGATGAAGAAGACACGTCTTCCAACATTGATTTGTCTAC
53953 CC-AAAAAGAGGCACAA
66 CCAAAAAAGAGGCACAA
* * *
53969 ATCAAGTCTGATTTCCCCTGAATACATGCTGGAA-AAGACACGTCTTCCAATATTGATTTGTCTA
1 ATCAAGTCTGATTTCCCCTGAATGCATGAT-GAAGAAGACACGTCTTCCAACATTGATTTGTCTA
*
54033 -CCTAAAAAGAGGCACAA
65 CCCAAAAAAGAGGCACAA
* * * * * *
54050 ATCAAGTTTGATTTCCCCTAAATGCATGAT-AGAGAAGATACATCTTCCAACTTTGATTTGTATA
1 ATCAAGTCTGATTTCCCCTGAATGCATGATGA-AGAAGACACGTCTTCCAACATTGATTTGTCTA
* * * * *
54114 TCCGAAGAAGAGACACAT
65 CCCAAAAAAGAGGCACAA
* *
54132 ATCAAGTCTTATCT-CCCTGAAT
1 ATCAAGTCTGATTTCCCCTGAAT
54154 AAATAATGGA
Statistics
Matches: 861, Mismatches: 123, Indels: 36
0.84 0.12 0.04
Matches are distributed among these distances:
79 3 0.00
80 66 0.08
81 246 0.29
82 450 0.52
83 96 0.11
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.27
Consensus pattern (82 bp):
ATCAAGTCTGATTTCCCCTGAATGCATGATGAAGAAGACACGTCTTCCAACATTGATTTGTCTAC
CCAAAAAAGAGGCACAA
Found at i:54012 original size:571 final size:573
Alignment explanation
Indices: 53066--54149 Score: 1516
Period size: 571 Copynumber: 1.9 Consensus size: 573
53056 AAAAAAAAGA
* * * * * **
53066 ACATATCAAGTCTGATTTTCCCTAAATGCGTTATGGAGTAGGCACGTCTTCCAAAATAGATATGT
1 ACATATCAAGTCCGATTTCCCCTAAATGCATGATGGAGAAAACACGTCTTCCAAAATAGATATGT
* *
53131 CTACCTAAAAAAAGAGGCACAGATCAAGTCTGATTTCCCCTGAATGCATAATGAAGCAGACACGT
66 CTACCTAAAAAAAGAGGCACAGATCAAGTCTGATTTCCCCTGAATGCATAATGAAGAAGACACAT
* * *
53196 CTTCCAAAATATATTTGTCTACCCAAAAAAGAGGCACACATCAAGTCTGATTTCCCCTGAATGCA
131 CTTCCAAAATATATTTGTCTACCCAAAAAAGAGGCACAAATCAAGTCTGATTTCCCCTAAACGCA
*
53261 TGATGGAGCAGACACATCTTCCAACATTGATTTGTCTACTCGAAAAAGAGGCATAAATCAAGTCT
196 TGATGGAGCAGACACATCTTCCAACATTGATTTGTCTACTCGAAAAAGAGGCACAAATCAAGTCT
* * * * *
53326 GATTTCCCTTAAATGCATTATGGAATAGACACGTCTTCCAACATTGATTTGTCTACCCAAAATGA
261 GATTTCCCTGAAATGCATGATGGAACAGACACATCTTCCAACATTGATTTGTCTACCCAAAAAGA
* * * * * * *
53391 GGCACAGATCAAGTTTGATTTCCTCTGATTGCTTGATGGAGCAAACACGTCTTCCAAAATAGATT
326 GGCACAAATCAAGTCTGATTTCCCCTGAATACATGATGGAGAAAACACGTCTTCCAAAATAGATT
* ** * *
53456 TGTCTACCCGAAAA-AGGCACTGATCAAGTCTGATTTCCCCTCAATACATGATAGAGAAGACACG
391 TGTCTACCCAAAAAGAGGCACAAATCAAGTCTGATTTCCCCTAAATACATGATAGAGAAGACACA
