Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015802.1 Corchorus capsularis cultivar CVL-1 contig15823, 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: 25843
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Found at i:2954 original size:75 final size:76
Alignment explanation
Indices: 2860--3094 Score: 269
Period size: 75 Copynumber: 3.0 Consensus size: 76
2850 CTATTCAATT
* *
2860 TTTATTATTTATTTT-TTTCTTAAAATAACTCCTAAATCTTCCATAATTTGGCAAGATTTAGAAA
1 TTTATTA-TTATTTTATTTCTTAAAATATCTCCTAAATCTTCCACAATTTGGCAAGATTTAGAAA
*
2924 ATATTCTCA-AC
65 ATATTCTCATAA
* * *
2935 TTTATTATTATTTTATTTCTTGAAATATCTCCTAAATCTCCCACAATTTGGCTAGATTTAGAAAA
1 TTTATTATTATTTTATTTCTTAAAATATCTCCTAAATCTTCCACAATTTGGCAAGATTTAGAAAA
3000 TATTCTCATTATTAA
66 TATTCTC---A-TAA
* *
3015 TTCTATTTTTAATTTATTTGT-TTTCTTAAAATATCTCCTAAACCTTCCACAATTTGGTAAGATT
1 TT-TA---TT-A-TTATTT-TATTTCTTAAAATATCTCCTAAATCTTCCACAATTTGGCAAGATT
3079 TAGAAAATATTCTCAT
59 TAGAAAATATTCTCAT
3095 TATTAATTTT
Statistics
Matches: 136, Mismatches: 11, Indels: 19
0.82 0.07 0.11
Matches are distributed among these distances:
74 7 0.05
75 59 0.43
78 1 0.01
80 3 0.02
81 2 0.01
82 1 0.01
83 1 0.01
84 2 0.01
85 1 0.01
86 58 0.43
87 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.46
Consensus pattern (76 bp):
TTTATTATTATTTTATTTCTTAAAATATCTCCTAAATCTTCCACAATTTGGCAAGATTTAGAAAA
TATTCTCATAA
Found at i:3032 original size:86 final size:86
Alignment explanation
Indices: 2942--3102 Score: 263
Period size: 86 Copynumber: 1.9 Consensus size: 86
2932 AACTTTATTA
* *
2942 TTATTT-TATTTCTTGAAATATCTCCTAAATCTCCCACAATTTGGCT-AGATTTAGAAAATATTC
1 TTATTTGT-TTTCTTAAAATATCTCCTAAACCTCCCACAATTTGG-TAAGATTTAGAAAATATTC
3005 TCATTATTAATTCTATTTTTAAT
64 TCATTATTAATTCTATTTTTAAT
*
3028 TTATTTGTTTTCTTAAAATATCTCCTAAACCTTCCACAATTTGGTAAGATTTAGAAAATATTCTC
1 TTATTTGTTTTCTTAAAATATCTCCTAAACCTCCCACAATTTGGTAAGATTTAGAAAATATTCTC
3093 ATTATTAATT
66 ATTATTAATT
3103 TTGTTAATCT
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
85 1 0.01
86 68 0.97
87 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.06, T:0.47
Consensus pattern (86 bp):
TTATTTGTTTTCTTAAAATATCTCCTAAACCTCCCACAATTTGGTAAGATTTAGAAAATATTCTC
ATTATTAATTCTATTTTTAAT
Found at i:3071 original size:161 final size:161
Alignment explanation
Indices: 2796--3093 Score: 474
Period size: 161 Copynumber: 1.8 Consensus size: 161
2786 ATTATTATTT
*
2796 AATATCTCCTAAATCTCCCACAATCTGGCAAGATTTAGAGAAATATTCTTATTACTATTCAATTT
1 AATATCTCCTAAATCTCCCACAATCTGGCAAGATTTAGAGAAATATTCTCATTACTATTCAATTT
* *
2861 TTATTATTTATTTTTTTCTTAAAATAACTCCTAAATCTTCCATAATTTGGCAAGATTTAGAAAAT
66 TTA-TATTTATTTTTTTCTTAAAATAACTCCTAAACCTTCCACAATTTGGCAAGATTTAGAAAAT
2926 ATTCTCAACTTTATTATTATTTTATTTCTTGA
130 ATTCTCAACTTTATTATTATTTTATTTCTTGA
* * * *
2958 AATATCTCCTAAATCTCCCACAATTTGGCTAGATTTAGA-AAATATTCTCATTATTAATTCTATT
1 AATATCTCCTAAATCTCCCACAATCTGGCAAGATTTAGAGAAATATTCTCATTACT-ATTCAATT
* *
3022 TTTA-ATTTATTTGTTTTCTTAAAATATCTCCTAAACCTTCCACAATTTGGTAAGATTTAGAAAA
65 TTTATATTTATTT-TTTTCTTAAAATAACTCCTAAACCTTCCACAATTTGGCAAGATTTAGAAAA
3086 TATTCTCA
129 TATTCTCA
3094 TTATTAATTT
Statistics
Matches: 125, Mismatches: 9, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
160 8 0.06
161 69 0.55
162 48 0.38
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (161 bp):
AATATCTCCTAAATCTCCCACAATCTGGCAAGATTTAGAGAAATATTCTCATTACTATTCAATTT
TTATATTTATTTTTTTCTTAAAATAACTCCTAAACCTTCCACAATTTGGCAAGATTTAGAAAATA
TTCTCAACTTTATTATTATTTTATTTCTTGA
Found at i:13083 original size:33 final size:33
Alignment explanation
Indices: 13008--13119 Score: 113
Period size: 33 Copynumber: 3.4 Consensus size: 33
12998 AGACAAAGGA
* * *
13008 TCGCGTGGCCGGTTGTGGCCGGGCATGGCCGA-G
1 TCGCGTGGCCGGTTGTAGCCGGACATGTCC-ATG
**
13041 TCGTTTGGCCGGTTGTAGCCGGACATGTCCATG
1 TCGCGTGGCCGGTTGTAGCCGGACATGTCCATG
*
13074 TCGCATGGCCGG-TG-ATGACCGGACATGTCCATG
1 TCGCGTGGCCGGTTGTA-G-CCGGACATGTCCATG
*
13107 TCACGTGGCCGGT
1 TCGCGTGGCCGGT
13120 CTAGTGGCCG
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
31 1 0.02
32 4 0.06
33 61 0.92
ACGTcount: A:0.12, C:0.27, G:0.38, T:0.23
Consensus pattern (33 bp):
TCGCGTGGCCGGTTGTAGCCGGACATGTCCATG
Found at i:13749 original size:28 final size:28
Alignment explanation
Indices: 13717--13789 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
13707 GGGTCATCCA
13717 GGGGCATTTTGGTCATTTTCACATCTAG
1 GGGGCATTTTGGTCATTTTCACATCTAG
** *
13745 GGGGCATTTTGGTCATTTTTGCATTTAG
1 GGGGCATTTTGGTCATTTTCACATCTAG
*
13773 GGGGTATTTTGGTCATT
1 GGGGCATTTTGGTCATT
13790 CTTAATCTAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.15, C:0.12, G:0.29, T:0.44
Consensus pattern (28 bp):
GGGGCATTTTGGTCATTTTCACATCTAG
Found at i:17465 original size:40 final size:38
Alignment explanation
Indices: 17374--17469 Score: 113
Period size: 38 Copynumber: 2.5 Consensus size: 38
17364 AGTGAAAAGA
* *
17374 AAAAGTAGTAATCAGTCAATTAGTAACTAAGAGGAAGT
1 AAAAGTAGTAATCAGTAAATTAGTAACCAAGAGGAAGT
* *
17412 AAAAGGATTAATCAGTAAATT-GATAACCAAGAGAAGAAGT
1 AAAAGTAGTAATCAGTAAATTAG-TAACCAAGAG--GAAGT
*
17452 AAAAGTAGCAATCAGTAA
1 AAAAGTAGTAATCAGTAA
17470 GTAAGGGTCA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 1 0.02
38 27 0.56
40 20 0.42
ACGTcount: A:0.51, C:0.08, G:0.20, T:0.21
Consensus pattern (38 bp):
AAAAGTAGTAATCAGTAAATTAGTAACCAAGAGGAAGT
Found at i:17531 original size:32 final size:31
Alignment explanation
Indices: 17461--17533 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 31
17451 TAAAAGTAGC
*
17461 AATCAGTAAGTAAGGGTCAAAGTAAAAGGGT
