Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001530.1 Hibiscus syriacus cultivar Beakdansim tig00002999_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: 78241
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:889 original size:10 final size:10
Alignment explanation
Indices: 864--921 Score: 71
Period size: 10 Copynumber: 5.6 Consensus size: 10
854 TTTATATTAT
*
864 ATTTTTATTG
1 ATTTTTATTC
*
874 AATTTTATTC
1 ATTTTTATTC
884 ATTTTTAATTC
1 ATTTTT-ATTC
895 ATTTTTATTAC
1 ATTTTTATT-C
*
906 ATTTTTATTT
1 ATTTTTATTC
916 ATTTTT
1 ATTTTT
922 TAAATAATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
10 22 0.52
11 20 0.48
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (10 bp):
ATTTTTATTC
Found at i:919 original size:21 final size:21
Alignment explanation
Indices: 858--921 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
848 ATTAGCTTTA
* * *
858 TATTATATTTTTATTGAATTT
1 TATTACATTTTTATTCATTTT
879 TATT-CATTTTTAATTCATTTT
1 TATTACATTTTT-ATTCATTTT
*
900 TATTACATTTTTATTTATTTT
1 TATTACATTTTTATTCATTTT
921 T
1 T
922 TAAATAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.16
21 24 0.65
22 7 0.19
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.69
Consensus pattern (21 bp):
TATTACATTTTTATTCATTTT
Found at i:11268 original size:27 final size:26
Alignment explanation
Indices: 11198--11260 Score: 108
Period size: 26 Copynumber: 2.4 Consensus size: 26
11188 GTTTTGTTCA
*
11198 AAAAAAATAAAAAGCAATTAAATTTC
1 AAAAACATAAAAAGCAATTAAATTTC
11224 AAAAACATAAAAAGCAATTAAATTTC
1 AAAAACATAAAAAGCAATTAAATTTC
*
11250 AAAAACTTAAA
1 AAAAACATAAA
11261 GAATCAATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.65, C:0.10, G:0.03, T:0.22
Consensus pattern (26 bp):
AAAAACATAAAAAGCAATTAAATTTC
Found at i:13192 original size:60 final size:59
Alignment explanation
Indices: 13124--13275 Score: 184
Period size: 60 Copynumber: 2.6 Consensus size: 59
13114 TTTGAGTTGG
*
13124 TCCTTAAACTTTTGAATATTCCAATTTCATCCCTAAACTATGA-CTCTGATTCTAAATT-A
1 TCCTTAAACTTTTGAATATTCCAATTTCATCCCTAAACTACGACCTCT--TTCTAAATTGA
* * * *
13183 GTTCTTAAACTTTT-TATCATTCTAATTTTATCCCTAAACTACGACCTCTTTCTAAATTGA
1 -TCCTTAAACTTTTGAAT-ATTCCAATTTCATCCCTAAACTACGACCTCTTTCTAAATTGA
* *
13243 TCCCTAAACTTTTGAATATTCCAAGTTCATCCC
1 TCCTTAAACTTTTGAATATTCCAATTTCATCCC
13276 CAAATTCATC
Statistics
Matches: 77, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
59 35 0.45
60 38 0.49
61 4 0.05
ACGTcount: A:0.30, C:0.24, G:0.05, T:0.41
Consensus pattern (59 bp):
TCCTTAAACTTTTGAATATTCCAATTTCATCCCTAAACTACGACCTCTTTCTAAATTGA
Found at i:13541 original size:60 final size:61
Alignment explanation
Indices: 13446--13563 Score: 143
Period size: 60 Copynumber: 2.0 Consensus size: 61
13436 TTTGGGGATC
* * *
13446 AATTTAGAATGCATGTCATAGTTTGAGGATGAAATTAAAATATTCAAAAGTTT-GAGAAGT
1 AATTTAGAATGCATGTCATACTTTGAGGATAAAATTAAAATATTCAAAAATTTAGAGAAGT
* * *
13506 AATTTAGAATG-ATAGTTATACTTT-AGGAATAAAATTAGAATATTTAAAAATTTAGAGA
1 AATTTAGAATGCAT-GTCATACTTTGAGG-ATAAAATTAAAATATTCAAAAATTTAGAGA