* * *
53520 TCTTCCAACATTGATTTGTCTACCCAAAAAAGAGTCACAAATCAAGTCTGATTTCCCTAAATGCA
456 TCTTCCAACATTGATTTGTATACCCAAAAAAGAGACACAAATCAAGTCTGATCTCCCTAAATGCA
53585 TGATGAAAAAGACACGTCTTCCAACATTGATTGTTTCTACCCAAAAAAGAGGC
521 TGATGAAAAAGACACGTCTTCCAACATTGATTGTTTCTACCCAAAAAAGAGGC
* * * * *
53638 ACATATCAAGTCCGATTTCCCCTGAATGCATGATGGAGAAAATACGTCTTCCAACATTGATTTGT
1 ACATATCAAGTCCGATTTCCCCTAAATGCATGATGGAGAAAACACGTCTTCCAAAATAGATATGT
* * * * * *
53703 CTA-CTCAAAAAAGAGGCACAGATCAATTTTGATTTCTCCTGAATGCATGATGGAGAAGACACAT
66 CTACCTAAAAAAAGAGGCACAGATCAAGTCTGATTTCCCCTGAATGCATAATGAAGAAGACACAT
* * *
53767 CTTCCAACAT-TAATTTGTCTACCCGAAAAAGAGGCACAAATCAAGTCTGATTTTCCCTAAACGC
131 CTTCCAAAATAT-ATTTGTCTACCCAAAAAAGAGGCACAAATCAAGTCTGATTTCCCCTAAACGC
53831 ATGATGGAGCAGACACATCTTCCAACATTGATTTGTCTAC-CTGAAAAAGAGGCACAAATCAAGT
195 ATGATGGAGCAGACACATCTTCCAACATTGATTTGTCTACTC-GAAAAAGAGGCACAAATCAAGT
* *
53895 CTGATTTCCCCTGAAA-GCATGAT-GAAGCAGATACATCTTCTAACATTGATTTGTCTACCCAAA
259 CTGATTT-CCCTGAAATGCATGATGGAA-CAGACACATCTTCCAACATTGATTTGTCTACCCAAA
* *
53958 AAGAGGCACAAATCAAGTCTGATTTCCCCTGAATACATGCTGGA-AAAGACACGTCTTCCAATAT
322 AAGAGGCACAAATCAAGTCTGATTTCCCCTGAATACATGATGGAGAAA-ACACGTCTTCCAAAAT
* * * *
54022 TGATTTGTCTACCTAAAAAGAGGCACAAATCAAGTTTGATTTCCCCTAAATGCATGATAGAGAAG
386 AGATTTGTCTACCCAAAAAGAGGCACAAATCAAGTCTGATTTCCCCTAAATACATGATAGAGAAG
* * * * * * *
54087 ATACATCTTCCAACTTTGATTTGTATATCCGAAGAAGAGACACATATCAAGTCTTATCTCCCT
451 ACACATCTTCCAACATTGATTTGTATACCCAAAAAAGAGACACAAATCAAGTCTGATCTCCCT
54150 GAATAAATAA
Statistics
Matches: 444, Mismatches: 62, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
570 7 0.02
571 282 0.64
572 155 0.35
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.27
Consensus pattern (573 bp):
ACATATCAAGTCCGATTTCCCCTAAATGCATGATGGAGAAAACACGTCTTCCAAAATAGATATGT
CTACCTAAAAAAAGAGGCACAGATCAAGTCTGATTTCCCCTGAATGCATAATGAAGAAGACACAT
CTTCCAAAATATATTTGTCTACCCAAAAAAGAGGCACAAATCAAGTCTGATTTCCCCTAAACGCA
TGATGGAGCAGACACATCTTCCAACATTGATTTGTCTACTCGAAAAAGAGGCACAAATCAAGTCT
GATTTCCCTGAAATGCATGATGGAACAGACACATCTTCCAACATTGATTTGTCTACCCAAAAAGA
GGCACAAATCAAGTCTGATTTCCCCTGAATACATGATGGAGAAAACACGTCTTCCAAAATAGATT
TGTCTACCCAAAAAGAGGCACAAATCAAGTCTGATTTCCCCTAAATACATGATAGAGAAGACACA