1 AATCAGTAAGTAAGAGTCAAAGTAAAAGGGT
* * * *
17492 AAGTCAGTAATTAAGAGTCAAGGTAGAAGGATT
1 AA-TCAGTAAGTAAGAGTCAAAGTAAAAGG-GT
17525 AATCAGTAA
1 AATCAGTAA
17534 ATTGATAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 2 0.06
32 30 0.86
33 3 0.09
ACGTcount: A:0.45, C:0.07, G:0.26, T:0.22
Consensus pattern (31 bp):
AATCAGTAAGTAAGAGTCAAAGTAAAAGGGT
Found at i:17682 original size:32 final size:32
Alignment explanation
Indices: 17607--17716 Score: 136
Period size: 32 Copynumber: 3.5 Consensus size: 32
17597 TTAAAAAAAA
* *
17607 AAAAGAAGTAATCAGTAGAAAGAAAT-AAA--
1 AAAAGAAGTAATCAGTAGAATGAAGTGAAAGT
* * *
17636 AGAGGAAGTGATCAGTAGAATGAAGTGAAAGT
1 AAAAGAAGTAATCAGTAGAATGAAGTGAAAGT
* *
17668 AAAAGAAGTAATCAGTAAAATGGAGTGAAAGT
1 AAAAGAAGTAATCAGTAGAATGAAGTGAAAGT
17700 AAAAGAAGTAATCAGTA
1 AAAAGAAGTAATCAGTA
17717 AGTTGGTAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
29 21 0.31
30 3 0.04
32 44 0.65
ACGTcount: A:0.55, C:0.04, G:0.25, T:0.17
Consensus pattern (32 bp):
AAAAGAAGTAATCAGTAGAATGAAGTGAAAGT
Found at i:17740 original size:40 final size:40
Alignment explanation
Indices: 17695--17837 Score: 259
Period size: 40 Copynumber: 3.6 Consensus size: 40
17685 AAATGGAGTG
17695 AAAGTAAAAGAAGTAATCAGTAAGTTGGTAATTAAGAATA
1 AAAGTAAAAGAAGTAATCAGTAAGTTGGTAATTAAGAATA
17735 AAAGTAAAAGAAGTAATCAGTAAGTTGGTAATTAAGAATA
1 AAAGTAAAAGAAGTAATCAGTAAGTTGGTAATTAAGAATA
** *
17775 AAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAAGAGTA
1 AAAGTAAAAGAAGTAATCAGTAAGTTGGTAATTAAGAATA
17815 AAAGTAAAAGAAGTAATCAGTAA
1 AAAGTAAAAGAAGTAATCAGTAA
17838 ATCGGTAAAG
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 100 1.00
ACGTcount: A:0.55, C:0.03, G:0.20, T:0.23
Consensus pattern (40 bp):
AAAGTAAAAGAAGTAATCAGTAAGTTGGTAATTAAGAATA
Found at i:17862 original size:16 final size:17
Alignment explanation
Indices: 17836--17890 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 17
17826 AGTAATCAGT
17836 AAATCGGTAAAGAGTAA
1 AAATCGGTAAAGAGTAA
*
17853 AAAT-GGTAAAAAGTAA
1 AAATCGGTAAAGAGTAA
*
17869 GAGTAATCAGTAAAGAGTAA
1 -A--AATCGGTAAAGAGTAA
17889 AA
1 AA
17891 TGGTAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 11 0.35
17 6 0.19
19 4 0.13
20 10 0.32
ACGTcount: A:0.56, C:0.04, G:0.22, T:0.18
Consensus pattern (17 bp):
AAATCGGTAAAGAGTAA
Found at i:17862 original size:40 final size:39
Alignment explanation
Indices: 17695--17890 Score: 153
Period size: 40 Copynumber: 5.0 Consensus size: 39
17685 AAATGGAGTG
* *
17695 AAAGTAAAAGAAGTAATCAGTAAGTTGGTAATTA-AG-AATA
1 AAAGTAAAAGAAGTAATCAGTAAATCGGTAA--AGAGTAA-A
* *
17735 AAAGTAAAAGAAGTAATCAGTAAGTTGGTAATTA-AG-AATA
1 AAAGTAAAAGAAGTAATCAGTAAATCGGTAA--AGAGTAA-A
17775 AAAGTAAAAGAAGTAATCAGTAAAAT-GGTAATTAAGAGT--A
1 AAAGTAAAAGAAGTAATCAGT-AAATCGGT-A--AAGAGTAAA
17815 AAAGTAAAAGAAGTAATCAGTAAATCGGTAAAGAGTAAA
1 AAAGTAAAAGAAGTAATCAGTAAATCGGTAAAGAGTAAA
* * *
17854 AATGGT-AAA-AAGTAA-GAGT-AATCAGTAAAGAGTAAA
1 AA-AGTAAAAGAAGTAATCAGTAAATCGGTAAAGAGTAAA
17890 A
1 A
17891 TGGTAAAAAT
Statistics
Matches: 142, Mismatches: 4, Indels: 24
0.84 0.02 0.14
Matches are distributed among these distances:
36 17 0.12
37 9 0.06
38 6 0.04
39 11 0.08
40 91 0.64
41 5 0.04
42 2 0.01
43 1 0.01
ACGTcount: A:0.55, C:0.03, G:0.20, T:0.22
Consensus pattern (39 bp):
AAAGTAAAAGAAGTAATCAGTAAATCGGTAAAGAGTAAA
Found at i:17919 original size:35 final size:36
Alignment explanation
Indices: 17844--17968 Score: 116
Period size: 35 Copynumber: 3.5 Consensus size: 36
17834 GTAAATCGGT
* * *
17844 AAAGAGTAAAAATGGTAAAAA--GTAAGAGTAATCAGT
1 AAAGAGTAAAAATGGTAAAAATGGTAA-ATTAATTA-C
17880 AAAGAGT-AAAATGGTAAAAATGGTAAATTAATTAC
1 AAAGAGTAAAAATGGTAAAAATGGTAAATTAATTAC
* * *
17915 AAAGAGTAAAAATAG-ACAAATGGTGAATTAAATT-C
1 AAAGAGTAAAAATGGTAAAAATGGTAAATT-AATTAC
*
17950 AAAGAGTGAAAAATAGTAA
1 AAAGAGT-AAAAATGGTAA
17969 TTAAATTCAA
Statistics
Matches: 76, Mismatches: 7, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
35 40 0.53
36 31 0.41
37 5 0.07
ACGTcount: A:0.56, C:0.03, G:0.19, T:0.22
Consensus pattern (36 bp):
AAAGAGTAAAAATGGTAAAAATGGTAAATTAATTAC
Found at i:17988 original size:26 final size:26
Alignment explanation
Indices: 17940--17995 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 26
17930 ACAAATGGTG
17940 AATTAAATTCAAAGAGTGAAAAATAGT
1 AATTAAATTCAAAGAGT-AAAAATAGT
17967 AATTAAATTCAAGAGAGT-AAAATAGT
1 AATTAAATTCAA-AGAGTAAAAATAGT
17993 AAT
1 AAT
17996 CAGTAAAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 11 0.39
27 12 0.43
28 5 0.18
ACGTcount: A:0.55, C:0.04, G:0.14, T:0.27
Consensus pattern (26 bp):
AATTAAATTCAAAGAGTAAAAATAGT
Found at i:18020 original size:7 final size:7
Alignment explanation
Indices: 17997--18071 Score: 64
Period size: 7 Copynumber: 10.9 Consensus size: 7
17987 AATAGTAATC
17997 AGTAAAG
1 AGTAAAG
*
18004 AGAAAAG
1 AGTAAAG
18011 AGTAAAG
1 AGTAAAG
**
18018 AGTAATC
1 AGTAAAG
18025 AGT-AAG
1 AGTAAAG
*
18031 AGTAAAA
1 AGTAAAG
*
18038 AGGTAAAA
1 A-GTAAAG
18046 AGTAAAG
1 AGTAAAG
**
18053 AGTAATC
1 AGTAAAG
18060 AGTAAA-
1 AGTAAAG
18066 AGTAAA
1 AGTAAA
18072 AGAATAATTA
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
6 10 0.18
7 38 0.69
8 7 0.13
ACGTcount: A:0.59, C:0.03, G:0.23, T:0.16
Consensus pattern (7 bp):
AGTAAAG
Found at i:18029 original size:28 final size:28
Alignment explanation
Indices: 17980--18050 Score: 92
Period size: 28 Copynumber: 2.5 Consensus size: 28
17970 TAAATTCAAG
17980 AGAGTAAAATAGTAATCAGTAAAGAG-AAA
1 AGAGTAAAA-AGTAATCAGT-AAGAGTAAA
*
18009 AGAGTAAAGAGTAATCAGTAAGAGTAAA