13564 CCAATTTAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
59 5 0.10
60 40 0.82
61 4 0.08
ACGTcount: A:0.45, C:0.03, G:0.17, T:0.35
Consensus pattern (61 bp):
AATTTAGAATGCATGTCATACTTTGAGGATAAAATTAAAATATTCAAAAATTTAGAGAAGT
Found at i:13674 original size:12 final size:13
Alignment explanation
Indices: 13637--13666 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
13627 AGTTCCCTCC
13637 ACAAAGGAACAAT
1 ACAAAGGAACAAT
13650 ACAAAGGAACAAT
1 ACAAAGGAACAAT
13663 ACAA
1 ACAA
13667 GGATCAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.63, C:0.17, G:0.13, T:0.07
Consensus pattern (13 bp):
ACAAAGGAACAAT
Found at i:15349 original size:30 final size:30
Alignment explanation
Indices: 15268--15552 Score: 140
Period size: 30 Copynumber: 9.7 Consensus size: 30
15258 TTAAATTCAC
*
15268 ATCTTAACTTA-AAAATATATTTTATTCTT
1 ATCTTAACTTATTAAATATATTTTATTCTT
*
15297 ATCTTAACTT-TTAAAAATATATTTTATTTTT
1 ATCTTAACTTATT--AAATATATTTTATTCTT
* *
15328 ATCTTAACTTATTACATATA--TTA-T-AT
1 ATCTTAACTTATTAAATATATTTTATTCTT
* *
15354 -TCTTAAC---TTAAAT-TATTATGTTCTT
1 ATCTTAACTTATTAAATATATTTTATTCTT
* * *
15379 ACCTTAAATTTTTAAATAT-TATTTATTCTT
1 ATCTTAACTTATTAAATATAT-TTTATTCTT
*
15409 ATTTTAACTTA--AAATATATGTTCTATTCTT
1 ATCTTAACTTATTAAATATAT-TT-TATTCTT
**
15439 ATCTTAACTTAAAAAATATATATTTTATT-TT
1 ATCTTAACTT-ATTAA-ATATATTTTATTCTT
* * * *
15470 AATTTTGA-TTAATATATATATATATATTATTTTT
1 -ATCTTAACTT-AT-TA-A-ATATATTTTATTCTT
* * ** *
15504 ATTTTAATTTAAGAAATATATTTTATTTTT
1 ATCTTAACTTATTAAATATATTTTATTCTT
15534 ATCTTAA-TT-TTAAA-ATATT
1 ATCTTAACTTATTAAATATATT
15553 ATAAGAATAA
Statistics
Matches: 201, Mismatches: 30, Indels: 52
0.71 0.11 0.18
Matches are distributed among these distances:
21 2 0.01
22 5 0.02
23 1 0.00
24 1 0.00
25 8 0.04
26 6 0.03
27 6 0.03
28 12 0.06
29 22 0.11
30 57 0.28
31 34 0.17
32 13 0.06
33 24 0.12
34 10 0.05
ACGTcount: A:0.36, C:0.07, G:0.01, T:0.55
Consensus pattern (30 bp):
ATCTTAACTTATTAAATATATTTTATTCTT
Found at i:15371 original size:21 final size:21
Alignment explanation
Indices: 15346--15388 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
15336 TTATTACATA
15346 TATTATATTCTTAACTTAAAT
1 TATTATATTCTTAACTTAAAT
* *
15367 TATTATGTTCTTACCTTAAAT
1 TATTATATTCTTAACTTAAAT
15388 T
1 T
15389 TTTAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.53
Consensus pattern (21 bp):
TATTATATTCTTAACTTAAAT
Found at i:15436 original size:81 final size:83
Alignment explanation
Indices: 15269--15445 Score: 189
Period size: 81 Copynumber: 2.1 Consensus size: 83
15259 TAAATTCACA
* * *
15269 TCTTAACTTAAAAATATATTTTATTCTTATCTTAACTTTTAAAAATATATTTTATTTTTATCTTA
1 TCTTAACTT--AAATATATTATATTCTTACCTTAACTTTTAAAAATATATTTTATTCTTATCTTA
**
15334 ACTTATTACATATATTATAT
64 ACTTAAAACATATATTATAT
* * * *
15354 TCTTAACTTAAAT-TATTATGTTCTTACCTTAAATTTT-TAAATAT-TATTTATTCTTATTTTAA
1 TCTTAACTTAAATATATTATATTCTTACCTTAACTTTTAAAAATATAT-TTTATTCTTATCTTAA
* * *
15416 CTTAAAATATATGTTCTAT
65 CTTAAAACATATATTATAT
*
15435 TCTTATCTTAA
1 TCTTAACTTAA