TCTTCCAACATTGATTTGTATACCCAAAAAAGAGACACAAATCAAGTCTGATCTCCCTAAATGCA
TGATGAAAAAGACACGTCTTCCAACATTGATTGTTTCTACCCAAAAAAGAGGC
Found at i:54341 original size:326 final size:326
Alignment explanation
Indices: 52876--54308 Score: 987
Period size: 328 Copynumber: 4.4 Consensus size: 326
52866 GTCCTCTGAA
* * * * ***
52876 ATTGATCTGAT-TACCTGAAAAAGAGGAACAAGTCAAGTCTGATCTCCCCTGAAAGAA-AAGCGG
1 ATTGATCTG-TCTACCCGAAAAAGAGGCACAAATCAAGTCTGATCTCCCCTGAAAGAATGA-TAA
* * * * * * * * *
52939 AGCAGCCCCTTCTTCTAAAATTGATATGACTACACGAAAAAGAGG-AAAAGATCAAGTTTGATTT
64 AGCAGACACATCGTCTAAAATTGATCTGTCTAC-CCAAAAAGAGGCACAA-ATCAAGTCTGATTT
* * * * * * * * * * *
53003 ACCCTGAA-AGAA-AAGTGGAGCAAACCACATCTTCAAAAATAGATCTGTCTTCT-AAAAAA-AA
127 CCCCTGAATACAAGAA--GGA-AAAAACACGTCTTCCAACATTGATTTGTCTACTCAAAAAAGAG
* * * * * * * * * * * *
53064 GAACATATCAAGTCTGATTTTCCCTAAATGCGTTATGGAGTAGGCACGTCTTCCAA-AATAGATA
189 GCACAAATCAAGTTTGATTTCCCCTAAATGCATGATAGAGAAGACACATCTTCCAACATTA-ATT
* ** * * * *** *
53128 TGTCTACCTAAAAAAAGAGGCACAGATCAAGTCTGATT-TCCCCTGAATGCATAATGAAGCAGAC
253 TGTATACC-CGAAAAAGAGACACAAATCAAGTCTGATTCT-CCCTAAACAAATAATGGAGCAGA-
* * *
53192 ACGTCTTCCAAA
315 ACATCATCCAAC
* * * * * * **
53204 ATAT-ATTTGTCTACCCAAAAAAGAGGCACACATCAAGTCTGATTTCCCCTGAATGCATGATGGA
1 AT-TGATCTGTCTACCCGAAAAAGAGGCACAAATCAAGTCTGATCTCCCCTGAAAGAATGATAAA
* * * * * *
53268 GCAGACACATCTTCCAACATTGATTTGTCTACTCGAAAAAGAGGCATAAATCAAGTCTGATTTCC
65 GCAGACACATCGTCTAAAATTGATCTGTCTAC-CCAAAAAGAGGCACAAATCAAGTCTGATTTCC
* * * ** * * * * *
53333 CTTAAATGCATTATGGAATAGACACGTCTTCCAACATTGATTTGTCTAC-CCAAAATGAGGCACA
129 CCTGAATACAAGAAGGAAAAAACACGTCTTCCAACATTGATTTGTCTACTCAAAAAAGAGGCACA
* * * * * * * * *
53397 GATCAAGTTTGATTTCCTCTGATTGCTTGATGGAGCAA-ACACGTCTTCCAA-AATAGATTTGTC
194 AATCAAGTTTGATTTCCCCTAAATGCATGATAGAG-AAGACACATCTTCCAACATTA-ATTTGTA
** * * * * * * *
53460 TACCCGAAAAAG-G-CACTGATCAAGTCTGATT-TCCCCTCAATACATGATAGAGAAGACACGTC
257 TACCCGAAAAAGAGACACAAATCAAGTCTGATTCT-CCCTAAACAAATAATGGAGCAGA-ACATC
*
53522 TTCCAAC
320 ATCCAAC
* * * * *
53529 ATTGATTTGTCTACCCAAAAAAGAGTCACAAATCAAGTCTGAT-TTCCCT-AAATGCATGATGAA
1 ATTGATCTGTCTACCCGAAAAAGAGGCACAAATCAAGTCTGATCTCCCCTGAAA-GAATGAT-AA