1 AGAGTAAAAAGTAATCAGTAAGAGTAAA
18037 A-AGGTAAAAAGTAA
1 AGA-GTAAAAAGTAA
18051 AGAGTAATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
27 6 0.16
28 24 0.63
29 8 0.21
ACGTcount: A:0.58, C:0.03, G:0.23, T:0.17
Consensus pattern (28 bp):
AGAGTAAAAAGTAATCAGTAAGAGTAAA
Found at i:18056 original size:28 final size:30
Alignment explanation
Indices: 17980--18066 Score: 76
Period size: 28 Copynumber: 3.0 Consensus size: 30
17970 TAAATTCAAG
*
17980 AGAGTAAAATAGTAATCAGTAA--AG-AGAAA
1 AGAGTAAAA-AGTAAACAGTAATCAGTA-AAA
* * *
18009 AGAGTAAAGAGTAATCAGTAA-GAGTAAAA
1 AGAGTAAAAAGTAAACAGTAATCAGTAAAA
*
18038 AG-GTAAAAAGTAAAGAGTAATCAGTAAAA
1 AGAGTAAAAAGTAAACAGTAATCAGTAAAA
18067 GTAAAAGAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
28 27 0.54
29 22 0.44
30 1 0.02
ACGTcount: A:0.57, C:0.03, G:0.22, T:0.17
Consensus pattern (30 bp):
AGAGTAAAAAGTAAACAGTAATCAGTAAAA
Found at i:18160 original size:32 final size:32
Alignment explanation
Indices: 18118--18197 Score: 133
Period size: 32 Copynumber: 2.5 Consensus size: 32
18108 AATAAAAGAG
* *
18118 GAAGTGATCAGTAGAACGGAGTGAAAGTAAAA
1 GAAGTAATCAGTAAAACGGAGTGAAAGTAAAA
*
18150 GAAGTAATCAGTAAAATGGAGTGAAAGTAAAA
1 GAAGTAATCAGTAAAACGGAGTGAAAGTAAAA
18182 GAAGTAATCAGTAAAA
1 GAAGTAATCAGTAAAA
18198 GAGTAAAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.51, C:0.05, G:0.26, T:0.17
Consensus pattern (32 bp):
GAAGTAATCAGTAAAACGGAGTGAAAGTAAAA
Found at i:18162 original size:16 final size:16
Alignment explanation
Indices: 18143--18203 Score: 74
Period size: 16 Copynumber: 3.9 Consensus size: 16
18133 ACGGAGTGAA
18143 AGTAAAAGAAGTAATC
1 AGTAAAAGAAGTAATC
*
18159 AGTAAAATGGAGTGAA--
1 AGTAAAA-GAAGT-AATC
18175 AGTAAAAGAAGTAATC
1 AGTAAAAGAAGTAATC
18191 AGTAAAAG-AGTAA
1 AGTAAAAGAAGTAA
18204 AAATGGTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
14 2 0.05
15 9 0.23
16 22 0.56
17 4 0.10
18 2 0.05
ACGTcount: A:0.56, C:0.03, G:0.23, T:0.18
Consensus pattern (16 bp):
AGTAAAAGAAGTAATC
Found at i:18274 original size:33 final size:32
Alignment explanation
Indices: 18232--18340 Score: 115
Period size: 32 Copynumber: 3.5 Consensus size: 32
18222 AGTAATCCGT
18232 AAAGAGTAAAATGGTAAAATGGTAATTAAATTC
1 AAAGAGTAAAAT-GTAAAATGGTAATTAAATTC
*
18265 AAAGAGTAAAATG-ACAAATGGTGATTAAATTC
1 AAAGAGTAAAATGTA-AAATGGTAATTAAATTC
*
18297 AAAGAG-----TG-AAAATAGTAATTAAATTC
1 AAAGAGTAAAATGTAAAATGGTAATTAAATTC
18323 AAGAGAGTAAAATAGTAA
1 AA-AGAGTAAAAT-GTAA
18341 TCAGTAAAGA
Statistics
Matches: 64, Mismatches: 3, Indels: 17
0.76 0.04 0.20
Matches are distributed among these distances:
26 17 0.27
27 7 0.11
31 1 0.02
32 24 0.38
33 13 0.20
34 2 0.03
ACGTcount: A:0.53, C:0.04, G:0.18, T:0.25
Consensus pattern (32 bp):
AAAGAGTAAAATGTAAAATGGTAATTAAATTC
Found at i:18292 original size:32 final size:33
Alignment explanation
Indices: 18232--18314 Score: 116
Period size: 32 Copynumber: 2.5 Consensus size: 33
18222 AGTAATCCGT
18232 AAAGAGTAAAATGGTAAAATGGTAATTAAATTC
1 AAAGAGTAAAATGGTAAAATGGTAATTAAATTC
*
18265 AAAGAGTAAAAT-G-ACAAATGGTGATTAAATTC
1 AAAGAGTAAAATGGTA-AAATGGTAATTAAATTC
*
18297 AAAGAGTGAAAATAGTAA
1 AAAGAGT-AAAATGGTAA
18315 TTAAATTCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
31 1 0.02
32 24 0.53
33 17 0.38
34 2 0.04
35 1 0.02
ACGTcount: A:0.53, C:0.04, G:0.19, T:0.24
Consensus pattern (33 bp):
AAAGAGTAAAATGGTAAAATGGTAATTAAATTC
Found at i:18317 original size:26 final size:26
Alignment explanation
Indices: 18247--18341 Score: 93
Period size: 26 Copynumber: 3.4 Consensus size: 26
18237 GTAAAATGGT
*
18247 AAAATGGTAATTAAATTCAAAGAGTAAAATG
1 AAAATAGTAATTAAATTCAAAGAG-----TG
* *
18278 ACAAATGGTGATTAAATTCAAAGAGTG
1 A-AAATAGTAATTAAATTCAAAGAGTG
18305 AAAATAGTAATTAAATTCAAGAGAGT-
1 AAAATAGTAATTAAATTCAA-AGAGTG
18331 AAAATAGTAAT
1 AAAATAGTAAT
18342 CAGTAAAGAG
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
26 28 0.47
27 8 0.14
31 1 0.02
32 22 0.37
ACGTcount: A:0.53, C:0.04, G:0.17, T:0.26
Consensus pattern (26 bp):
AAAATAGTAATTAAATTCAAAGAGTG
Found at i:18366 original size:7 final size:7
Alignment explanation
Indices: 18343--18417 Score: 64
Period size: 7 Copynumber: 10.9 Consensus size: 7
18333 AATAGTAATC
18343 AGTAAAG
1 AGTAAAG
*
18350 AGAAAAG
1 AGTAAAG
18357 AGTAAAG
1 AGTAAAG
**
18364 AGTAATC
1 AGTAAAG
18371 AGT-AAG
1 AGTAAAG
*
18377 AGTAAAA
1 AGTAAAG
*
18384 AGGTAAAA
1 A-GTAAAG
18392 AGTAAAG
1 AGTAAAG
**
18399 AGTAATC
1 AGTAAAG
18406 AGTAAA-
1 AGTAAAG
18412 AGTAAA
1 AGTAAA
18418 AGAATAAATT
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
6 10 0.18
7 38 0.69
8 7 0.13
ACGTcount: A:0.59, C:0.03, G:0.23, T:0.16
Consensus pattern (7 bp):
AGTAAAG
Found at i:18375 original size:28 final size:28
Alignment explanation
Indices: 18326--18396 Score: 92
Period size: 28 Copynumber: 2.5 Consensus size: 28
18316 TAAATTCAAG
18326 AGAGTAAAATAGTAATCAGTAAAGAG-AAA
1 AGAGTAAAA-AGTAATCAGT-AAGAGTAAA
*
18355 AGAGTAAAGAGTAATCAGTAAGAGTAAA
1 AGAGTAAAAAGTAATCAGTAAGAGTAAA
18383 A-AGGTAAAAAGTAA
1 AGA-GTAAAAAGTAA
18397 AGAGTAATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
27 6 0.16
28 24 0.63
29 8 0.21
ACGTcount: A:0.58, C:0.03, G:0.23, T:0.17
Consensus pattern (28 bp):
AGAGTAAAAAGTAATCAGTAAGAGTAAA
Found at i:18402 original size:28 final size:30
Alignment explanation
Indices: 18326--18412 Score: 76
Period size: 28 Copynumber: 3.0 Consensus size: 30
18316 TAAATTCAAG
*
18326 AGAGTAAAATAGTAATCAGTAA--AG-AGAAA
1 AGAGTAAAA-AGTAAACAGTAATCAGTA-AAA
* * *
18355 AGAGTAAAGAGTAATCAGTAA-GAGTAAAA
