Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005077.1 Hibiscus syriacus cultivar Beakdansim tig00011406_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: 68577
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:3199 original size:30 final size:28
Alignment explanation
Indices: 3165--3404 Score: 243
Period size: 30 Copynumber: 8.2 Consensus size: 28
3155 GTAGGTCAAC
3165 CCTTTAAGTTATATTTTTTACTATTTTAGT
1 CCTTTAAGTT-TATTTTTT-CTATTTTAGT
* * *
3195 CCTTTAATTTTATGTTTTTGTTATTTTAAT
1 CCTTTAAGTTTAT-TTTTT-CTATTTTAGT
* *
3225 CTTTTAAGTTTCTATTTTT-TATTTTAGT
1 CCTTTAAGTTTAT-TTTTTCTATTTTAGT
* * *
3253 CCTTTAAATTTTTTTTTTCTTTTTTAGT
1 CCTTTAAGTTTATTTTTTCTATTTTAGT
3281 CCTTTAAGTTTTTATTTTTTCTATTTTAGT
1 CCTTTAAG--TTTATTTTTTCTATTTTAGT
3311 CCTTTAAGTTTA-TTTTTCTATTTTAGT
1 CCTTTAAGTTTATTTTTTCTATTTTAGT
*
3338 CCTTTAACTTTCTATTTTTTCTATTTTAGT
1 CCTTTAA-GTT-TATTTTTTCTATTTTAGT
* *
3368 CCCTTAAGTTCCTATTTTTGT-TATTTTGGT
1 CCTTTAAGTT--TATTTTT-TCTATTTTAGT
*
3398 CCATTAA
1 CCTTTAA
3405 ATCACTGAGT
Statistics
Matches: 180, Mismatches: 21, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
27 27 0.15
28 39 0.22
29 7 0.04
30 106 0.59
31 1 0.01
ACGTcount: A:0.18, C:0.12, G:0.07, T:0.63
Consensus pattern (28 bp):
CCTTTAAGTTTATTTTTTCTATTTTAGT
Found at i:3256 original size:58 final size:59
Alignment explanation
Indices: 3165--3404 Score: 278
Period size: 57 Copynumber: 4.1 Consensus size: 59
3155 GTAGGTCAAC
* * *
3165 CCTTTAAG-TTATATTTTTTACTATTTTAGTCCTTTAATTTTATGTTTTTGTTATTTTAAT
1 CCTTTAAGTTTCTATTTTTT-CTATTTTAGTCCTTTAAGTTTAT-TTTTTGTTATTTTAGT
* * * *
3225 CTTTTAAGTTTCTA-TTTTT-TATTTTAGTCCTTTAAATTTTTTTTTTCTT-TTTTAGT
1 CCTTTAAGTTTCTATTTTTTCTATTTTAGTCCTTTAAGTTTATTTTTTGTTATTTTAGT
* *
3281 CCTTTAAGTTTTTATTTTTTCTATTTTAGTCCTTTAAGTTTA-TTTTT-CTATTTTAGT
1 CCTTTAAGTTTCTATTTTTTCTATTTTAGTCCTTTAAGTTTATTTTTTGTTATTTTAGT
* * *
3338 CCTTTAACTTTCTATTTTTTCTATTTTAGTCCCTTAAGTTCCTA-TTTTTGTTATTTTGGT
1 CCTTTAAGTTTCTATTTTTTCTATTTTAGTCCTTTAAGTT--TATTTTTTGTTATTTTAGT
*
3398 CCATTAA
1 CCTTTAA
3405 ATCACTGAGT
Statistics
Matches: 156, Mismatches: 17, Indels: 14
0.83 0.09 0.07
Matches are distributed among these distances:
56 19 0.12
57 61 0.39
58 39 0.25
59 7 0.04
60 26 0.17
61 4 0.03
ACGTcount: A:0.18, C:0.12, G:0.07, T:0.63
Consensus pattern (59 bp):
CCTTTAAGTTTCTATTTTTTCTATTTTAGTCCTTTAAGTTTATTTTTTGTTATTTTAGT
Found at i:8808 original size:27 final size:27
Alignment explanation
Indices: 8773--8827 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
8763 ATTTCAAAAT
8773 TATAATTATGAAA-AAAATATTAATTTA
1 TATAATTAT-AAATAAAATATTAATTTA
* *
8800 TATATTTATAAATAAAATATTTATTTA
1 TATAATTATAAATAAAATATTAATTTA
8827 T
1 T
8828 TTAGAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 3 0.12
27 22 0.88
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
TATAATTATAAATAAAATATTAATTTA
Found at i:8921 original size:20 final size:19
Alignment explanation
Indices: 8882--8931 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
8872 TTTCTTCGAT
8882 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
8901 ATTAAAATAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
8921 ATTTAAAAATA
1 ATTAAAAAATA
8932 GGATATTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:8981 original size:117 final size:116
Alignment explanation
Indices: 8786--9022 Score: 273
Period size: 117 Copynumber: 2.0 Consensus size: 116
8776 AATTATGAAA
* * * *
8786 AAAATATTAATTTATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTT
1 AAAATATTAATATATATATTTAAAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACAT
* * *
8851 CTAGGTGCCTTAAGACAGCTC-TTTCTTCGATATTAAAAAATAAATAAATAATT
66 CCAAGTGCCTTAAGACAGC-CATTTCTT-AATATTAAAAAATAAATAAAT-ATT
** * *
8904 AAAATAATTAATATATA-ATTTAAAAATAGGATATTTA-TTATTTAAAAATATCAGAAAATGTCA
1 AAAAT-ATTAATATATATATTTAAAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACA
* ** * *
8967 TCCAATTGTTTTAAGACTGCCATTTCTTAATATTGAAAAATAAATAAATATT
65 TCCAAGTGCCTTAAGACAGCCATTTCTTAATATTAAAAAATAAATAAATATT
9019 AAAA
1 AAAA
9023 CAGGATTAAA
Statistics