* * * * * * *
53592 A-AAGACACGTCTTCCAACATTGAT-TGTTTCTACCCAAAAAAGAGGCACATATCAAGTCCGATT
64 AGCAGACACATCGTCTAAAATTGATCTG--TCTACCC-AAAAAGAGGCACAAATCAAGTCTGATT
* * * * *
53655 TCCCCTGAATGCATGATGGAGAAAATACGTCTTCCAACATTGATTTGTCTACTCAAAAAAGAGGC
126 TCCCCTGAATACAAGAAGGAAAAAACACGTCTTCCAACATTGATTTGTCTACTCAAAAAAGAGGC
* * * * *
53720 ACAGATCAATTTTGATTTCTCCTGAATGCATGATGGAGAAGACACATCTTCCAACATTAATTTGT
191 ACAAATCAAGTTTGATTTCCCCTAAATGCATGATAGAGAAGACACATCTTCCAACATTAATTTGT
* * * ** *
53785 CTACCCGAAAAAGAGGCACAAATCAAGTCTGATTTTCCCTAAACGCATGATGGAGCAGACACATC
256 ATACCCGAAAAAGAGACACAAATCAAGTCTGATTCTCCCTAAACAAATAATGGAGCAGA-ACATC
*
53850 TTCCAAC
320 ATCCAAC
* * * * *
53857 ATTGATTTGTCTACCTGAAAAAGAGGCACAAATCAAGTCTGATTTCCCCTGAAAGCATGATGAAG
1 ATTGATCTGTCTACCCGAAAAAGAGGCACAAATCAAGTCTGATCTCCCCTGAAAGAATGATAAAG
* * * *
53922 CAGATACATCTTCTAACATTGATTTGTCTACCCAAAAAGAGGCACAAATCAAGTCTGATTTCCCC
66 CAGACACATCGTCTAAAATTGATCTGTCTACCCAAAAAGAGGCACAAATCAAGTCTGATTTCCCC
* ** * * *
53987 TGAATACATGCTGGAAAAGACACGTCTTCCAATATTGATTTGTCTAC-CTAAAAAGAGGCACAAA
131 TGAATACAAGAAGGAAAAAACACGTCTTCCAACATTGATTTGTCTACTCAAAAAAGAGGCACAAA
* * * *
54051 TCAAGTTTGATTTCCCCTAAATGCATGATAGAGAAGATACATCTTCCAACTTTGATTTGTATATC
196 TCAAGTTTGATTTCCCCTAAATGCATGATAGAGAAGACACATCTTCCAACATTAATTTGTATACC
* * * * * * *
54116 CGAAGAAGAGACACATATCAAGTCTTA-TCTCCCTGAATAAATAATGGAGTAG-ATAT-ATCCAA
261 CGAAAAAGAGACACAAATCAAGTCTGATTCTCCCTAAACAAATAATGGAGCAGAACATCATCCAA
54178 -
326 C
* * * * * * *
54178 AGTT-ATCTGTCTACCCGAAGAAGTGGCACAGATCGAGTCTTATCT-CCCTGAATGAATTATAAA
1 A-TTGATCTGTCTACCCGAAAAAGAGGCACAAATCAAGTCTGATCTCCCCTGAAAGAATGATAAA
* * * *
54241 GCA-AGCACATCGTCTAAAATTGATCTGTCTACCTGAAAAAGAGGCACATATCAAGTTTGGTTTC
65 GCAGA-CACATCGTCTAAAATTGATCTGTCTACC-CAAAAAGAGGCACAAATCAAGTCTGATTTC
54305 CCCT
128 CCCT
54309 TGAGTGAAAG
Statistics
Matches: 917, Mismatches: 160, Indels: 63
0.80 0.14 0.06
Matches are distributed among these distances:
319 1 0.00
320 41 0.04
321 64 0.07
322 7 0.01
323 7 0.01
324 35 0.04
325 182 0.20
326 169 0.18
327 108 0.12
328 258 0.28
329 39 0.04
330 6 0.01
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (326 bp):
ATTGATCTGTCTACCCGAAAAAGAGGCACAAATCAAGTCTGATCTCCCCTGAAAGAATGATAAAG