1 AGAGTAAAAAGTAAACAGTAATCAGTAAAA
*
18384 AG-GTAAAAAGTAAAGAGTAATCAGTAAAA
1 AGAGTAAAAAGTAAACAGTAATCAGTAAAA
18413 GTAAAAGAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
28 27 0.54
29 22 0.44
30 1 0.02
ACGTcount: A:0.57, C:0.03, G:0.22, T:0.17
Consensus pattern (30 bp):
AGAGTAAAAAGTAAACAGTAATCAGTAAAA
Found at i:18507 original size:32 final size:32
Alignment explanation
Indices: 18465--18542 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 32
18455 AATAAAAGAG
* *
18465 GAAGTGATCAGTAGAACGGAGTGAAAGTAAAA
1 GAAGTAATCAGTAAAACGGAGTGAAAGTAAAA
*
18497 GAAGTAATCAGTAAAATGGAGTGAAAGTAAAA
1 GAAGTAATCAGTAAAACGGAGTGAAAGTAAAA
18529 GAAGTAATCAGTAA
1 GAAGTAATCAGTAA
18543 GTTGGTAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.50, C:0.05, G:0.27, T:0.18
Consensus pattern (32 bp):
GAAGTAATCAGTAAAACGGAGTGAAAGTAAAA
Found at i:18509 original size:16 final size:16
Alignment explanation
Indices: 18490--18542 Score: 65
Period size: 16 Copynumber: 3.3 Consensus size: 16
18480 ACGGAGTGAA
18490 AGTAAAAGAAGTAATC
1 AGTAAAAGAAGTAATC
*
18506 AGTAAAATGGAGTGAA--
1 AGTAAAA-GAAGT-AATC
18522 AGTAAAAGAAGTAATC
1 AGTAAAAGAAGTAATC
18538 AGTAA
1 AGTAA
18543 GTTGGTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 2 0.06
15 4 0.13
16 19 0.61
17 4 0.13
18 2 0.06
ACGTcount: A:0.55, C:0.04, G:0.23, T:0.19
Consensus pattern (16 bp):
AGTAAAAGAAGTAATC
Found at i:18565 original size:40 final size:40
Alignment explanation
Indices: 18515--18623 Score: 182
Period size: 40 Copynumber: 2.7 Consensus size: 40
18505 CAGTAAAATG
* **
18515 GAGTGAAAGTAAAAGAAGTAATCAGTAAGTTGGTAATTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
18555 GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
*
18595 GAGTAAAAGTAAAAGAAATAATCAGTAAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAA
18624 TCGGTAAAGA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.54, C:0.03, G:0.21, T:0.22
Consensus pattern (40 bp):
GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
Found at i:18567 original size:347 final size:352
Alignment explanation
Indices: 17844--18542 Score: 1315
Period size: 347 Copynumber: 2.0 Consensus size: 352
17834 GTAAATCGGT
17844 AAAGAGTAAAAATGGTAAAAAGT-AAGAGTAATCAGTAAAGAGTAAAATGGTAAAAATGGTAAAT
1 AAAGAGTAAAAATGGTAAAAAGTAAAGAGTAATCAGTAAAGAGTAAAATGGTAAAAATGGTAAAT
17908 TAATTACAAAGAGTAAAAATAGACAAATGGTGAATTAAATTCAAAGAGTGAAAAATAGTAATTAA
66 TAATTACAAAGAGTAAAAATAGACAAATGGTGAATTAAATTCAAAGAGTGAAAAATAGTAATTAA
17973 ATTCAAGAGAGTAAAATAGTAATCAGTAAAGAGAAAAGAGTAAAGAGTAATCAGTAAGAGTAAAA
131 ATTCAAGAGAGTAAAATAGTAATCAGTAAAGAGAAAAGAGTAAAGAGTAATCAGTAAGAGTAAAA
18038 AGGTAAAAAGTAAAGAGTAATCAGTAAAAGTAAAAGAATAATTAAAAAAAAAAAGTAATCAGTAG
196 AGGTAAAAAGTAAAGAGTAATCAGTAAAAGTAAAAGAATAATTAAAAAAAAAAAGTAATCAGTAG
18103 AAAGAAATAAAAGAGGAAGTGATCAGTAGAACGGAGTGAAAGTAAAAGAAGTAATCAGTAAAATG
261 AAAGAAATAAAAGAGGAAGTGATCAGTAGAACGGAGTGAAAGTAAAAGAAGTAATCAGTAAAATG
18168 GAGTGAAAGTAAAAGAAGTAATCAGTA
326 GAGTGAAAGTAAAAGAAGTAATCAGTA
*
18195 AAAGAGTAAAAATGGTAAAAAGTAAAGAGTAATCCGTAAAGAGTAAAATGGT-AAAATGGT-AAT
1 AAAGAGTAAAAATGGTAAAAAGTAAAGAGTAATCAGTAAAGAGTAAAATGGTAAAAATGGTAAAT
18258 TAAATT-CAAAGAGT-AAAAT-GACAAATGGTG-ATTAAATTCAAAGAGTG-AAAATAGTAATTA
66 T-AATTACAAAGAGTAAAAATAGACAAATGGTGAATTAAATTCAAAGAGTGAAAAATAGTAATTA
18318 AATTCAAGAGAGTAAAATAGTAATCAGTAAAGAGAAAAGAGTAAAGAGTAATCAGTAAGAGTAAA
130 AATTCAAGAGAGTAAAATAGTAATCAGTAAAGAGAAAAGAGTAAAGAGTAATCAGTAAGAGTAAA
18383 AAGGTAAAAAGTAAAGAGTAATCAGTAAAAGTAAAAGAATAAATTAAAAAAAAAAAGTAATCAGT
195 AAGGTAAAAAGTAAAGAGTAATCAGTAAAAGTAAAAGAAT-AATTAAAAAAAAAAAGTAATCAGT
18448 AGAAAGAAATAAAAGAGGAAGTGATCAGTAGAACGGAGTGAAAGTAAAAGAAGTAATCAGTAAAA
259 AGAAAGAAATAAAAGAGGAAGTGATCAGTAGAACGGAGTGAAAGTAAAAGAAGTAATCAGTAAAA
18513 TGGAGTGAAAGTAAAAGAAGTAATCAGTA
324 TGGAGTGAAAGTAAAAGAAGTAATCAGTA
18542 A
1 A
18543 GTTGGTAATT
Statistics
Matches: 344, Mismatches: 1, Indels: 10
0.97 0.00 0.03
Matches are distributed among these distances:
346 118 0.34
347 136 0.40
348 11 0.03
349 5 0.01
350 12 0.03
351 35 0.10
352 27 0.08
ACGTcount: A:0.56, C:0.04, G:0.21, T:0.19
Consensus pattern (352 bp):
AAAGAGTAAAAATGGTAAAAAGTAAAGAGTAATCAGTAAAGAGTAAAATGGTAAAAATGGTAAAT
TAATTACAAAGAGTAAAAATAGACAAATGGTGAATTAAATTCAAAGAGTGAAAAATAGTAATTAA
ATTCAAGAGAGTAAAATAGTAATCAGTAAAGAGAAAAGAGTAAAGAGTAATCAGTAAGAGTAAAA
AGGTAAAAAGTAAAGAGTAATCAGTAAAAGTAAAAGAATAATTAAAAAAAAAAAGTAATCAGTAG
AAAGAAATAAAAGAGGAAGTGATCAGTAGAACGGAGTGAAAGTAAAAGAAGTAATCAGTAAAATG
GAGTGAAAGTAAAAGAAGTAATCAGTA
Found at i:18647 original size:16 final size:17
Alignment explanation
Indices: 18621--18654 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
18611 AATAATCAGT
*
18621 AAATCGGTAAAGAGTAA
1 AAATCGGTAAAAAGTAA
18638 AAAT-GGTAAAAAGTAA
1 AAATCGGTAAAAAGTAA
18654 A
1 A
18655 GAGTAATCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.59, C:0.03, G:0.21, T:0.18
Consensus pattern (17 bp):
AAATCGGTAAAAAGTAA
Found at i:18648 original size:40 final size:39
Alignment explanation
Indices: 18515--18639 Score: 166
Period size: 40 Copynumber: 3.2 Consensus size: 39
18505 CAGTAAAATG
* * *
18515 GAGTGAAAGTAAAAGAAGTAATCAGTAAGTTGGTAATTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAATCGGTAA-TAA
18555 GAGTAAAAGTAAAAGAAGTAATCAGTAAAAT-GGTAATTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGT-AAATCGGTAA-TAA
*
18595 GAGTAAAAGTAAAAGAAATAATCAGTAAATCGGT-A-AA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAATCGGTAATAA
18632 GAGTAAAA
1 GAGTAAAA
18640 ATGGTAAAAA
Statistics
Matches: 80, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