Matches: 101, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
115 7 0.07
116 20 0.20
117 42 0.42
118 22 0.22
119 10 0.10
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.38
Consensus pattern (116 bp):
AAAATATTAATATATATATTTAAAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACAT
CCAAGTGCCTTAAGACAGCCATTTCTTAATATTAAAAAATAAATAAATATT
Found at i:10887 original size:76 final size:76
Alignment explanation
Indices: 10761--11703 Score: 1676
Period size: 76 Copynumber: 12.4 Consensus size: 76
10751 AGGTCCTAAA
* *
10761 AAACATCATGCACTGAAGGGA-TTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGTA-GGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
10825 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* * *
10837 AAACATGATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTAAAAACATC-AAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
10901 AGGCTTTTTGG
66 AGGCTTTTTGG
*
10912 AAATATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
10977 AGGCTTTTTGG
66 AGGCTTTTTGG
10988 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCCAAAAAGCTCCCG
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACAT-CAAAAAGCTCCCG
11053 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* * *
11065 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
11130 AGGCTTTTTGG
66 AGGCTTTTTGG
*
11141 AAATATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
11205 AGGCTTTTTGG
66 AGGCTTTTTGG
*
11216 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
11281 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
11292 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCTGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
11357 AGGCTTTTTGG
66 AGGCTTTTTGG
*
11368 AAACATCATGCATTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
11433 AGGCTTTTTGG
66 AGGCTTTTTGG
11444 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
11509 AGGCTTTTTTG
66 AGGCTTTTTGG
*
11520 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAATATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
11585 AGGCTTTTTGG
66 AGGCTTTTTGG
*
11596 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCCAAAAAGCTCCCG
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACAT-CAAAAAGCTCCCG
11661 AAGGCTTTTTGG
65 AAGGCTTTTTGG
*
11673 AAACATCATGCACTGCAGGACTTACAGATGA
1 AAACATCATGCACTGTAGGACTTACAGATGA
11704 GAAATAGTTT
Statistics
Matches: 834, Mismatches: 28, Indels: 9
0.96 0.03 0.01
Matches are distributed among these distances:
75 147 0.18
76 559 0.67
77 128 0.15
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:17174 original size:17 final size:16
Alignment explanation
Indices: 17154--17264 Score: 71
Period size: 17 Copynumber: 6.6 Consensus size: 16
17144 ATTTCTCCCC
17154 TTTTTCTTTTTCCCTTT
1 TTTTTCTTTTT-CCTTT
*
17171 TTTTCCTTTTTTCTCATTT
1 TTTTTC-TTTTTC-C-TTT
* * *
17190 TTCTT-TTTTTCATCT
1 TTTTTCTTTTTCCTTT
*
17205 TTTTCCTTTTTTCCTTT
1 TTTTTC-TTTTTCCTTT
* *
17222 TTTCTCATTTTCCTTT
1 TTTTTCTTTTTCCTTT
* *
17238 TTTCATCTTTTTTCTTT
1 TTT-TTCTTTTTCCTTT
17255 TTCTTTCTTT
1 TT-TTTCTTT
17265 GCTGGATGAG
Statistics
Matches: 71, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
15 5 0.07
16 12 0.17
17 41 0.58
18 7 0.10
19 6 0.08
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTCTTTTTCCTTT
Found at i:17195 original size:25 final size:25
Alignment explanation
Indices: 17167--17251 Score: 84
Period size: 25 Copynumber: 3.4 Consensus size: 25
17157 TTCTTTTTCC
*
17167 CTTTTTTTCCT-TTTTTCTCATTTTT
1 CTTTTTTTCATCTTTTTC-CATTTTT
*
17192 CTTTTTTTCATCTTTTTCCTTTTTT
1 CTTTTTTTCATCTTTTTCCATTTTT
* * *
17217 CCTTTTTTC-TCATTTTCCTTTTTT
1 CTTTTTTTCATCTTTTTCCATTTTT
17241 CATCTTTTTTC
1 C-T-TTTTTTC
17252 TTTTTCTTTC
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
24 15 0.29
25 24 0.46
26 13 0.25
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (25 bp):
CTTTTTTTCATCTTTTTCCATTTTT
Found at i:17228 original size:42 final size:41
Alignment explanation
Indices: 17158--17256 Score: 153
Period size: 41 Copynumber: 2.3 Consensus size: 41