15446 CTTAAAAAAT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
80 1 0.01
81 44 0.56
82 20 0.26
83 4 0.05
85 9 0.12
ACGTcount: A:0.34, C:0.10, G:0.01, T:0.54
Consensus pattern (83 bp):
TCTTAACTTAAATATATTATATTCTTACCTTAACTTTTAAAAATATATTTTATTCTTATCTTAAC
TTAAAACATATATTATAT
Found at i:16673 original size:20 final size:20
Alignment explanation
Indices: 16629--16674 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
16619 CTTAAAGTTA
* *
16629 TAATTTTAAAAAATATTTTG
1 TAATTTTAAAAAAAATTGTG
16649 TAATTTTAAAAACAAATTGTG
1 TAATTTTAAAAA-AAATTGTG
16670 -AATTT
1 TAATTT
16675 ATATATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (20 bp):
TAATTTTAAAAAAAATTGTG
Found at i:19035 original size:117 final size:117
Alignment explanation
Indices: 18886--19122 Score: 327
Period size: 117 Copynumber: 2.0 Consensus size: 117
18876 TTATAGCTAA
* * * * *
18886 AAATGATCTTCTTTTGAAAGCTAAAATAGATTTTGAAAATCAAAATGAAATGTTGAAAAAGGAGT
1 AAATGATCTTCTTCTAAAAACTAAAATAGATTTGGAAAATCAAAATGAAATATTGAAAAAGGA-T
*
18951 -TAGAGCTTTTAAAAATGAAATCTGAAAAACT-TTGAAAAAG-AAATTTTGAATT
65 CTAGAGCTTTCAAAAATGAAATCTG--AAACTATTGAAAAAGAAAATTTTGAATT
* *
19003 AAATGATCTTCTTCTAAAAACTAAAATAGATTTGGAGAATCAAAATGAAATATTGAAGAAGGATC
1 AAATGATCTTCTTCTAAAAACTAAAATAGATTTGGAAAATCAAAATGAAATATTGAAAAAGGATC
* * *
19068 TAGAGCTTTCAAAAATGAAATTTGAAAGTATTGAAAAAGAAAATTTTGATTT
66 TAGAGCTTTCAAAAATGAAATCTGAAACTATTGAAAAAGAAAATTTTGAATT
19120 AAA
1 AAA
19123 AGTGTCAGAA
Statistics
Matches: 106, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
115 4 0.04
116 10 0.09
117 92 0.87
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.31
Consensus pattern (117 bp):
AAATGATCTTCTTCTAAAAACTAAAATAGATTTGGAAAATCAAAATGAAATATTGAAAAAGGATC
TAGAGCTTTCAAAAATGAAATCTGAAACTATTGAAAAAGAAAATTTTGAATT
Found at i:19569 original size:14 final size:14
Alignment explanation
Indices: 19550--19587 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
19540 ACACAATAAG
19550 TAAATAAAATAAAC
1 TAAATAAAATAAAC
19564 TAAATAAAATAAAC
1 TAAATAAAATAAAC
*
19578 AAAATGAAAA
1 TAAAT-AAAA
19588 GAAATAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (14 bp):
TAAATAAAATAAAC
Found at i:19698 original size:2 final size:2
Alignment explanation
Indices: 19691--19739 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
19681 CAATAAAAAC
19691 AT AT AT 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 AT AT AT
*
19733 AC AT AT A
1 AT AT AT A
19740 CAAATAATGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:19859 original size:18 final size:18
Alignment explanation
Indices: 19828--19869 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
19818 AGAAAAAGAG
19828 AAAAT-AATAATAATAAA
1 AAAATAAATAATAATAAA
*
19845 AAAATAAATATTAATAAA
1 AAAATAAATAATAATAAA
*
19863 GAAATAA
1 AAAATAA
19870 TTAAACATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
AAAATAAATAATAATAAA
Found at i:21161 original size:19 final size:19
Alignment explanation
Indices: 21137--21174 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
21127 GATACATATA
21137 TTATATAATATAATATAAT