37 10 0.12
39 5 0.06
40 62 0.77
41 3 0.04
ACGTcount: A:0.54, C:0.03, G:0.22, T:0.22
Consensus pattern (39 bp):
GAGTAAAAGTAAAAGAAGTAATCAGTAAATCGGTAATAA
Found at i:18726 original size:32 final size:33
Alignment explanation
Indices: 18666--18748 Score: 116
Period size: 32 Copynumber: 2.5 Consensus size: 33
18656 AGTAATCCGT
18666 AAAGAGTAAAATGGTAAAATGGTAATTAAATTC
1 AAAGAGTAAAATGGTAAAATGGTAATTAAATTC
*
18699 AAAGAGTAAAAT-G-ACAAATGGTGATTAAATTC
1 AAAGAGTAAAATGGTA-AAATGGTAATTAAATTC
*
18731 AAAGAGTGAAAATAGTAA
1 AAAGAGT-AAAATGGTAA
18749 TTAAATTCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
31 1 0.02
32 24 0.53
33 17 0.38
34 2 0.04
35 1 0.02
ACGTcount: A:0.53, C:0.04, G:0.19, T:0.24
Consensus pattern (33 bp):
AAAGAGTAAAATGGTAAAATGGTAATTAAATTC
Found at i:18771 original size:24 final size:26
Alignment explanation
Indices: 18681--18773 Score: 91
Period size: 32 Copynumber: 3.4 Consensus size: 26
18671 GTAAAATGGT
*
18681 AAAATGGTAATTAAATTCAAAGAGTAAAATG
1 AAAATAGTAATTAAATTCAAAGAG-----TG
* *
18712 ACAAATGGTGATTAAATTCAAAGAGTG
1 A-AAATAGTAATTAAATTCAAAGAGTG
18739 AAAATAGTAATTAAATTC-AAGAGT-
1 AAAATAGTAATTAAATTCAAAGAGTG
18763 AAAATAGTAAT
1 AAAATAGTAAT
18774 CAGTAAAGAG
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
24 11 0.19
25 6 0.10
26 15 0.26
27 3 0.05
31 1 0.02
32 22 0.38
ACGTcount: A:0.53, C:0.04, G:0.16, T:0.27
Consensus pattern (26 bp):
AAAATAGTAATTAAATTCAAAGAGTG
Found at i:18813 original size:7 final size:7
Alignment explanation
Indices: 18775--18850 Score: 64
Period size: 7 Copynumber: 10.9 Consensus size: 7
18765 AATAGTAATC
18775 AGTAAAG
1 AGTAAAG
*
18782 AGAAAAG
1 AGTAAAG
18789 AGTAAAG
1 AGTAAAG
* **
18796 AATAATC
1 AGTAAAG
18803 AGTAAAG
1 AGTAAAG
*
18810 AGTAAAA
1 AGTAAAG
*
18817 AGGTAAAA
1 A-GTAAAG
18825 AGTAAAG
1 AGTAAAG
**
18832 AGTAATC
1 AGTAAAG
18839 AGTAAA-
1 AGTAAAG
18845 AGTAAA
1 AGTAAA
18851 AATGGCAAAG
Statistics
Matches: 55, Mismatches: 13, Indels: 3
0.77 0.18 0.04
Matches are distributed among these distances:
6 6 0.11
7 42 0.76
8 7 0.13
ACGTcount: A:0.61, C:0.03, G:0.21, T:0.16
Consensus pattern (7 bp):
AGTAAAG
Found at i:18838 original size:36 final size:37
Alignment explanation
Indices: 18784--18957 Score: 138
Period size: 40 Copynumber: 4.8 Consensus size: 37
18774 CAGTAAAGAG
* *
18784 AAAAGAGTAAAGAATAATCAGTAAAGAGTAAAAA-GGT
1 AAAAGAGTAAAGAGTAATCAGTAAA-AGTAAAAATGGC
18821 AAAA-AGTAAAGAGTAATCAGTAAAAGTAAAAATGGC
1 AAAAGAGTAAAGAGTAATCAGTAAAAGTAAAAATGGC
*
18857 AAAGAGCAGTAAAAAGTAATCAGGTAAAAGT---AAT---
1 AAA-AG-AGTAAAGAGTAATCA-GTAAAAGTAAAAATGGC
* *
18891 ----TAGTAAAGAGTAATCAGTAAAAAGTAAAAATGAC
1 AAAAGAGTAAAGAGTAATCAGT-AAAAGTAAAAATGGC
*
18925 AAAGAGTAGTAAAAAGTAATCAGGTAAAAGTAA
1 AAA-AG-AGTAAAGAGTAATCA-GTAAAAGTAA
18958 TCAGTAAAGA
Statistics
Matches: 111, Mismatches: 7, Indels: 35
0.73 0.05 0.23
Matches are distributed among these distances:
27 2 0.02
28 20 0.18
31 3 0.03
35 8 0.07
36 24 0.22
37 8 0.07
39 14 0.13
40 30 0.27
41 2 0.02
ACGTcount: A:0.57, C:0.05, G:0.20, T:0.18
Consensus pattern (37 bp):
AAAAGAGTAAAGAGTAATCAGTAAAAGTAAAAATGGC
Found at i:18852 original size:7 final size:7
Alignment explanation
Indices: 18803--18920 Score: 51
Period size: 7 Copynumber: 16.1 Consensus size: 7
18793 AAGAATAATC
*
18803 AGTAAAG
1 AGTAAAA
18810 AGTAAAA
1 AGTAAAA
18817 AGGTAAAA
1 A-GTAAAA
*
18825 AGTAAAG
1 AGTAAAA
**
18832 AGTAATC
1 AGTAAAA
18839 AGT-AAA
1 AGTAAAA
18845 AGTAAAA
1 AGTAAAA
*
18852 ATGGCAAAGA
1 A--GTAAA-A
18862 GCAGTAAAA
1 --AGTAAAA
*
18871 AGTAATCA
1 AGTAA-AA
*
18879 GGT-AAA
1 AGTAAAA
**
18885 AGTAATT
1 AGTAAAA
*
18892 AGTAAAG
1 AGTAAAA
**
18899 AGTAATC
1 AGTAAAA
18906 AGTAAAA
1 AGTAAAA
18913 AGTAAAA
1 AGTAAAA
18920 A
1 A
18921 TGACAAAGAG
Statistics
Matches: 82, Mismatches: 20, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
6 7 0.09
7 54 0.66
8 10 0.12
9 5 0.06
10 5 0.06
12 1 0.01
ACGTcount: A:0.58, C:0.04, G:0.20, T:0.18
Consensus pattern (7 bp):
AGTAAAA
Found at i:18887 original size:14 final size:13
Alignment explanation
Indices: 18863--18971 Score: 80
Period size: 14 Copynumber: 7.9 Consensus size: 13
18853 TGGCAAAGAG
18863 CAGTAAAAAGTAAT
1 CAGT-AAAAGTAAT
18877 CAGGTAAAAGTAAT
1 CA-GTAAAAGTAAT
*
18891 TAGTAAAGAGTAAT
1 CAGTAAA-AGTAAT
18905 CAGTAAAAAGTAA-
1 CAGT-AAAAGTAAT
* * *
18918 AAATGACAAAG-AGT
1 CAGT-A-AAAGTAAT
18932 -AGTAAAAAGTAAT
1 CAGT-AAAAGTAAT
18945 CAGGTAAAAGTAAT
1 CA-GTAAAAGTAAT
18959 CAGTAAAGAGTAA
1 CAGTAAA-AGTAA
18972 AAGAGAAGAG
Statistics
Matches: 77, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
12 4 0.05
13 19 0.25
14 47 0.61
15 7 0.09
ACGTcount: A:0.55, C:0.06, G:0.19, T:0.20
Consensus pattern (13 bp):
CAGTAAAAGTAAT
Found at i:18902 original size:28 final size:28
Alignment explanation
Indices: 18864--18971 Score: 91
Period size: 28 Copynumber: 3.9 Consensus size: 28
18854 GGCAAAGAGC
18864 AGTAAAAAGTAATCAGGT-AAAAGTAATT
1 AGTAAAAAGTAATCA-GTAAAAAGTAATT
* *
18892 AGTAAAGAGTAATCAGTAAAAAGTAA-A
1 AGTAAAAAGTAATCAGTAAAAAGTAATT
* * * *
18919 AATGACAAAG-AGT-AGTAAAAAGTAATC
1 AGT-AAAAAGTAATCAGTAAAAAGTAATT
*
18946 AGGT-AAAAGTAATCAGTAAAGAGTAA
1 A-GTAAAAAGTAATCAGTAAAAAGTAA
18972 AAGAGAAGAG
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
26 16 0.25
27 9 0.14
28 38 0.60
ACGTcount: A:0.56, C:0.05, G:0.19, T:0.20
Consensus pattern (28 bp):
AGTAAAAAGTAATCAGTAAAAAGTAATT
Found at i:18920 original size:68 final size:67
Alignment explanation
Indices: 18825--18971 Score: 258