CAGACACATCGTCTAAAATTGATCTGTCTACCCAAAAAGAGGCACAAATCAAGTCTGATTTCCCC
TGAATACAAGAAGGAAAAAACACGTCTTCCAACATTGATTTGTCTACTCAAAAAAGAGGCACAAA
TCAAGTTTGATTTCCCCTAAATGCATGATAGAGAAGACACATCTTCCAACATTAATTTGTATACC
CGAAAAAGAGACACAAATCAAGTCTGATTCTCCCTAAACAAATAATGGAGCAGAACATCATCCAA
C
Found at i:54362 original size:571 final size:571
Alignment explanation
Indices: 53115--54383 Score: 1429
Period size: 571 Copynumber: 2.2 Consensus size: 571
53105 AGGCACGTCT
* * * * *
53115 TCCAAAATAGATATGTCTACCTAAAAAAAGAGGCACAGATCAAGTCTGATTTCCCCTGAATG-CA
1 TCCAAAATTGATCTGTCTA-CTCAAAAAAGAGGCACAGATCAAGTTTGATTTCCCCTGAATGAAA
* * * *
53179 TAA--TGAAGCAGACACGTCTTCCAAAA-TATATTTGTCTACCCAAAAAAGAGGCACACATCAAG
65 GAAGGAGAAGCA-ACACGTCTTCCAAAATTA-ATTTGTCTACCCGAAAAAGAGGCACAAATCAAG
* *
53241 TCTGATTTCCCCTGAATGCATGATGGAGCAGACACATCTTCCAACATTGATTTGTCTACTCGAAA
128 TCTGATTTCCCCTAAACGCATGATGGAGCAGACACATCTTCCAACATTGATTTGTCTACTCGAAA
* * * * *
53306 AAGAGGCATAAATCAAGTCTGATTTCCCTTAAATGCATTATGGAATAGACACGTCTTCCAACATT
193 AAGAGGCACAAATCAAGTCTGATTTCCCTGAAATGCATGATGGAACAGACACATCTTCCAACATT
* * * * * * * *
53371 GATTTGTCTACCCAAAATGAGGCACAGATCAAGTTTGATTTCCTCTGATTGCTTGATGGAGCAAA
258 GATTTGTCTACCCAAAAAGAGGCACAAATCAAGTCTGATTTCCCCTGAATACATGATGGAGAAAA
* ** *
53436 CACGTCTTCCAAAATAGATTTGTCTACCCGAAAAAGGCACTGATCAAGTCTGATTTCCCCTCAAT
323 CACGTCTTCCAAAATAGATTTGTCTACCCAAAAAAGGCACAAATCAAGTCTGATTTCCCCTAAAT
* * *
53501 ACATGATAGAGAAGACACGTCTTCCAACATTGATTTGTCTACCCAAAAAAGAGTCACAAATCAAG
388 ACATGATAGAGAAGACACATCTTCCAACATTGATTTGTATACCCAAAAAAGAGACACAAATCAAG
* ** * *
53566 TCTGATTTCCCTAAATGCATGATGAAAAAGACACGTCTTCCAACATTGATTGTTTCTACCCAAAA
453 TCTGATCTCCCTAAATAAATAATGAAAAAGACAC-TCATCCAACATTGATTG-TTCTACCCAAAA
* * * ** * * *
53631 AAGAGGCACATATCAAGTCCGATTTCCCCTGAATGCATGATGGAGAAAATACGTCT
516 AAGAGGCACAGATCAAGTCCGATCTCCCCTGAATGAATGATAAAGAAAACACATCG
* * * * * *
53687 TCCAACATTGATTTGTCTACTCAAAAAAGAGGCACAGATCAATTTTGATTTCTCCTGAATGCATG
1 TCCAAAATTGATCTGTCTACTCAAAAAAGAGGCACAGATCAAGTTTGATTTCCCCTGAATGAAAG
* * *
53752 ATGGAGAAG--ACACATCTTCCAACATTAATTTGTCTACCCGAAAAAGAGGCACAAATCAAGTCT
66 AAGGAGAAGCAACACGTCTTCCAAAATTAATTTGTCTACCCGAAAAAGAGGCACAAATCAAGTCT
*