1 TTATATAATATAATATAAT
* *
21156 TTATATTATATAATGTAAT
1 TTATATAATATAATATAAT
21175 AACATTAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TTATATAATATAATATAAT
Found at i:21996 original size:251 final size:249
Alignment explanation
Indices: 21553--22151 Score: 831
Period size: 251 Copynumber: 2.4 Consensus size: 249
21543 GAAGTTGGGT
* * *
21553 ACGATATCTTTCGTTGTGAAGTTAAAATCGTAGATGGCTCATTCGTTGTGAAGTTGA-CCTTTGA
1 ACGATATCATTCATTGTGAAGTTGAAATCGTAGATGGCTCATTCGTTGTGAAGTTGAGCC-TTGA
* *
21617 ATTAGATATCCTTAGTCGTGAAGTTGAAATCCAATTTTATGTAAGTTGCATTGTTTCAAGTCCAA
65 ATTAGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTATGTAAGTTGCATTGTTTCAAGTCCAA
* * * * *
21682 TATCCTTCACTGTGAAGTTGAAATTGGCTTTGAATGAAACTGGGATGCCCCTTCGCTGTGAAGTT
130 TATCCTTCACCGTGAAGTTGAAATTGGCTCTGAATAAAACTGGGAAGACCCTTCGCTGTGAAGTT
* * * *
21747 GAGCTTTGAATTGGATATCCTTCGCCGTGAAGTTGAAATCCAATTTTGTGTATAAGC
195 GAGCTTCGAATTGGATATCCTTCGCCATGAACTTGAAATCCAATTTTGAGT-T-AGC
* * * * *
21804 ACGATATCATTCCTCGTGAAGTTGAAATTGTAAATGGCTCGTTCGTTGTGAAGTTGAGCCTTGAA
1 ACGATATCATTCATTGTGAAGTTGAAATCGTAGATGGCTCATTCGTTGTGAAGTTGAGCCTTGAA
* * * ** *
21869 TTAGATATCATTCGTCGTGAAGTTGAAATCTAATCTTGTGTAAGTTTTATTGTTTCGAGTCCAAT
66 TTAGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTATGTAAGTTGCATTGTTTCAAGTCCAAT
*
21934 ATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAATAAAACTGGGAAGACCCTTCGCTGTGAAGTTG
131 ATCCTTCACCGTGAAGTTGAAATTGGCTCTGAATAAAACTGGGAAGACCCTTCGCTGTGAAGTTG
* ** *
21999 AGCTTCGAATTGGATATCTTTCTTCATGAACTTGAAATCCAATTTTGAGTTGGC
196 AGCTTCGAATTGGATATCCTTCGCCATGAACTTGAAATCCAATTTTGAGTTAGC
* * * * *
22053 ACAATATCCTTCATTGTGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAGTTAAGCCTTGAA
1 ACGATATCATTCATTGTGAAGTTGAAATCGTAGATGGCTCATTCGTTGTGAAGTTGAGCCTTGAA
* *
22118 TTGGATATCCTTCATCGTGAAGTTGAAATCCAAT
66 TTAGATATCCTTCGTCGTGAAGTTGAAATCCAAT
22152 ATGAAGATTA
Statistics
Matches: 304, Mismatches: 43, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
249 87 0.29
250 1 0.00
251 214 0.70
252 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.36
Consensus pattern (249 bp):
ACGATATCATTCATTGTGAAGTTGAAATCGTAGATGGCTCATTCGTTGTGAAGTTGAGCCTTGAA
TTAGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTATGTAAGTTGCATTGTTTCAAGTCCAAT
ATCCTTCACCGTGAAGTTGAAATTGGCTCTGAATAAAACTGGGAAGACCCTTCGCTGTGAAGTTG
AGCTTCGAATTGGATATCCTTCGCCATGAACTTGAAATCCAATTTTGAGTTAGC
Found at i:23258 original size:13 final size:13
Alignment explanation
Indices: 23226--23270 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
23216 CCTAAACGTT
*
23226 TTTTTTCTTTTTGC
1 TTTTTTATTTTT-C
*
23240 TCTTTTATTTTTC
1 TTTTTTATTTTTC
23253 TTTTTTATTTTTC
1 TTTTTTATTTTTC
23266 TTTTT
1 TTTTT
23271 CGTCTTAGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 18 0.64
14 10 0.36
ACGTcount: A:0.04, C:0.11, G:0.02, T:0.82
Consensus pattern (13 bp):
TTTTTTATTTTTC
Found at i:23270 original size:20 final size:20
Alignment explanation
Indices: 23227--23271 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
23217 CTAAACGTTT
*