Period size: 68 Copynumber: 2.2 Consensus size: 67
18815 AAAGGTAAAA
*
18825 AGTAAAGAGTAATCAGTAAAAGTAAAAATGGCAAAGAGCAGTAAAAAGTAATCAGGTAAAAGTAA
1 AGTAAAGAGTAATCAGTAAAAGTAAAAATGACAAAGAGCAGTAAAAAGTAATCAGGTAAAAGTAA
*
18890 TT
66 TC
*
18892 AGTAAAGAGTAATCAGTAAAAAGTAAAAATGACAAAGAGTAGTAAAAAGTAATCAGGTAAAAGTA
1 AGTAAAGAGTAATCAGT-AAAAGTAAAAATGACAAAGAGCAGTAAAAAGTAATCAGGTAAAAGTA
18957 ATC
65 ATC
18960 AGTAAAGAGTAA
1 AGTAAAGAGTAA
18972 AAGAGAAGAG
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
67 17 0.22
68 59 0.78
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.19
Consensus pattern (67 bp):
AGTAAAGAGTAATCAGTAAAAGTAAAAATGACAAAGAGCAGTAAAAAGTAATCAGGTAAAAGTAA
TC
Found at i:18970 original size:7 final size:7
Alignment explanation
Indices: 18960--19092 Score: 51
Period size: 7 Copynumber: 18.9 Consensus size: 7
18950 AAAAGTAATC
18960 AGTAAAG
1 AGTAAAG
18967 AGTAAAAG
1 AGT-AAAG
18975 AG-AAGAG
1 AGTAA-AG
18982 AGTAAAG
1 AGTAAAG
**
18989 AGTAATC
1 AGTAAAG
18996 AGTAAAAG
1 AGT-AAAG
*
19004 AAG-AATG
1 -AGTAAAG
*
19011 -GTAAAA
1 AGTAAAG
19017 AGTAAAG
1 AGTAAAG
**
19024 AGTAATC
1 AGTAAAG
19031 AGTAAAGG
1 AGTAAA-G
* *
19039 AGGAATG
1 AGTAAAG
19046 -GT-AAG
1 AGTAAAG
19051 AGTAAAG
1 AGTAAAG
* **
19058 GGTAATC
1 AGTAAAG
*
19065 AGTAAAA
1 AGTAAAG
**
19072 AGATAATC
1 AG-TAAAG
19080 AGTAAAG
1 AGTAAAG
19087 AGTAAA
1 AGTAAA
19093 ATAGTAAAAG
Statistics
Matches: 89, Mismatches: 26, Indels: 22
0.65 0.19 0.16
Matches are distributed among these distances:
5 3 0.03
6 7 0.08
7 58 0.65
8 19 0.21
9 2 0.02
ACGTcount: A:0.54, C:0.03, G:0.26, T:0.17
Consensus pattern (7 bp):
AGTAAAG
Found at i:19000 original size:36 final size:35
Alignment explanation
Indices: 18955--19036 Score: 71
Period size: 35 Copynumber: 2.3 Consensus size: 35
18945 CAGGTAAAAG
* *
18955 TAATCAGTAAAGAGT-AAAAGAG-AAGAGAGTAAAGAG
1 TAATCAGTAAA-AGTAAAAAG-GTAA-AAAGTAAAGAA
* *
18991 TAATCAGTAAAAG-AAGAATGGTAAAAAGTAAAGAG
1 TAATCAGTAAAAGTAA-AAAGGTAAAAAGTAAAGAA
19026 TAATCAGTAAA
1 TAATCAGTAAA
19037 GGAGGAATGG
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
35 25 0.61
36 16 0.39
ACGTcount: A:0.56, C:0.04, G:0.23, T:0.17
Consensus pattern (35 bp):
TAATCAGTAAAAGTAAAAAGGTAAAAAGTAAAGAA
Found at i:19021 original size:35 final size:34
Alignment explanation
Indices: 18982--19071 Score: 135
Period size: 35 Copynumber: 2.6 Consensus size: 34
18972 AAGAGAAGAG
18982 AGTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAA
1 AGTAAAGAGTAATCAGTAAAAGAAGAATGGT-AAA
* * *
19017 AGTAAAGAGTAATCAGTAAAGGAGGAATGGTAAG
1 AGTAAAGAGTAATCAGTAAAAGAAGAATGGTAAA
*
19051 AGTAAAGGGTAATCAGTAAAA
1 AGTAAAGAGTAATCAGTAAAA
19072 AGATAATCAG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
34 21 0.42
35 29 0.58
ACGTcount: A:0.52, C:0.03, G:0.27, T:0.18
Consensus pattern (34 bp):
AGTAAAGAGTAATCAGTAAAAGAAGAATGGTAAA
Found at i:19028 original size:14 final size:14
Alignment explanation
Indices: 18757--19028 Score: 65
Period size: 14 Copynumber: 18.6 Consensus size: 14
18747 AATTAAATTC
18757 AAGAGTAAAATAGTA
1 AAGAGTAAAA-AGTA
** * *
18772 ATCAGTAAAGAGAA
1 AAGAGTAAAAAGTA
18786 AAGAGTAAAGAA-TA
1 AAGAGTAAA-AAGTA
** *
18800 ATCAGTAAAGAGTA
1 AAGAGTAAAAAGTA
*
18814 AAAAGGTAAAAAGTA
1 AAGA-GTAAAAAGTA
**
18829 AAGAGTAATCAGTA
1 AAGAGTAAAAAGTA
*
18843 AA-AGTAAAAATGGCAA
1 AAGAGTAAAAA--G-TA
18859 AGAGCAGTAAAAAGTA
1 A-AG-AGTAAAAAGTA
18875 ATCAG-GT-AAAAGTA
1 A--AGAGTAAAAAGTA
** *
18889 ATTAGTAAAGAGTA
1 AAGAGTAAAAAGTA
**
18903 ATCAGTAAAAAGTA
1 AAGAGTAAAAAGTA
* *
18917 AAAATGACAAAGAGTAGTA
1 AAGA-G-TAAA-A--AGTA
* * *
18936 AAAAGTAATCAGGTA
1 AAGAGTAA-AAAGTA
**
18951 AA-AGTAATCAGTA
1 AAGAGTAAAAAGTA
18964 AAGAGTAAAAGAG-A
1 AAGAGTAAAA-AGTA
*
18978 AGAGAGTAAAGAGTA
1 A-AGAGTAAAAAGTA
**
18993 ATCAGTAAAAGAAG-A
1 AAGAGT-AAA-AAGTA
*
19008 ATG-GTAAAAAGTA
1 AAGAGTAAAAAGTA
19021 AAGAGTAA
1 AAGAGTAA
19029 TCAGTAAAGG
Statistics
Matches: 187, Mismatches: 44, Indels: 53
0.66 0.15 0.19
Matches are distributed among these distances:
12 3 0.02
13 20 0.11
14 83 0.44
15 47 0.25
16 9 0.05
17 8 0.04
18 1 0.01
19 16 0.09
ACGTcount: A:0.57, C:0.04, G:0.22, T:0.17
Consensus pattern (14 bp):
AAGAGTAAAAAGTA
Found at i:19084 original size:29 final size:28
Alignment explanation
Indices: 19051--19114 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
19041 GAATGGTAAG
*
19051 AGTAAAGGGT-AATCAGTAAAAAGATAATC
1 AGTAAAGAGTAAAT-AGT-AAAAGATAATC
*
19080 AGTAAAGAGTAAAATAGTAAAAGGTAATC
1 AGTAAAGAGT-AAATAGTAAAAGATAATC
19109 AGTAAA
1 AGTAAA
19115 AAAGTAATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 25 0.81
30 3 0.10
31 3 0.10
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (28 bp):
AGTAAAGAGTAAATAGTAAAAGATAATC
Found at i:19121 original size:15 final size:14
Alignment explanation
Indices: 19059--19122 Score: 67
Period size: 15 Copynumber: 4.4 Consensus size: 14
19049 AGAGTAAAGG
19059 GTAATCAGTAAAAA
1 GTAATCAGTAAAAA
*
19073 GATAATCAGTAAAGA
1 G-TAATCAGTAAAAA
*
19088 GTAAAAT-AGTAAAAG
1 GT--AATCAGTAAAAA
19103 GTAATCAGTAAAAAA
1 GTAATCAGT-AAAAA
19118 GTAAT
1 GTAAT
19123 GATAATCAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
13 3 0.07
14 5 0.12
15 30 0.73
16 3 0.07
ACGTcount: A:0.56, C:0.05, G:0.17, T:0.22
Consensus pattern (14 bp):
GTAATCAGTAAAAA
Found at i:19150 original size:43 final size:43
Alignment explanation
Indices: 19059--19490 Score: 237
Period size: 43 Copynumber: 10.3 Consensus size: 43
19049 AGAGTAAAGG
* ** *
19059 GTAATCAGT-AAAAAGATAATCAGTAAAGAGTAAAATAGTAAAA-G
1 GTAATCAGTAAAAAAG-TAATGAGTAATCAGT-AAA-AGTAAAATA