17148 CTCCCCTTTT
*
17158 TCTTTTTCCCTTTTTTTCCTTTTTTCTCATTTTTCTTTTTTTCA
1 TCTTTTT-CC-TTTTTTCCTTTTTTCTCA-TTTTCCTTTTTTCA
17202 TCTTTTTCCTTTTTTCCTTTTTTCTCATTTTCCTTTTTTCA
1 TCTTTTTCCTTTTTTCCTTTTTTCTCATTTTCCTTTTTTCA
*
17243 TCTTTTTTCTTTTT
1 TCTTTTTCCTTTTT
17257 CTTTCTTTGC
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
41 26 0.49
42 18 0.34
43 2 0.04
44 7 0.13
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (41 bp):
TCTTTTTCCTTTTTTCCTTTTTTCTCATTTTCCTTTTTTCA
Found at i:17232 original size:9 final size:9
Alignment explanation
Indices: 17160--17262 Score: 85
Period size: 9 Copynumber: 11.8 Consensus size: 9
17150 CCCCTTTTTC
*
17160 TTTTTCCCT
1 TTTTTCTCT
17169 TTTTT-TCCT
1 TTTTTCT-CT
*
17178 TTTTTCTCA
1 TTTTTCTCT
17187 TTTTTCT-T
1 TTTTTCTCT
17195 TTTTTCATC-
1 TTTTTC-TCT
17204 TTTTTC-CT
1 TTTTTCTCT
17212 TTTTTC-CT
1 TTTTTCTCT
17220 TTTTTCTC-
1 TTTTTCTCT
*
17228 ATTTTC-CT
1 TTTTTCTCT
17236 TTTTTCATCT
1 TTTTTC-TCT
*
17246 TTTTTCTTT
1 TTTTTCTCT
17255 TTCTTTCT
1 TT-TTTCT
17263 TTGCTGGATG
Statistics
Matches: 78, Mismatches: 6, Indels: 19
0.76 0.06 0.18
Matches are distributed among these distances:
7 2 0.03
8 30 0.38
9 32 0.41
10 14 0.18
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTTCTCT
Found at i:17232 original size:24 final size:24
Alignment explanation
Indices: 17187--17252 Score: 87
Period size: 24 Copynumber: 2.6 Consensus size: 24
17177 TTTTTTCTCA
* *
17187 TTTTTCTTTTTTTCATCTTTTTCCT
1 TTTTTCCTTTTTTC-TCATTTTCCT
17212 TTTTTCCTTTTTTCTCATTTTCCT
1 TTTTTCCTTTTTTCTCATTTTCCT
17236 TTTTTCATCTTTTTTCT
1 TTTTTC--CTTTTTTCT
17253 TTTTCTTTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
24 15 0.41
25 13 0.35
26 9 0.24
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (24 bp):
TTTTTCCTTTTTTCTCATTTTCCT
Found at i:17256 original size:24 final size:22
Alignment explanation
Indices: 17154--17260 Score: 56
Period size: 25 Copynumber: 4.4 Consensus size: 22
17144 ATTTCTCCCC
17154 TTTTTCTTTTTCCCTTTTTTTCCTT
1 TTTTTCTTTTT-CC-TTTTTTCC-T
*
17179 TTTTCTCATTTTTCTTTTTTTCATCT
1 TTTT-TC-TTTTTCCTTTTTTC--CT
* *
17205 TTTTCCTTTTTTCCTTTTTTCTCA
1 TTTTTC-TTTTTCCTTTTTTC-CT
*
17229 TTTTCCTTTTTTCATCTTTTTT-C-
1 TTTTTC-TTTTTC--CTTTTTTCCT
17252 TTTTTCTTT
1 TTTTTCTTT
17261 CTTTGCTGGA
Statistics
Matches: 70, Mismatches: 6, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
22 3 0.04
23 5 0.07
24 16 0.23
25 25 0.36
26 15 0.21
27 6 0.09
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTTCTTTTTCCTTTTTTCCT
Found at i:17257 original size:16 final size:16
Alignment explanation
Indices: 17169--17256 Score: 83
Period size: 17 Copynumber: 5.3 Consensus size: 16
17159 CTTTTTCCCT
17169 TTTTTTC-CTTTTTTC
1 TTTTTTCTCTTTTTTC
17184 TCATTTTTCT-TTTTTTC
1 T--TTTTTCTCTTTTTTC
17201 ATCTTTTTC-CTTTTTTCC
1 -T-TTTTTCTCTTTTTT-C
* *
17219 TTTTTTCTCATTTTCC
1 TTTTTTCTCTTTTTTC
17235 TTTTTTCATCTTTTTTC
1 TTTTTTC-TCTTTTTTC
17252 TTTTT
1 TTTTT
17257 CTTTCTTTGC
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
15 1 0.02
16 14 0.23
17 43 0.72
18 2 0.03
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTTCTCTTTTTTC
Found at i:20160 original size:36 final size:36
Alignment explanation
Indices: 20083--20172 Score: 94
Period size: 36 Copynumber: 2.5 Consensus size: 36
20073 GTAAATGCGA
* *
20083 AAATGCATAA-ATGCAAAAATAAGAATGCAAATTGTG
1 AAATGCA-AAGATGCAAAAATAAGAATACAAAATGTG
* *
20119 TAATGCAAAGATGTAAAAAGTAAGAATACAAAATG-G
1 AAATGCAAAGATGCAAAAA-TAAGAATACAAAATGTG
* *
20155 AAATGCACAGATACAAAA
1 AAATGCAAAGATGCAAAA
20173 TGTAAATGCA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
35 2 0.05
36 29 0.66
37 13 0.30
ACGTcount: A:0.56, C:0.09, G:0.17, T:0.19
Consensus pattern (36 bp):
AAATGCAAAGATGCAAAAATAAGAATACAAAATGTG
Found at i:22479 original size:13 final size:14
Alignment explanation
Indices: 22463--22500 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
22453 TTAATACCTG
*
22463 AATAAAATAAAT-A
1 AATAATATAAATAA
*
22476 AATAATATTAATAA
1 AATAATATAAATAA
22490 AATAATATAAA
1 AATAATATAAA