23227 TTTTTCTTTTTGCTCTTTTA
1 TTTTTCTTTTTGATCTTTTA
* *
23247 TTTTTCTTTTTTAT-TTTTC
1 TTTTTCTTTTTGATCTTTTA
23266 TTTTTC
1 TTTTTC
23272 GTCTTAGGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.80
Consensus pattern (20 bp):
TTTTTCTTTTTGATCTTTTA
Found at i:31560 original size:19 final size:19
Alignment explanation
Indices: 31536--31572 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
31526 GTTTGTATCT
31536 TCTTTTCACTTTAACTTTA
1 TCTTTTCACTTTAACTTTA
*
31555 TCTTTTTACTTTAACTTT
1 TCTTTTCACTTTAACTTT
31573 CTTTCATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (19 bp):
TCTTTTCACTTTAACTTTA
Found at i:45980 original size:57 final size:55
Alignment explanation
Indices: 45897--46032 Score: 166
Period size: 57 Copynumber: 2.4 Consensus size: 55
45887 AACGAGTAAA
* *
45897 GAAAGATAAAGAAAAGAATAAAAATAAAGATAACAAGTAAATAACATAAACAAAAT
1 GAAA-ATAAAGAAAAGAATAAAAATAAAGACAACAAGTAAATAAAATAAACAAAAT
* * *
45953 GAAAATAAAGAAACAAGAATAAGAATAAAGACAATAAGTAAATAAAATAAACTAAAT
1 GAAAATAAAG-AA-AAGAATAAAAATAAAGACAACAAGTAAATAAAATAAACAAAAT
* *
46010 -AAAATAAACAAAATGAAAAAAAA
1 GAAAATAAAGAAAA-GAATAAAAA
46033 ATTAAAAGGA
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
54 2 0.03
55 15 0.22
56 14 0.20
57 38 0.55
ACGTcount: A:0.71, C:0.05, G:0.10, T:0.14
Consensus pattern (55 bp):
GAAAATAAAGAAAAGAATAAAAATAAAGACAACAAGTAAATAAAATAAACAAAAT
Found at i:46010 original size:14 final size:14
Alignment explanation
Indices: 45934--46028 Score: 59
Period size: 14 Copynumber: 6.6 Consensus size: 14
45924 AGATAACAAG
*
45934 TAAATAACATAAAC
1 TAAATAAAATAAAC
*
45948 AAAATGAAAATAAA-
1 TAAAT-AAAATAAAC
* * *
45962 GAAACAAGAATAAGAA
1 TAAATAA-AATAA-AC
* * *
45978 TAAAGACAAT-AAG
1 TAAATAAAATAAAC
45991 TAAATAAAATAAAC
1 TAAATAAAATAAAC
46005 TAAATAAAATAAAC
1 TAAATAAAATAAAC
*
46019 AAAATGAAAA
1 TAAAT-AAAA
46029 AAAAATTAAA
Statistics
Matches: 63, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
13 11 0.17
14 33 0.52
15 15 0.24
16 4 0.06
ACGTcount: A:0.71, C:0.06, G:0.07, T:0.16
Consensus pattern (14 bp):
TAAATAAAATAAAC
Found at i:46096 original size:2 final size:2
Alignment explanation
Indices: 46089--46166 Score: 149
Period size: 2 Copynumber: 39.5 Consensus size: 2
46079 AACAATAAAA
46089 AT AT AT 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 AT AT AT
46131 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
46167 AAAAAATAAA
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 74 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:46179 original size:17 final size:17
Alignment explanation
Indices: 46159--46197 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
46149 ATATATATAT
46159 AATATATAAAAA-AATAA
1 AATA-ATAAAAATAATAA
46176 AATAATAAAAATAATAA
1 AATAATAAAAATAATAA
46193 AATAA
1 AATAA
46198 ATTTAAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (17 bp):
AATAATAAAAATAATAA
Found at i:46211 original size:22 final size:22
Alignment explanation
Indices: 46164--46269 Score: 61
Period size: 24 Copynumber: 4.5 Consensus size: 22