19103 GTAATCAGTAAAAAAGTAATGA-TAATCAGTAAAAGGTAAAATA
1 GTAATCAGTAAAAAAGTAATGAGTAATCAGTAAAA-GTAAAATA
* * * **
19146 GTAATCAGTAAGAGCAA--AATG-GTGATCAGTAAAAATGTAATA
1 GTAATCAGTAA-A-AAAGTAATGAGTAATCAGTAAAAGTAAAATA
* * * * *
19188 ATAATCAGT-AAAAGGTAAAAT-AGTAATCAGTAAGAGCAAAATG
1 GTAATCAGTAAAAAAGT--AATGAGTAATCAGTAAAAGTAAAATA
*
19231 GTGATCAGTAAAAGCAA--AATG-GTAATCAGTAAAGAGTAAAATA
1 GTAATCAGTAAAA--AAGTAATGAGTAATCAGTAAA-AGTAAAATA
19274 GTAATCAGT-AAAAAGTAA-GAAGGTAATCAGTAAAGAGTAAAATA
1 GTAATCAGTAAAAAAGTAATG-A-GTAATCAGTAAA-AGTAAAATA
*
19318 GTAATCAGT----AA--AA-G-GTAATCAGTAAGAGTAAAATA
1 GTAATCAGTAAAAAAGTAATGAGTAATCAGTAAAAGTAAAATA
* * *
19353 GTAATCGGCAAAAAAGTAAAGAGTAATCAGTAAGAAGTCAAAAT-
1 GTAATCAGTAAAAAAGTAATGAGTAATCAGTAA-AAGT-AAAATA
* * *
19397 GTAATCAGTAAAAATGTGAA-AAGGCAATCAGTAAAGAGTAAAAT-
1 GTAATCAGTAAAAAAGT-AATGA-GTAATCAGTAAA-AGTAAAATA
* *
19441 G------GT-AAAAAGTAATG-GTGATCAGTAAAGAGT-AAAGA
1 GTAATCAGTAAAAAAGTAATGAGTAATCAGTAAA-AGTAAAATA
19476 GTAATCAGTAAAAAA
1 GTAATCAGTAAAAAA
19491 AAATGGTAAA
Statistics
Matches: 305, Mismatches: 40, Indels: 88
0.70 0.09 0.20
Matches are distributed among these distances:
34 3 0.01
35 31 0.10
36 13 0.04
37 6 0.02
38 2 0.01
39 6 0.02
40 3 0.01
41 9 0.03
42 47 0.15
43 82 0.27
44 74 0.24
45 28 0.09
46 1 0.00
ACGTcount: A:0.53, C:0.06, G:0.20, T:0.21
Consensus pattern (43 bp):
GTAATCAGTAAAAAAGTAATGAGTAATCAGTAAAAGTAAAATA
Found at i:19153 original size:22 final size:22
Alignment explanation
Indices: 19125--19335 Score: 204
Period size: 22 Copynumber: 9.8 Consensus size: 22
19115 AAAGTAATGA
19125 TAATCAGTAAAAGGTAAAATAG
1 TAATCAGTAAAAGGTAAAATAG
* * *
19147 TAATCAGTAAGA-GCAAAATGG
1 TAATCAGTAAAAGGTAAAATAG
* * *
19168 TGATCAGTAAAAATGT--AATAA
1 TAATCAGT-AAAAGGTAAAATAG
19189 TAATCAGTAAAAGGTAAAATAG
1 TAATCAGTAAAAGGTAAAATAG
* * *
19211 TAATCAGTAAGA-GCAAAATGG
1 TAATCAGTAAAAGGTAAAATAG
* * *
19232 TGATCAGTAAAA-GCAAAATGG
1 TAATCAGTAAAAGGTAAAATAG
19253 TAATCAGT-AAAGAGTAAAATAG
1 TAATCAGTAAAAG-GTAAAATAG
* *
19275 TAATCAGTAAAAAGTAAGAA-GG
1 TAATCAGTAAAAGGTAA-AATAG
19297 TAATCAGT-AAAGAGTAAAATAG
1 TAATCAGTAAAAG-GTAAAATAG
19319 TAATCAGTAAAAGGTAA
1 TAATCAGTAAAAGGTAA
19336 TCAGTAAGAG
Statistics
Matches: 155, Mismatches: 23, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
20 9 0.06
21 62 0.40
22 74 0.48
23 10 0.06
ACGTcount: A:0.52, C:0.06, G:0.20, T:0.22
Consensus pattern (22 bp):
TAATCAGTAAAAGGTAAAATAG
Found at i:19156 original size:15 final size:15
Alignment explanation
Indices: 19059--19156 Score: 50
Period size: 15 Copynumber: 6.7 Consensus size: 15
19049 AGAGTAAAGG
19059 GTAATCAGTAAAA-A
1 GTAATCAGTAAAATA
19073 GATAATCAGTAAAGAGTA
1 G-TAATCAGTAAA-A-TA
* *
19091 -AAAT-AGTAAAA-G
1 GTAATCAGTAAAATA
*
19103 GTAATCAGTAAAAAA
1 GTAATCAGTAAAATA
*
19118 GTAAT--G-ATAATCA
1 GTAATCAGTAAAAT-A
*
19131 GTAA-AAGGTAAAATA
1 GTAATCA-GTAAAATA
19146 GTAATCAGTAA
1 GTAATCAGTAA
19157 GAGCAAAATG
Statistics
Matches: 63, Mismatches: 8, Indels: 25
0.66 0.08 0.26
Matches are distributed among these distances:
12 3 0.05
13 9 0.14
14 9 0.14
15 32 0.51
16 9 0.14
18 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.17, T:0.22
Consensus pattern (15 bp):
GTAATCAGTAAAATA
Found at i:19186 original size:64 final size:62
Alignment explanation
Indices: 19098--19335 Score: 275
Period size: 64 Copynumber: 3.7 Consensus size: 62
19088 GTAAAATAGT
19098 AAAAGGTAATCAGTAAAAAAGTAATGATAATCAGTAAAAGGTAAAATAGTAATCAGTAAGAGC
1 AAAAGGTAATCAGT-AAAAAGTAATGATAATCAGTAAAAGGTAAAATAGTAATCAGTAAGAGC
* *
19161 AAAATGGTGATCAGTAAAAATGTAATAATAATCAGTAAAAGGTAAAATAGTAATCAGTAAGAGC
1 AAAA-GGTAATCAGTAAAAA-GTAATGATAATCAGTAAAAGGTAAAATAGTAATCAGTAAGAGC
* * * *
19225 AAAATGGTGATCAGT-AAAAGCAAAATGGTAATCAGT-AAAGAGTAAAATAGTAATCAGTAAAAA
1 AAAA-GGTAATCAGTAAAAAG--TAATGATAATCAGTAAAAG-GTAAAATAGTAATCAGT-AAGA
*
19288 GT
61 GC
*
19290 AAGAAGGTAATCAGTAAAGAGTAAAAT-AGTAATCAGTAAAAGGTAA
1 AA-AAGGTAATCAGTAAAAAGT--AATGA-TAATCAGTAAAAGGTAA
19336 TCAGTAAGAG
Statistics
Matches: 152, Mismatches: 11, Indels: 21
0.83 0.06 0.11
Matches are distributed among these distances:
62 1 0.01
63 17 0.11
64 94 0.62
65 15 0.10
66 21 0.14
67 4 0.03
ACGTcount: A:0.53, C:0.06, G:0.20, T:0.21
Consensus pattern (62 bp):
AAAAGGTAATCAGTAAAAAGTAATGATAATCAGTAAAAGGTAAAATAGTAATCAGTAAGAGC
Found at i:19378 original size:101 final size:101
Alignment explanation
Indices: 19120--19409 Score: 261
Period size: 101 Copynumber: 2.8 Consensus size: 101
19110 GTAAAAAAGT
* * * * * *
19120 AATGATAATCAGTAAAAGGTAAAATAGTAATCAG-TAAGAGCAAAATG-GTGATCAGTAAAAATG
1 AATGGTAATCAGTAAAA-GCAAAATAGTAATCAGAAAAAAGTAAAA-GAGTAATCAGTAAAAA-G
19183 TAATAA-TAATCAGTAAAAGGTAAAATAGTAATCAGTAAGAGCAA
63 TAA-AAGTAATCAGTAAAAGGTAAAATAGTAATCAGT---A--AA
* * * * *
19227 AATGGTGATCAGTAAAAGCAAAATGGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAAAGTAA
1 AATGGTAATCAGTAAAAGCAAAATAGTAATCAGAAAAAAGTAAAAGAGTAATCAGTAAAAAGTAA
19292 GAAGGTAATCAGT-AAAGAGTAAAATAGTAATCAGT-AA
66 -AA-GTAATCAGTAAAAG-GTAAAATAGTAATCAGTAAA
* * * *
19329 AA-GGTAATCAGTAAGAGTAAAATAGTAATCGGCAAAAAAGT-AAAGAGTAATCAGTAAGAAGTC
1 AATGGTAATCAGTAAAAGCAAAATAGTAATCAG-AAAAAAGTAAAAGAGTAATCAGTAAAAAGT-
19392 AAAATGTAATCAGTAAAA
64 AAAA-GTAATCAGTAAAA
19410 ATGTGAAAAG
Statistics
Matches: 156, Mismatches: 19, Indels: 21
0.80 0.10 0.11
Matches are distributed among these distances:
101 55 0.35
102 15 0.10
106 20 0.13
107 41 0.26
108 25 0.16
ACGTcount: A:0.52, C:0.07, G:0.20, T:0.21
Consensus pattern (101 bp):
AATGGTAATCAGTAAAAGCAAAATAGTAATCAGAAAAAAGTAAAAGAGTAATCAGTAAAAAGTAA
