Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006129.1 Hibiscus syriacus cultivar Beakdansim tig00014531_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: 66444
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2418 original size:27 final size:27
Alignment explanation
Indices: 2388--2439 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
2378 TTTTAGGTAA
*
2388 TTGGGTGGGTTTGGGTTTTATTTTGGT
1 TTGGGTGGGTTTGGGTCTTATTTTGGT
* *
2415 TTGGTTTGGTTTGGGTCTTATTTTG
1 TTGGGTGGGTTTGGGTCTTATTTTG
2440 ATTTAGTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.04, C:0.02, G:0.37, T:0.58
Consensus pattern (27 bp):
TTGGGTGGGTTTGGGTCTTATTTTGGT
Found at i:2448 original size:27 final size:27
Alignment explanation
Indices: 2395--2450 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
2385 TAATTGGGTG
* * *
2395 GGTTTGGGTTTTATTTTGGTTTGGTTT
1 GGTTTGGGTCTTATTTTGATTTAGTTT
2422 GGTTTGGGTCTTATTTTGATTTAGTTT
1 GGTTTGGGTCTTATTTTGATTTAGTTT
2449 GG
1 GG
2451 GCTTGAGGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.07, C:0.02, G:0.32, T:0.59
Consensus pattern (27 bp):
GGTTTGGGTCTTATTTTGATTTAGTTT
Found at i:4619 original size:28 final size:28
Alignment explanation
Indices: 4574--4629 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
4564 AGTTGATGGT
* *
4574 AAAAAAAGAGTAGCAAGAAGAA-AAAAAG
1 AAAAAAAGAGAAGAAAGAA-AACAAAAAG
4602 AAAAAAAGAGAAGAAAGAAAACAAAAAG
1 AAAAAAAGAGAAGAAAGAAAACAAAAAG
4630 CAAATTGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.08
28 23 0.92
ACGTcount: A:0.75, C:0.04, G:0.20, T:0.02
Consensus pattern (28 bp):
AAAAAAAGAGAAGAAAGAAAACAAAAAG
Found at i:4855 original size:3 final size:3
Alignment explanation
Indices: 4847--4906 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
4837 GTCCGCAATT
4847 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
4895 GAA GAA GAA GAA
1 GAA GAA GAA GAA
4907 ATCAAGTAAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:4969 original size:15 final size:15
Alignment explanation
Indices: 4949--4978 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4939 CTACTTGGAG
4949 TGATGAGGATGTCAT
1 TGATGAGGATGTCAT
4964 TGATGAGGATGTCAT
1 TGATGAGGATGTCAT
4979 CAATGACGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.33, T:0.33
Consensus pattern (15 bp):
TGATGAGGATGTCAT
Found at i:4984 original size:15 final size:15
Alignment explanation
Indices: 4951--4984 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4941 ACTTGGAGTG
**
4951 ATGAGGATGTCATTG
1 ATGAGGATGTCATCA
4966 ATGAGGATGTCATCA
1 ATGAGGATGTCATCA
4981 ATGA
1 ATGA
4985 CGAAGAGGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.29
Consensus pattern (15 bp):
ATGAGGATGTCATCA
Found at i:7154 original size:13 final size:13
Alignment explanation
Indices: 7136--7160 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7126 GTGCTGAATA
7136 TAAACGAACAAAG
1 TAAACGAACAAAG
7149 TAAACGAACAAA
1 TAAACGAACAAA
7161 CATAAATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.16, G:0.12, T:0.08
Consensus pattern (13 bp):
TAAACGAACAAAG
Found at i:9292 original size:14 final size:16
Alignment explanation
Indices: 9261--9300 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
9251 ACCAAGTTTA
*
9261 TTATATATATATTATT
1 TTATATTTATATTATT
9277 TTATATTTA-ATT-TT
1 TTATATTTATATTATT
9291 TT-TATTTATA
1 TTATATTTATA
9301 ATTCTCAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 6 0.27
14 5 0.23
15 3 0.14
16 8 0.36
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATATTTATATTATT
Found at i:9403 original size:39 final size:38
Alignment explanation
Indices: 9322--9412 Score: 105
Period size: 39 Copynumber: 2.3 Consensus size: 38
9312 ATTTCATTCG
9322 AACATTCA-AAATTCCTAATTTCTTAAATTTTATCATCAT
1 AACATT-ATAAATTCCTAATTTCTTAAATTTTATCAT-AT
* * *
9361 AACATTTTAAATTCTTAATTTCTTAAATTATTTTACAT-T
1 AACATTATAAATTCCTAATTTCTTAAATT-TTAT-CATAT
9400 AACATTATAAATT
1 AACATTATAAATT
9413 ATTTTTTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
39 39 0.87
40 3 0.07
41 3 0.07
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (38 bp):
AACATTATAAATTCCTAATTTCTTAAATTTTATCATAT
Found at i:10740 original size:20 final size:20
Alignment explanation
Indices: 10717--10779 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
10707 GGGTCTTTTT
* *
10717 GACCCGAACTAAGTGAACCC
1 GACCCGAACCAAGTCAACCC
10737 GACCCGAACCAAGTCAA-CC
1 GACCCGAACCAAGTCAACCC
* * *
10756 AACCCGAATCAAGTCAACTC
1 GACCCGAACCAAGTCAACCC
10776 GACC
1 GACC
10780 TCACCCGTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
19 17 0.47
20 19 0.53
ACGTcount: A:0.37, C:0.38, G:0.16, T:0.10
Consensus pattern (20 bp):
GACCCGAACCAAGTCAACCC
Found at i:10762 original size:19 final size:19