46154 TATATAATAT
46164 ATAAAAAAATAAAATAATAAAA
1 ATAAAAAAATAAAATAATAAAA
* * *
46186 ATAATAAAATAAATTTAA-AAAC
1 ATAAAAAAATAAA-ATAATAAAA
** *
46208 ATAAAGAGGGATAATAATAATAATA
1 ATAAA-A-AAATAA-AATAATAAAA
* *
46233 ATAATAATAATAAAGAAAATAAATA
1 ATAA-AAAAATAAA-ATAATAAA-A
*
46258 ATAAAGAAATAA
1 ATAAAAAAATAA
46270 TTATATATAT
Statistics
Matches: 61, Mismatches: 15, Indels: 14
0.68 0.17 0.16
Matches are distributed among these distances:
22 19 0.31
23 5 0.08
24 23 0.38
25 13 0.21
26 1 0.02
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.23
Consensus pattern (22 bp):
ATAAAAAAATAAAATAATAAAA
Found at i:46261 original size:3 final size:3
Alignment explanation
Indices: 46218--46245 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
46208 ATAAAGAGGG
46218 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
46246 AGAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:54347 original size:18 final size:19
Alignment explanation
Indices: 54324--54361 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
54314 GAATGCAATA
54324 AGGGTA-CGAATA-CCCTAT
1 AGGGTACCG-ATACCCCTAT
54342 AGGGTACCGATACCCCTAT
1 AGGGTACCGATACCCCTAT
54361 A
1 A
54362 CAAAGAGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (19 bp):
AGGGTACCGATACCCCTAT
Found at i:55876 original size:5 final size:5
Alignment explanation
Indices: 55866--55890 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
55856 ATTATTTTAA
55866 ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT
55891 TTATCTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:55945 original size:102 final size:104
Alignment explanation
Indices: 55754--55953 Score: 350
Period size: 102 Copynumber: 1.9 Consensus size: 104
55744 TTAAACTCAA
*
55754 ATTTTAAGATATTATTTTAAATATTATATTATATTTTATCTTATCTTTGTTTTAGGTATTTTAGT
1 ATTTTAAGATATTATATT-AATATTATATTATATTTTATCTTATCTTTGTTTTAGGTATTTTAGT
*
55819 TAAAATAGTTTTAAGTATTTTAATTAGGATTTAGGATATT
65 TAAAATAGTTTTAAGTATTTTAATTAGAATTTAGGATATT
55859 ATTTTAA-ATATTATATT-ATATTATATTATATTTTATCTTATCTTTGTTTTAGGTATTTTAGTT
1 ATTTTAAGATATTATATTAATATTATATTATATTTTATCTTATCTTTGTTTTAGGTATTTTAGTT
*
55922 TAAATAGTTTTAAGTATTTTAATTAGAATTTA
66 AAAATAGTTTTAAGTATTTTAATTAGAATTTA
55954 TTTTCTTTAT
Statistics
Matches: 92, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
102 76 0.83
104 9 0.10
105 7 0.08
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (104 bp):
ATTTTAAGATATTATATTAATATTATATTATATTTTATCTTATCTTTGTTTTAGGTATTTTAGTT
AAAATAGTTTTAAGTATTTTAATTAGAATTTAGGATATT
Found at i:56139 original size:18 final size:18
Alignment explanation
Indices: 56116--56150 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
56106 CTCTTTCAAG
56116 TTTTAAAATTTTATTTTA
1 TTTTAAAATTTTATTTTA
* *
56134 TTTTAAAGTTTTGTTTT
1 TTTTAAAATTTTATTTT
56151 CAAATATGCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TTTTAAAATTTTATTTTA
Found at i:63373 original size:54 final size:54
Alignment explanation
Indices: 63307--63435 Score: 233
Period size: 54 Copynumber: 2.4 Consensus size: 54
63297 GCATTGATGC
*