22501 AATAATAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AATAATATAAATAA
Found at i:22491 original size:22 final size:22
Alignment explanation
Indices: 22463--22504 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
22453 TTAATACCTG
22463 AATAAAATAA-ATAAATAATATT
1 AATAAAATAATATAAA-AATATT
22485 AATAAAATAATATAAAAATA
1 AATAAAATAATATAAAAATA
22505 ATAAGTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
AATAAAATAATATAAAAATATT
Found at i:23028 original size:29 final size:29
Alignment explanation
Indices: 22996--23052 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
22986 ATTTCAAAAT
22996 TATAATTATGAAA-AAAATATTAATTTATA
1 TATAATTAT-AAATAAAATATTAATTTATA
* *
23025 TATATTTATAAATAAAATATTTATTTAT
1 TATAATTATAAATAAAATATTAATTTAT
23053 TTAGAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
TATAATTATAAATAAAATATTAATTTATA
Found at i:23147 original size:20 final size:19
Alignment explanation
Indices: 23108--23149 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
23098 TTTCTTCGAT
23108 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
23127 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
23147 ATT
1 ATT
23150 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:23260 original size:120 final size:120
Alignment explanation
Indices: 23021--23253 Score: 305
Period size: 120 Copynumber: 2.0 Consensus size: 120
23011 AATATTAATT
* * *
23021 TATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGTGCCT
1 TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAAGACTACTAGGTGCCT
*
23086 TAAGACAGCTCTTTTCTTCGATATTAAAAAATAAATAAATAATTAAAACAATTAA
66 TAAGACAGCTCTTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACAATTAA
** *
23141 TATATA-ATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATAGACATAC-AGTTG
1 TATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAA-AGAC-TACTAGGTG
** * *
23204 TTTTAAGACTGCTC-TTTCTT-AATATTGAAAAATAAATAAAT-ATTAAAACA
63 CCTTAAGACAGCTCTTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACA
23254 TGATTAAAAT
Statistics
Matches: 99, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
118 9 0.09
119 25 0.25
120 45 0.45
121 18 0.18
122 2 0.02
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.37
Consensus pattern (120 bp):
TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAAGACTACTAGGTGCCT
TAAGACAGCTCTTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACAATTAA
Found at i:23323 original size:2 final size:2
Alignment explanation
Indices: 23316--23340 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23306 TATTATTTAT
23316 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
23341 TTATGGCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24818 original size:15 final size:15
Alignment explanation
Indices: 24798--24845 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
24788 TAGGGTTTTG
24798 TAATATTTAATTTAA
1 TAATATTTAATTTAA
24813 TAATA-TTAA-TTAA
1 TAATATTTAATTTAA
*
24826 TAATATAT-ATTGTAA
1 TAATATTTAATT-TAA
24841 TAATA
1 TAATA
24846 ATAATAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 10 0.34
14 6 0.21
15 13 0.45
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
TAATATTTAATTTAA
Found at i:24866 original size:21 final size:24
Alignment explanation
Indices: 24813--24871 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 24
24803 TTTAATTTAA
*
24813 TAATATTAATTAATAATATATATTG
1 TAATAATAA-TAATAATATATATTG
*
24838 TAATAATAATAATAATA-AT-TTT
1 TAATAATAATAATAATATATATTG
24860 TAA-AATAATAAT
1 TAATAATAATAAT
24872 TTAAATAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 9 0.28
22 5 0.16
23 2 0.06
24 8 0.25
25 8 0.25
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TAATAATAATAATAATATATATTG
Found at i:31501 original size:14 final size:15
Alignment explanation
Indices: 31482--31510 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
31472 CGAGAGTACT
31482 CAGGATATGG-CGGA
1 CAGGATATGGACGGA
31496 CAGGATATGGACGGA
1 CAGGATATGGACGGA
31511 AGTCAGGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.31, C:0.14, G:0.41, T:0.14