53815 GATTTTCCCTAAACGCATGATGGAGCAGACACATCTTCCAACATTGATTTGTCTAC-CTGAAAAA
131 GATTTCCCCTAAACGCATGATGGAGCAGACACATCTTCCAACATTGATTTGTCTACTC-GAAAAA
* *
53879 GAGGCACAAATCAAGTCTGATTTCCCCTGAAA-GCATGAT-GAAGCAGATACATCTTCTAACATT
195 GAGGCACAAATCAAGTCTGATTT-CCCTGAAATGCATGATGGAA-CAGACACATCTTCCAACATT
*
53942 GATTTGTCTACCCAAAAAGAGGCACAAATCAAGTCTGATTTCCCCTGAATACATGCTGGA-AAAG
258 GATTTGTCTACCCAAAAAGAGGCACAAATCAAGTCTGATTTCCCCTGAATACATGATGGAGAAA-
* * * *
54006 ACACGTCTTCCAATATTGATTTGTCTACCTAAAAAGAGGCACAAATCAAGTTTGATTTCCCCTAA
322 ACACGTCTTCCAAAATAGATTTGTCTACCCAAAAA-AGGCACAAATCAAGTCTGATTTCCCCTAA
* * * * * * *
54071 ATGCATGATAGAGAAGATACATCTTCCAACTTTGATTTGTATATCCGAAGAAGAGACACATATCA
386 ATACATGATAGAGAAGACACATCTTCCAACATTGATTTGTATACCCAAAAAAGAGACACAAATCA
* * * ** * *
54136 AGTCTTATCTCCCTGAATAAATAATGGAGTAGATA-T-ATCCAA-AGTT-ATCTG-TCTACCCGA
451 AGTCTGATCTCCCTAAATAAATAATGAAAAAGACACTCATCCAACA-TTGAT-TGTTCTACCCAA
* * * ** * * *
54196 AGAAGTGGCACAGATCGAGTCTTATCT-CCCTGAATGAATTATAAAGCAAGCACATCG
514 AAAAGAGGCACAGATCAAGTCCGATCTCCCCTGAATGAATGATAAAGAAAACACATCG
* * * * *
54253 TCTAAAATTGATCTGTCTAC-CTGAAAAAGAGGCACATATCAAGTTTGGTTTCCCCTTGAGTGAA
1 TCCAAAATTGATCTGTCTACTC-AAAAAAGAGGCACAGATCAAGTTTGATTTCCCC-TGAATGAA
* * * * * *
54317 AGAAGAGAGAAGCAAACACGTCTTCTAAAATTAATCTGACTACCCGAAAAAGTGGAACATATCAA
64 AGAAG-GAGAAGC-AACACGTCTTCCAAAATTAATTTGTCTACCCGAAAAAGAGGCACAAATCAA
54382 GT
127 GT
54384 TTAACCTACC
Statistics
Matches: 579, Mismatches: 101, Indels: 35
0.81 0.14 0.05
Matches are distributed among these distances:
565 1 0.00
566 66 0.11
567 37 0.06
568 9 0.02
569 9 0.02
570 7 0.01
571 315 0.54
572 131 0.23
574 4 0.01
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (571 bp):
TCCAAAATTGATCTGTCTACTCAAAAAAGAGGCACAGATCAAGTTTGATTTCCCCTGAATGAAAG
AAGGAGAAGCAACACGTCTTCCAAAATTAATTTGTCTACCCGAAAAAGAGGCACAAATCAAGTCT
GATTTCCCCTAAACGCATGATGGAGCAGACACATCTTCCAACATTGATTTGTCTACTCGAAAAAG
AGGCACAAATCAAGTCTGATTTCCCTGAAATGCATGATGGAACAGACACATCTTCCAACATTGAT
TTGTCTACCCAAAAAGAGGCACAAATCAAGTCTGATTTCCCCTGAATACATGATGGAGAAAACAC
GTCTTCCAAAATAGATTTGTCTACCCAAAAAAGGCACAAATCAAGTCTGATTTCCCCTAAATACA
TGATAGAGAAGACACATCTTCCAACATTGATTTGTATACCCAAAAAAGAGACACAAATCAAGTCT
GATCTCCCTAAATAAATAATGAAAAAGACACTCATCCAACATTGATTGTTCTACCCAAAAAAGAG