Alignment explanation
Indices: 10718--10773 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
10708 GGTCTTTTTG
* * *
10718 ACCCGAACTAAGTGAACCCG
1 ACCCGAACCAAGTCAA-CCA
10738 ACCCGAACCAAGTCAACCA
1 ACCCGAACCAAGTCAACCA
*
10757 ACCCGAATCAAGTCAAC
1 ACCCGAACCAAGTCAAC
10774 TCGACCTCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.39, C:0.38, G:0.14, T:0.09
Consensus pattern (19 bp):
ACCCGAACCAAGTCAACCA
Found at i:11688 original size:27 final size:27
Alignment explanation
Indices: 11631--11688 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
11621 GATTAGATTG
* * *
11631 AAGTGTAAAATGACCAAAATTCCCCTG
1 AAGTGTAAAATGACCAAAAGTACCCTC
* *
11658 AAGTGTAAAATGACCCAAAGTACCTTC
1 AAGTGTAAAATGACCAAAAGTACCCTC
11685 AAGT
1 AAGT
11689 CTTGGAATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (27 bp):
AAGTGTAAAATGACCAAAAGTACCCTC
Found at i:18328 original size:26 final size:27
Alignment explanation
Indices: 18299--18357 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
18289 CAAGTCTAGG
*
18299 AATGACTAAAT-ACCCTAAAGCT-CCAA
1 AATGACTAAATCAACCTAAAG-TACCAA
* *
18325 AATGAATAAATCAACCTAGAGTACCAA
1 AATGACTAAATCAACCTAAAGTACCAA
18352 AATGAC
1 AATGAC
18358 CTAGAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.49, C:0.22, G:0.10, T:0.19
Consensus pattern (27 bp):
AATGACTAAATCAACCTAAAGTACCAA
Found at i:27269 original size:35 final size:35
Alignment explanation
Indices: 27218--27318 Score: 141
Period size: 35 Copynumber: 2.9 Consensus size: 35
27208 TGGAGTATGA
*
27218 AGGTTCAACTCAGTCAAAATAGTAATTCCTTATAT
1 AGGTTCAACTCGGTCAAAATAGTAATTCCTTATAT
*
27253 AGGTTCAACTCGGTCAAACTAGTAATTCCTTATAT
1 AGGTTCAACTCGGTCAAAATAGTAATTCCTTATAT
* * *
27288 AGGTTCAGAC-CGATCAAGATGGTAATTCCTT
1 AGGTTCA-ACTCGGTCAAAATAGTAATTCCTT
27319 GCGGACCTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
35 57 0.97
36 2 0.03
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (35 bp):
AGGTTCAACTCGGTCAAAATAGTAATTCCTTATAT
Found at i:32883 original size:12 final size:12
Alignment explanation
Indices: 32868--32913 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
32858 TTTAAATTAG
* *
32868 TATTTATTTATT
1 TATTTATTCATA
32880 TATTTATTCATA
1 TATTTATTCATA
32892 TATTTATT-ATA
1 TATTTATTCATA
32903 TATTTTATTCA
1 TA-TTTATTCA
32914 CTAATATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
11 5 0.17
12 24 0.80
13 1 0.03
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (12 bp):
TATTTATTCATA
Found at i:32895 original size:24 final size:24
Alignment explanation
Indices: 32868--32913 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
32858 TTTAAATTAG
*
32868 TATTTATT-TATTTATTTATTCATA
1 TATTTATTATATAT-TTTATTCATA
32892 TATTTATTATATATTTTATTCA
1 TATTTATTATATATTTTATTCA
32914 CTAATATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (24 bp):
TATTTATTATATATTTTATTCATA
Found at i:33749 original size:24 final size:23
Alignment explanation
Indices: 33706--33753 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
33696 TAATTTATAA
33706 TTTTATATATATATACATATTAT
1 TTTTATATATATATACATATTAT
* *
33729 TTTTATAGTATTTATATATATTAT
1 TTTTATA-TATATATACATATTAT
33753 T
1 T
33754 AATATTACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
TTTTATATATATATACATATTAT
Found at i:35161 original size:15 final size:14
Alignment explanation
Indices: 35136--35177 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
35126 TTTTCATGCA
35136 TACAT-TTGCATTT
1 TACATCTTGCATTT
35149 TACATCCTTGCATTT
1 TACAT-CTTGCATTT
* *
35164 TTCATTTTGCATTT
1 TACATCTTGCATTT
35178 ATACTGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 5 0.20
14 8 0.32
15 12 0.48
ACGTcount: A:0.19, C:0.19, G:0.07, T:0.55
Consensus pattern (14 bp):
TACATCTTGCATTT
Found at i:41136 original size:114 final size:114
Alignment explanation
Indices: 40936--41248 Score: 527
Period size: 114 Copynumber: 2.7 Consensus size: 114
40926 CCATATGCTC
*
40936 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCTAAAACCAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAACCAAT
*
41001 CATTAGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGAAGACCCA
66 CATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGAAGACCCA
*
41050 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAACTAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAACCAAT
*
41115 CATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCCA
66 CATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGAAGACCCA
* * * * * *
41164 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGATTCGGTAGGAACCCCAGAACCGAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAACCAAT
*
41229 CATTGGAATTGAAAGATGAA
66 CATTGGATTTGAAAGATGAA
41249 CTGCATGATC
Statistics