Consensus pattern (15 bp):
CAGGATATGGACGGA
Found at i:33898 original size:15 final size:17
Alignment explanation
Indices: 33878--33909 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
33868 GTTTAAAGCA
33878 ATTTT-AAGA-AAAAAT
1 ATTTTAAAGATAAAAAT
33893 ATTTTAAAGATAAAAAT
1 ATTTTAAAGATAAAAAT
33910 TAATCGGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 4 0.27
17 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (17 bp):
ATTTTAAAGATAAAAAT
Found at i:34054 original size:22 final size:22
Alignment explanation
Indices: 34026--34070 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
34016 CGTCTTAAAT
34026 GTGGAACTTGCAAATTCGAGTA
1 GTGGAACTTGCAAATTCGAGTA
34048 GTGGAACTTGCAAATTCGAGTA
1 GTGGAACTTGCAAATTCGAGTA
34070 G
1 G
34071 AAAGTTGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (22 bp):
GTGGAACTTGCAAATTCGAGTA
Found at i:39494 original size:15 final size:16
Alignment explanation
Indices: 39468--39503 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
39458 TATTATCAAC
39468 AAATAGATTTTTATAT
1 AAATAGATTTTTATAT
*
39484 AAATA-ATTTTTATTT
1 AAATAGATTTTTATAT
39499 AAATA
1 AAATA
39504 TTTAGAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
AAATAGATTTTTATAT
Found at i:41131 original size:20 final size:20
Alignment explanation
Indices: 41106--41148 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
41096 TAAGTAAATT
*
41106 TTTAATATTTGTATTATAAA
1 TTTAATATTTGTATTAAAAA
*
41126 TTTAATATTTTTATTAAAAA
1 TTTAATATTTGTATTAAAAA
41146 TTT
1 TTT
41149 TAACTTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTAATATTTGTATTAAAAA
Found at i:41245 original size:17 final size:17
Alignment explanation
Indices: 41223--41267 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
41213 CTTTATTTAA
41223 AATTTGTG-TCTCATGTT
1 AATTTGTGTTC-CATGTT
41240 AATTTGTGTTCCATGTT
1 AATTTGTGTTCCATGTT
*
41257 ATTTTGTGTTC
1 AATTTGTGTTC
41268 GTAAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 24 0.92
18 2 0.08
ACGTcount: A:0.16, C:0.11, G:0.18, T:0.56
Consensus pattern (17 bp):
AATTTGTGTTCCATGTT
Found at i:41541 original size:33 final size:33
Alignment explanation
Indices: 41499--41589 Score: 130
Period size: 33 Copynumber: 2.8 Consensus size: 33
41489 AATAATAAAC
41499 TATTAAATTATTATCAAACGTGGTACT-AGTGGT
1 TATTAAATTATTATCAAACGTGGTACTGA-TGGT
*
41532 TATTAAATTATTATCAAATGTGGTACTGATGGT
1 TATTAAATTATTATCAAACGTGGTACTGATGGT
* * *
41565 TACTAAACTATTATCAAAGGTGGTA
1 TATTAAATTATTATCAAACGTGGTA
41590 ATTAACTATT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 52 0.98
34 1 0.02
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (33 bp):
TATTAAATTATTATCAAACGTGGTACTGATGGT
Found at i:41809 original size:16 final size:16
Alignment explanation
Indices: 41786--41926 Score: 72
Period size: 16 Copynumber: 8.9 Consensus size: 16
41776 TTTGAGTTGC
41786 TTTT-GGTTCAGG-TTA
1 TTTTCGGTTC-GGATTA
* *
41801 TTTTCGGTTCAGATTG
1 TTTTCGGTTCGGATTA
*
41817 TTTTCGATTCGGATTA
1 TTTTCGGTTCGGATTA
* * *
41833 ATTTCGATTCGGTTTA
1 TTTTCGGTTCGGATTA
** *
41849 TTTTCGGTTATGATTG
1 TTTTCGGTTCGGATTA
** *
41865 TTTTTTGTTC-GAGTTG
1 TTTTCGGTTCGGA-TTA
* *
41881 CTTTCGATTCGGATTA
1 TTTTCGGTTCGGATTA
* ** *
41897 TTTTTGGTTCAAACTA
1 TTTTCGGTTCGGATTA
*
41913 TTTTCGATTCGGAT
1 TTTTCGGTTCGGAT
41927 CAAATTGGAT
Statistics
Matches: 90, Mismatches: 32, Indels: 7
0.70 0.25 0.05
Matches are distributed among these distances:
15 7 0.08
16 81 0.90
17 2 0.02
ACGTcount: A:0.16, C:0.11, G:0.21, T:0.52
Consensus pattern (16 bp):
TTTTCGGTTCGGATTA
Found at i:41838 original size:32 final size:32
Alignment explanation
Indices: 41798--41926 Score: 98
Period size: 32 Copynumber: 4.0 Consensus size: 32
41788 TTGGTTCAGG
*
41798 TTATTTTCGGTTCAGATTGTTTTCGATTCGGA
1 TTATTTTCGGTTCAGATTATTTTCGATTCGGA
* * * * * **
41830 TTAATTTCGATTCGGTTTATTTTCGGTTATGA
1 TTATTTTCGGTTCAGATTATTTTCGATTCGGA
* ** **
41862 TTGTTTTTTGTTC-GAGTTGCTTTCGATTCGGA
1 TTATTTTCGGTTCAGA-TTATTTTCGATTCGGA
* * *
41894 TTATTTTTGGTTCAAACTATTTTCGATTCGGA
1 TTATTTTCGGTTCAGATTATTTTCGATTCGGA
41926 T