GCACAGATCAAGTCCGATCTCCCCTGAATGAATGATAAAGAAAACACATCG
Found at i:58035 original size:2 final size:2
Alignment explanation
Indices: 58030--58072 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
58020 TATTATTCTT
58030 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58072 T
1 T
58073 TATCTTCATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:58320 original size:12 final size:14
Alignment explanation
Indices: 58171--58313 Score: 57
Period size: 14 Copynumber: 9.9 Consensus size: 14
58161 TATATCATTA
*
58171 TTTATATATTTTTT
1 TTTATATATTTTAT
*
58185 TATTACTATAATTATAT
1 T-TTA-TAT-ATTTTAT
58202 GTTATATATATTTATTAT
1 -TT-TATATA-TT-TTAT
*
58220 TTTATATATTTCA-
1 TTTATATATTTTAT
*
58233 TTT-TATCTTTTA-
1 TTTATATATTTTAT
*
58245 --TCTAT-TTTTAT
1 TTTATATATTTTAT
*
58256 TTT-TGTATTGTTAT
1 TTTATATATT-TTAT
*
58270 TGTTATTATCTTCTTTAT
1 T-TTA-TAT-AT-TTTAT
*
58288 TTTATGTATTTTAT
1 TTTATATATTTTAT
58302 TTTATATATTTT
1 TTTATATATTTT
58314 TTTATATTTG
Statistics
Matches: 99, Mismatches: 12, Indels: 36
0.67 0.08 0.24
Matches are distributed among these distances:
10 6 0.06
11 3 0.03
12 9 0.09
13 6 0.06
14 24 0.24
15 8 0.08
16 12 0.12
17 18 0.18
18 12 0.12
19 1 0.01
ACGTcount: A:0.24, C:0.04, G:0.03, T:0.68
Consensus pattern (14 bp):
TTTATATATTTTAT
Found at i:58322 original size:33 final size:32
Alignment explanation
Indices: 58171--58322 Score: 96
Period size: 32 Copynumber: 4.6 Consensus size: 32
58161 TATATCATTA
* * *
58171 TTTATATA-TTTTTTTATTACTAT-AATTATAT
1 TTTATATATTTTTTTTATT-TTATGTATTTTAT
* * * * *
58202 GTTATATATATTTATTATTTTATATATTTCAT
1 TTTATATATTTTTTTTATTTTATGTATTTTAT
* *
58234 TTTATCTTTTATCTATTTTTATTTT-TGTATTGTTAT
1 TTTA---TATAT-TTTTTTTATTTTATGTATT-TTAT
* *
58270 TGTTAT-TATCTTCTTTATTTTATGTATTTTAT
1 T-TTATATATTTTTTTTATTTTATGTATTTTAT
58302 TTTATATATTTTTTTATATTT
1 TTTATATATTTTTTT-TATTT
58323 GTTTTTGTGC
Statistics
Matches: 91, Mismatches: 19, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
31 14 0.15
32 37 0.41
33 14 0.15
34 1 0.01
35 9 0.10
36 13 0.14
37 3 0.03
ACGTcount: A:0.24, C:0.04, G:0.03, T:0.68
Consensus pattern (32 bp):
TTTATATATTTTTTTTATTTTATGTATTTTAT
Done.