63307 ACACTT-AGTGCACCGATGCACTAAGTGTTCCAACGGTCAAAATATTTGAATTTT
1 ACACTTGA-TGCACCGATGCACTAAGTGTTCCAACGGTCAAAATATTTGAATATT
63361 ACACTTGATGCACCGATGCACTAAGTGTTCCAACGGTCAAAATATTTGAATATT
1 ACACTTGATGCACCGATGCACTAAGTGTTCCAACGGTCAAAATATTTGAATATT
63415 ACACTTGATGCACCGATGCAC
1 ACACTTGATGCACCGATGCAC
63436 CTTGTGTATA
Statistics
Matches: 73, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
54 72 0.99
55 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (54 bp):
ACACTTGATGCACCGATGCACTAAGTGTTCCAACGGTCAAAATATTTGAATATT
Found at i:68861 original size:23 final size:23
Alignment explanation
Indices: 68789--68870 Score: 82
Period size: 23 Copynumber: 3.6 Consensus size: 23
68779 ACACTTAACA
68789 GTGCATCGATGCA-TCCCTTTGAAT
1 GTGCATCGATGCACT-CC-TTGAAT
* *
68813 GTGCATCGAT--ACACCATGAA-
1 GTGCATCGATGCACTCCTTGAAT
*
68833 GATGCACCGATGCACTCCTTGAAT
1 G-TGCATCGATGCACTCCTTGAAT
68857 GTGCATCGATGCAC
1 GTGCATCGATGCAC
68871 AAAGCCATGC
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
20 1 0.02
21 12 0.26
22 3 0.06
23 20 0.43
24 11 0.23
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (23 bp):
GTGCATCGATGCACTCCTTGAAT
Found at i:70748 original size:20 final size:20
Alignment explanation
Indices: 70719--70756 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
70709 TTTTAAAGGG
70719 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
70739 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
70757 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:70974 original size:54 final size:54
Alignment explanation
Indices: 70908--71034 Score: 224
Period size: 54 Copynumber: 2.4 Consensus size: 54
70898 GCATTGATGC
70908 ACACTT-AGTGCACCGATGCACTAAGTGTTCCAACGGTCAAAATATTTGAATTTT
1 ACACTTGA-TGCACCGATGCACTAAGTGTTCCAACGGTCAAAATATTTGAATTTT
70962 ACACTTGATGCACCGATGCACTAAGTGTTCCAACGGTCAAAATATTTGAATTTT
1 ACACTTGATGCACCGATGCACTAAGTGTTCCAACGGTCAAAATATTTGAATTTT
71016 ACAC-TGATGCA-CGATGCAC
1 ACACTTGATGCACCGATGCAC
71035 CATGGGTATG
Statistics
Matches: 72, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
52 8 0.11
53 7 0.10
54 56 0.78
55 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (54 bp):
ACACTTGATGCACCGATGCACTAAGTGTTCCAACGGTCAAAATATTTGAATTTT
Found at i:77879 original size:57 final size:59
Alignment explanation
Indices: 77816--77955 Score: 204
Period size: 57 Copynumber: 2.5 Consensus size: 59
77806 ATATATTTTA
*
77816 TTGAGTCA-TCGACTATT-AAAGTTACACAATAGTCCCAAACTATGGAGAGTTGCTTT-G
1 TTGAGTCACTCGACTATTAAAAGTTACACAATAATCCCAAACTATGGAGAGTTG-TTTCG
77873 TTGAGTCACTC-ACTATTAAAAG-TACACAATAATCCCAAACTATGGAGAGTTGTTTCG
1 TTGAGTCACTCGACTATTAAAAGTTACACAATAATCCCAAACTATGGAGAGTTGTTTCG
*
77930 -TGAG-CACTCGACAATTAAAAGTTACA
1 TTGAGTCACTCGACTATTAAAAGTTACA
77956 AAATGGCATC
Statistics
Matches: 76, Mismatches: 2, Indels: 10
0.86 0.02 0.11
Matches are distributed among these distances:
55 5 0.07
56 17 0.22
57 48 0.63
58 6 0.08
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (59 bp):
TTGAGTCACTCGACTATTAAAAGTTACACAATAATCCCAAACTATGGAGAGTTGTTTCG
Done.