1 T
41927 CAAATTGGAT
Statistics
Matches: 70, Mismatches: 25, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
31 1 0.01
32 68 0.97
33 1 0.01
ACGTcount: A:0.16, C:0.12, G:0.20, T:0.52
Consensus pattern (32 bp):
TTATTTTCGGTTCAGATTATTTTCGATTCGGA
Found at i:41850 original size:48 final size:48
Alignment explanation
Indices: 41798--41926 Score: 138
Period size: 48 Copynumber: 2.7 Consensus size: 48
41788 TTGGTTCAGG
*
41798 TTATTTTCGGTTCAGATTGTTTTCGATTCGGATTAATTTCGATTCGGT
1 TTATTTTCGGTTCAGATTGTTTTCGATTCGGATTAATTTCGATTCGGA
* **
41846 TTATTTTCGGTT-ATGATTGTTTTTTG-TTC-GAGTTGCTTTCGATTCGGA
1 TTATTTTCGGTTCA-GATTG-TTTTCGATTCGGA-TTAATTTCGATTCGGA
* * * *
41894 TTATTTTTGGTTCAAACTATTTTCGATTCGGAT
1 TTATTTTCGGTTCAGATTGTTTTCGATTCGGAT
41927 CAAATTGGAT
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
47 8 0.12
48 50 0.76
49 8 0.12
ACGTcount: A:0.16, C:0.12, G:0.20, T:0.52
Consensus pattern (48 bp):
TTATTTTCGGTTCAGATTGTTTTCGATTCGGATTAATTTCGATTCGGA
Found at i:44194 original size:19 final size:19
Alignment explanation
Indices: 44170--44216 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
44160 TTTTACCTTT
44170 TCCGACGAGT-CTCATCACC
1 TCCGACGAGTGCTCA-CACC
* *
44189 TCCGACGACTGCTCACTCC
1 TCCGACGAGTGCTCACACC
44208 TCCGACGAG
1 TCCGACGAG
44217 GCTAAGTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.19, C:0.43, G:0.19, T:0.19
Consensus pattern (19 bp):
TCCGACGAGTGCTCACACC
Found at i:44886 original size:5 final size:5
Alignment explanation
Indices: 44877--45050 Score: 240
Period size: 5 Copynumber: 34.8 Consensus size: 5
44867 AATAATTACT
* * * * * *
44877 AGTAT AGTAT AGTAT AGTAT AGTAT AGTAC AGTAC AGTAC AATAC AGTAC
1 AGTAC AGTAC AGTAC AGTAC AGTAC AGTAC AGTAC AGTAC AGTAC AGTAC
* *
44927 AGTAC AATAC AGTAC AGTAC AATAC AGTAC AGTAC AGTAC AGTAC AGTAC
1 AGTAC AGTAC AGTAC AGTAC AGTAC AGTAC AGTAC AGTAC AGTAC AGTAC
* * *
44977 AGTAT AATAC AGTAC AGTAC AGTAT AGTAC AGTAC AGTAC AGTAC AGTAC
1 AGTAC AGTAC AGTAC AGTAC AGTAC AGTAC AGTAC AGTAC AGTAC AGTAC
*
45027 AGTAC AATAC AGTAC AGTAC AGTA
1 AGTAC AGTAC AGTAC AGTAC AGTA
45051 ATATAATATA
Statistics
Matches: 154, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 154 1.00
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (5 bp):
AGTAC
Found at i:45063 original size:7 final size:7
Alignment explanation
Indices: 45051--45126 Score: 50
Period size: 7 Copynumber: 10.6 Consensus size: 7
45041 CAGTACAGTA
45051 ATATAAT
1 ATATAAT
45058 ATATAAT
1 ATATAAT
**
45065 ATTATCTT
1 A-TATAAT
45073 ATATAAT
1 ATATAAT
45080 ATACTATAT
1 ATA-TA-AT
45089 AATATACAT
1 -ATATA-AT
*
45098 -TATACT
1 ATATAAT
*
45104 AAATAAT
1 ATATAAT
45111 ATAT-AT
1 ATATAAT
45117 ATAT-AT
1 ATATAAT
45123 ATAT
1 ATAT
45127 TATAAAAGGT
Statistics
Matches: 55, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
6 13 0.24
7 26 0.47
8 7 0.13
9 6 0.11
10 3 0.05
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (7 bp):
ATATAAT
Found at i:45066 original size:12 final size:12
Alignment explanation
Indices: 45049--45131 Score: 64
Period size: 12 Copynumber: 6.7 Consensus size: 12
45039 TACAGTACAG
45049 TAATATAATATA
1 TAATATAATATA
*
45061 TAATATTATCTTATA
1 TAATA-TA--ATATA
*
45076 TAATATACTATA
1 TAATATAATATA
45088 TAATATACATTATA
1 TAATATA-A-TATA
45102 CTAA-ATAATATA
1 -TAATATAATATA
45114 T-ATAT-ATATA
1 TAATATAATATA
*
45124 TATTATAA
1 TAATATAA
45132 AAGGTCTCGA
Statistics
Matches: 58, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
10 7 0.12
11 6 0.10
12 21 0.36
13 3 0.05
14 9 0.16
15 12 0.21
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.45
Consensus pattern (12 bp):
TAATATAATATA
Found at i:45077 original size:2 final size:2
Alignment explanation
Indices: 45051--45130 Score: 52
Period size: 2 Copynumber: 43.5 Consensus size: 2
45041 CAGTACAGTA
*
45051 AT AT A- AT AT AT A- AT AT -T AT CT -T AT AT A- AT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* *
45089 A- AT AT AC AT -T AT ACT AA AT A- AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
45128 AT A
1 AT A
45131 AAAGGTCTCG