AAGTAATCAGTAAAAGGTAAAATAGTAATCAGTAAA
Found at i:19400 original size:22 final size:21
Alignment explanation
Indices: 19324--19445 Score: 95
Period size: 22 Copynumber: 5.6 Consensus size: 21
19314 AATAGTAATC
*
19324 AGTAAAAGGTAATCAGT-AAG
1 AGTAAAAGGTAATCAGTAAAA
* * *
19344 AGTAAAATAGTAATCGGCAAAAA
1 AGTAAAA-GGTAATCAG-TAAAA
*
19367 AGT-AAAGAGTAATCAGTAAGA
1 AGTAAAAG-GTAATCAGTAAAA
*
19388 AGTCAAAATGTAATCAGTAAAA
1 AGT-AAAAGGTAATCAGTAAAA
* *
19410 ATGTGAAAAGGCAATCAGTAAAG
1 A-GT-AAAAGGTAATCAGTAAAA
19433 AGTAAAATGGTAA
1 AGTAAAA-GGTAA
19446 AAAGTAATGG
Statistics
Matches: 79, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
20 7 0.09
21 17 0.22
22 29 0.37
23 26 0.33
ACGTcount: A:0.52, C:0.07, G:0.21, T:0.20
Consensus pattern (21 bp):
AGTAAAAGGTAATCAGTAAAA
Found at i:19425 original size:23 final size:22
Alignment explanation
Indices: 19377--19439 Score: 65
Period size: 23 Copynumber: 2.9 Consensus size: 22
19367 AGTAAAGAGT
* * *
19377 AATCAGTAAGAAGTCAAAATGT
1 AATCAGTAAAAAGTCAAAAGGC
*
19399 AATCAGTAAAAATGTGAAAAGGC
1 AATCAGTAAAAA-GTCAAAAGGC
*
19422 AATCAGTAAAGAGT-AAAA
1 AATCAGTAAAAAGTCAAAA
19440 TGGTAAAAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 4 0.11
22 13 0.37
23 18 0.51
ACGTcount: A:0.54, C:0.08, G:0.19, T:0.19
Consensus pattern (22 bp):
AATCAGTAAAAAGTCAAAAGGC
Found at i:19528 original size:20 final size:20
Alignment explanation
Indices: 19476--19531 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 20
19466 AGAGTAAAGA
*
19476 GTAATCAGTAAAAAAAAATG
1 GTAATCAGTAGAAAAAAATG
*
19496 GTAA--AG-AGTAAAAAATG
1 GTAATCAGTAGAAAAAAATG
*
19513 GTAATCAGTAGGAAAAAAT
1 GTAATCAGTAGAAAAAAAT
19532 CAAATAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 13 0.43
18 2 0.07
19 2 0.07
20 13 0.43
ACGTcount: A:0.57, C:0.04, G:0.20, T:0.20
Consensus pattern (20 bp):
GTAATCAGTAGAAAAAAATG
Found at i:19558 original size:17 final size:17
Alignment explanation
Indices: 19471--19558 Score: 56
Period size: 17 Copynumber: 5.1 Consensus size: 17
19461 AGTAAAGAGT
19471 AAAGAGTAATCAGTAAAAAA
1 AAAG-GTAATCAGT--AAAA
**
19491 AAATGGTAAAGAGTAAAA
1 AAA-GGTAATCAGTAAAA
* **
19509 AATGGTAATCAGTAGGA
1 AAAGGTAATCAGTAAAA
*
19526 AAA---AATCAAATAAAA
1 AAAGGTAATC-AGTAAAA
19541 AAAGGTAATCAGTAAAA
1 AAAGGTAATCAGTAAAA
19558 A
1 A
19559 GGAAATTAAG
Statistics
Matches: 51, Mismatches: 12, Indels: 13
0.67 0.16 0.17
Matches are distributed among these distances:
14 4 0.08
15 7 0.14
17 19 0.37
18 10 0.20
20 10 0.20
21 1 0.02
ACGTcount: A:0.61, C:0.05, G:0.17, T:0.17
Consensus pattern (17 bp):
AAAGGTAATCAGTAAAA
Found at i:19985 original size:20 final size:21
Alignment explanation
Indices: 19942--19996 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
19932 GATAAAATAT
* * *
19942 TTTCTTTTTGTTTTTAAAGTC
1 TTTCATTTTGTTTTGAAAGAC
*
19963 TTTTATTTTGTTTTGAAA-AC
1 TTTCATTTTGTTTTGAAAGAC
19983 TTTCATTTTAGTTT
1 TTTCATTTT-GTTT
19997 CCCTAAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.18, C:0.07, G:0.09, T:0.65
Consensus pattern (21 bp):
TTTCATTTTGTTTTGAAAGAC
Found at i:20255 original size:17 final size:18
Alignment explanation
Indices: 20227--20274 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
20217 AATTTTTTTA
20227 TTTTTCCATTTTTCCAT-T
1 TTTTTCC-TTTTTCCATCT
*
20245 TTTTTCC-TTTTCCTTCT
1 TTTTTCCTTTTTCCATCT
*
20262 TTTTTTCTTTTTC
1 TTTTTCCTTTTTC
20275 TCCTTTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 7 0.27
17 7 0.27
18 12 0.46
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTCCTTTTTCCATCT
Found at i:20280 original size:17 final size:17
Alignment explanation
Indices: 20243--20292 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
20233 CATTTTTCCA
* *
20243 TTTTTTTCCTTTTCCTTC
1 TTTTTTT-CTTTTTCTCC
20261 TTTTTTTCTTTTTCTCC
1 TTTTTTTCTTTTTCTCC
20278 TTTTCTTTCATTTTT
1 TTTT-TTTC-TTTTT
20293 TTTATTCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 12 0.43
18 11 0.39
19 5 0.18
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTTCTTTTTCTCC
Found at i:20293 original size:26 final size:27
Alignment explanation
Indices: 20233--20293 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 27
20223 TTTATTTTTC
* *
20233 CATTTTTCCATTTTTTTCCTTTTCCTT
1 CATTTTTTCATTTTTCTCCTTTTCCTT
* *
20260 CTTTTTTTC-TTTTTCTCCTTTTCTTT
1 CATTTTTTCATTTTTCTCCTTTTCCTT
20286 CATTTTTT
1 CATTTTTT
20294 TTATTCAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 22 0.76
27 7 0.24
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (27 bp):
CATTTTTTCATTTTTCTCCTTTTCCTT
Found at i:22011 original size:19 final size:18
Alignment explanation
Indices: 21987--22022 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
21977 TGAAGATTTT
21987 TTGAAGATAATTTGAAGAC
1 TTGAAGATAA-TTGAAGAC
*
22006 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
22023 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAC
Found at i:23335 original size:22 final size:23
Alignment explanation
Indices: 23301--23374 Score: 60
Period size: 23 Copynumber: 3.1 Consensus size: 23
23291 ATTCACTGCT
* *
23301 TTTTAATTAATTGTTTTATTTAA
1 TTTTACTTGATTGTTTTATTTAA
*
23324 TTTT-CTTGATTGCTTTCTTAGTTAA
1 TTTTACTTGATTG--TT-TTATTTAA
* * *
23349 TTTTACTTGTTTGCTTGATTTAA
1 TTTTACTTGATTGTTTTATTTAA
23372 TTT
1 TTT
23375 AACTCTACTT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
22 6 0.15
23 13 0.32
24 3 0.08
25 11 0.28
26 7 0.17
ACGTcount: A:0.20, C:0.07, G:0.09, T:0.64
Consensus pattern (23 bp):
TTTTACTTGATTGTTTTATTTAA
Done.