Statistics
Matches: 62, Mismatches: 5, Indels: 22
0.70 0.06 0.25
Matches are distributed among these distances:
1 9 0.15
2 49 0.79
3 4 0.06
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:45101 original size:19 final size:18
Alignment explanation
Indices: 45051--45130 Score: 67
Period size: 17 Copynumber: 4.6 Consensus size: 18
45041 CAGTACAGTA
* *
45051 ATATAATATATA-ATATT
1 ATATAATATACATATACT
* *
45068 ATCTTATATA-ATATACT
1 ATATAATATACATATACT
45085 ATATAATATACATTATACT
1 ATATAATATACA-TATACT
* *
45104 AAATAATATATATATA-T
1 ATATAATATACATATACT
*
45121 ATATATTATA
1 ATATAATATA
45131 AAAGGTCTCG
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
16 1 0.02
17 29 0.57
18 5 0.10
19 16 0.31
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (18 bp):
ATATAATATACATATACT
Found at i:55802 original size:31 final size:30
Alignment explanation
Indices: 55754--55857 Score: 93
Period size: 31 Copynumber: 3.4 Consensus size: 30
55744 CTAATGTGAC
* *
55754 TCTTAGGTAGGCTCTGCGGCCCTGAGATTAT
1 TCTTAGGTAGGCCCTGCGGCCCTGAGACT-T
* * *
55785 TCTTGGGTAGGCCCTGCGACCCTAAGACGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTGAGAC-T-T
* * *
55817 TCTTAGGTAGGCCCCGTGGCCCCGA-ACTT
1 TCTTAGGTAGGCCCTGCGGCCCTGAGACTT
*
55846 TCTTGGGTAGGC
1 TCTTAGGTAGGC
55858 TCTCAAGCCC
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
29 12 0.20
30 1 0.02
31 25 0.42
32 21 0.36
ACGTcount: A:0.14, C:0.27, G:0.31, T:0.28
Consensus pattern (30 bp):
TCTTAGGTAGGCCCTGCGGCCCTGAGACTT
Found at i:57894 original size:13 final size:12
Alignment explanation
Indices: 57838--57927 Score: 57
Period size: 12 Copynumber: 7.8 Consensus size: 12
57828 ACTACAATAC
*
57838 AATATAATATAT
1 AATATATTATAT
* * *
57850 ATTATATAATAC
1 AATATATTATAT
*
57862 AA-ATTTATATAT
1 AATATAT-TATAT
57874 AATATATTATAT
1 AATATATTATAT
*
57886 AAGTATATTATCT
1 AA-TATATTATAT
57899 AATATA--A-A-
1 AATATATTATAT
*
57907 GATATATTATAT
1 AATATATTATAT
57919 -ATATATTAT
1 AATATATTAT
57928 TAGGGATGGG
Statistics
Matches: 59, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
8 5 0.08
10 2 0.03
11 13 0.22
12 25 0.42
13 14 0.24
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (12 bp):
AATATATTATAT
Found at i:58356 original size:27 final size:27
Alignment explanation
Indices: 58324--58472 Score: 121
Period size: 27 Copynumber: 5.6 Consensus size: 27
58314 TATACTATAC
*
58324 ATACTATATAACATAATATTATAAAAT
1 ATACTATATAATATAATATTATAAAAT
*
58351 ATACTATATAATATAA-A-TAT-ATAT
1 ATACTATATAATATAATATTATAAAAT
* *
58375 AGTA-TATATTATATACCATA-TAAAATAAT
1 A-TACTATATAATATA--ATATTATAA-AAT
* * *
58404 AAAC-ATATAATATTTATATTATAATAT
1 ATACTATATAATA-TAATATTATAAAAT
* * *
58431 ATACTATATAATATTATCTTATATAAT
1 ATACTATATAATATAATATTATAAAAT
58458 ATACTATATAATATA
1 ATACTATATAATATA
58473 CACCGTACTA
Statistics
Matches: 97, Mismatches: 15, Indels: 20
0.73 0.11 0.15
Matches are distributed among these distances:
24 14 0.14
25 5 0.05
26 2 0.02
27 51 0.53
28 21 0.22
29 4 0.04
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.42
Consensus pattern (27 bp):
ATACTATATAATATAATATTATAAAAT
Found at i:58491 original size:5 final size:5
Alignment explanation
Indices: 58329--58472 Score: 64
Period size: 5 Copynumber: 28.0 Consensus size: 5
58319 TATACATACT
* * *
58329 ATATA ACATA ATATT ATAAA ATATA CTATATA ATATA A-ATA TATATA
1 ATATA ATATA ATATA ATATA ATATA --ATATA ATATA ATATA -ATATA
* * * * *
58376 GTAT- ATATT ATATA CCATATA AAATA ATAAA CATATA ATAT- TTATA
1 ATATA ATATA ATATA --ATATA ATATA ATATA -ATATA ATATA ATATA
* * * *
58422 TTATA ATAT- ATACT- ATATA ATATT ATCTT ATATA ATATA CTATATA
1 ATATA ATATA ATA-TA ATATA ATATA ATATA ATATA ATATA --ATATA
58468 ATATA
1 ATATA
58473 CACCGTACTA
Statistics
Matches: 107, Mismatches: 19, Indels: 26
0.70 0.12 0.17
Matches are distributed among these distances:
4 13 0.12
5 72 0.67
6 7 0.07
7 15 0.14
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:58491 original size:7 final size:7
Alignment explanation
Indices: 58336--58472 Score: 77
Period size: 7 Copynumber: 19.1 Consensus size: 7
58326 ACTATATAAC
58336 ATAATATT
1 ATAATA-T
*
58344 ATAAAAT
1 ATAATAT
*
58351 ATACTAT
1 ATAATAT
58358 ATAATAT
1 ATAATAT
58365 A-AATAT
1 ATAATAT
58371 ATATAGTAT
1 ATA-A-TAT
*
58380 ATATTAT
1 ATAATAT
58387 ATACCATAT
1 ATA--ATAT
*
58396 AAAATA-
1 ATAATAT
*
58402 ATAAACAT
1 AT-AATAT
58410 ATAATAT
1 ATAATAT
*
58417 -TTATATT
1 ATAATA-T
58424 ATAATAT
1 ATAATAT
*
58431 ATACTAT
1 ATAATAT
58438 ATAATATT
1 ATAATA-T
**
58446 ATCTTAT
1 ATAATAT
58453 AT-A-AT
1 ATAATAT
*
58458 ATACTAT
1 ATAATAT
58465 ATAATAT
1 ATAATAT
58472 A
1 A
58473 CACCGTACTA
Statistics
Matches: 98, Mismatches: 19, Indels: 25
0.69 0.13 0.18
Matches are distributed among these distances:
5 4 0.04
6 11 0.11
7 55 0.56
8 17 0.17
9 11 0.11
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (7 bp):
ATAATAT
Found at i:58492 original size:2 final size:2
Alignment explanation
Indices: 58349--58472 Score: 56
Period size: 2 Copynumber: 65.5 Consensus size: 2
58339 ATATTATAAA
* *
58349 AT AT ACT AT AT A- AT AT AA AT AT AT AT AGT AT AT AT -T AT AT ACC
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T
* * * *
58392 AT AT A- AA AT A- AT AA AC AT AT A- AT AT TT AT AT -T AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
58429 AT AT ACT AT AT A- AT AT -T AT CT -T AT AT A- AT AT ACT AT AT A-
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
58468 AT AT A
1 AT AT A
58473 CACCGTACTA
Statistics
Matches: 94, Mismatches: 11, Indels: 34
0.68 0.08 0.24
Matches are distributed among these distances:
1 12 0.13
2 73 0.78
3 9 0.10
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.43
Consensus pattern (2 bp):
AT
Found at i:59648 original size:20 final size:21
Alignment explanation
Indices: 59623--59662 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
59613 CTTTACATAG
*
59623 TAGTATTGATACCAT-AGGCA
1 TAGTATCGATACCATCAGGCA
59643 TAGTATCGATACCATCAGGC
1 TAGTATCGATACCATCAGGC
59663 CCCAACGGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (21 bp):
TAGTATCGATACCATCAGGCA
Found at i:59802 original size:20 final size:21
Alignment explanation
Indices: 59763--59803 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
59753 TGTAGAGATT
**
59763 TCATCCCCAAACGGCTAGAAA
1 TCATCCCCAAACAACTAGAAA
59784 TCATCCCC-AACAACTAGAAA
1 TCATCCCCAAACAACTAGAAA
59804 CGGCCACAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.41, C:0.34, G:0.10, T:0.15
Consensus pattern (21 bp):
TCATCCCCAAACAACTAGAAA
Found at i:60555 original size:20 final size:20
Alignment explanation
Indices: 60532--60580 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
60522 CTCTAAATCA
* *
60532 TTTTTCAAAATTTCATTTTG
1 TTTTTCAAAATCTAATTTTG
60552 TTTTTCAAAATCTAATTTTG
1 TTTTTCAAAATCTAATTTTG
*
60572 -CTTTCAAAA
1 TTTTTCAAAA
60581 GAAAATCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.53
Consensus pattern (20 bp):
TTTTTCAAAATCTAATTTTG
Found at i:67293 original size:55 final size:54
Alignment explanation
Indices: 67209--67333 Score: 191
Period size: 55 Copynumber: 2.3 Consensus size: 54
67199 TCGAAATTGC
*
67209 AAGGTATCGATAC-CTCCCAGTGTACCGATACACATGT-AGCACTAAATGTTTTA
1 AAGGTATCGATACACTCCCAGTGTACCGATACACATATGA-CACTAAATGTTTTA
* *
67262 AGGGTATCGATACACTCCTCAGTGTACCGATACACATATGACACTCAATGTTTTA
1 AAGGTATCGATACACTCC-CAGTGTACCGATACACATATGACACTAAATGTTTTA
67317 AAGGTATCGATACACTC
1 AAGGTATCGATACACTC
67334 TCCCTTTTAA
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
53 12 0.18
54 4 0.06
55 48 0.74
56 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (54 bp):
AAGGTATCGATACACTCCCAGTGTACCGATACACATATGACACTAAATGTTTTA
Found at i:68354 original size:14 final size:14
Alignment explanation
Indices: 68330--68364 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
68320 TGAGACATTA
68330 CCCGCCCCGCATCCG
1 CCCG-CCCGCATCCG
*
68345 TCCGCCCGCATCCG
1 CCCGCCCGCATCCG
68359 CCCGCC
1 CCCGCC
68365 AGCTAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 15 0.83
15 3 0.17
ACGTcount: A:0.06, C:0.66, G:0.20, T:0.09
Consensus pattern (14 bp):
CCCGCCCGCATCCG
Done.