Matches: 187, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 187 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (114 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAACCAAT
CATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGAAGACCCA
Found at i:43962 original size:22 final size:22
Alignment explanation
Indices: 43931--43985 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
43921 ATCTACACTC
**
43931 TTCAAAGATGGTAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
43953 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
43975 TTCAAAGATGA
1 TTCAAAGATGA
43986 AAGCTTTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:44785 original size:76 final size:76
Alignment explanation
Indices: 44659--44839 Score: 299
Period size: 76 Copynumber: 2.4 Consensus size: 76
44649 CTATTTCCCA
44659 ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAA
1 ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAA
*
44724 GCCTTAGGGTC
66 ACCTTAGGGTC
*
44735 ATCTGTAAGTCCTACAGTGCATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAA
1 ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAA
*
44800 ACCTTCGGGTC
66 ACCTTAGGGTC
* * * *
44811 AGCTATAAGCCCTACAGTGCATAATGTTT
1 ATCTGTAAGTCCTACAGTGCATGATGTTT
44840 TTTCTTAAAA
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
76 98 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (76 bp):
ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAA
ACCTTAGGGTC
Found at i:45056 original size:111 final size:113
Alignment explanation
Indices: 44850--45267 Score: 715
Period size: 111 Copynumber: 3.8 Consensus size: 113
44840 TTTCTTAAAA
*
44850 CATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAA
1 CATTTCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAA
44915 GAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATCAG
66 GAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATCAG
*
44963 CATTTCCA-GAAGAGTTCATAATGAGAAGAACTCATCTGAAG-ATGAAGAAGAAGTTCATAATAA
1 CATTTCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAA
45026 GAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATCAG
66 GAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATCAG
*
45074 CATTTCCA-GAAGAGTTCATAATGAGAAGAACAT-ATCTGAAGAAGGAAGAAGAAGTTCATAATG
1 CATTTCCAGGAAGAGTTCATAATGAGAAGAAC-TCATCTGAAGAAGGAAGAAGAAGTTCATAATA
45137 AGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATCAG
65 AGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATCAG
* ** *
45186 CATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAG-AGG-AGAAG-AGTTCATAATGA
1 CATTTCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAA
45248 GAAGAACTTGTTCAACCTTT
66 GAAGAACTTGTTCAACCTTT
45268 GCATGACTCT
Statistics
Matches: 294, Mismatches: 7, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
110 32 0.11
111 113 0.38
112 112 0.38
113 37 0.13
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.28
Consensus pattern (113 bp):
CATTTCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAA
GAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATCAG
Found at i:45346 original size:223 final size:222
Alignment explanation
Indices: 44863--45273 Score: 623
Period size: 223 Copynumber: 1.9 Consensus size: 222
44853 TTCCAGGTAG
* * *
44863 AGTTCATAATGAGAAGAAC-TCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTT
1 AGTTCAGAATGAGAAGAACAT-ATCTCAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
44927 CAACCTTTTGCTTGAATTCATCATTCGATGGATCAGCATTTCCAGAAGAGTTCATAATGAGAAGA
65 CAACCTTTTGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGAAGAGTTCATAATGAGAAGA
*
44992 ACTCATCTGAAGATGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCTTGAATTC
130 ACTCATCTGAAGATGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCATGAATTC
* ** * *
45057 ATCATTCGATGGATCAGCATTTCCAGAAG
195 ATCA-TCGAGGGATCAGCATCACCACAAC
* *
45086 AGTTCATAATGAGAAGAACATATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCAGAATGAGAAGAACATATCTCAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
**
45151 AACCTTTTGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTCGAGTTCATAATGAGAAGA
66 AACCTTTTGCTTGAATTCATCATTCGATGGATCAGCATTGCCA-GAAGAGTTCATAATGAGAAGA
* *
45216 ACTCATCTGAAGA-GGAGAAG-AGTTCATAATGAGAAGAACTTGTTCAACC-TTTGCATGA
130 ACTCATCTGAAGATGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCATGA
45274 CTCTATCACA
Statistics
Matches: 179, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
221 8 0.04
222 28 0.16
223 110 0.61
224 33 0.18
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (222 bp):
AGTTCAGAATGAGAAGAACATATCTCAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTTTGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGAAGAGTTCATAATGAGAAGAA
CTCATCTGAAGATGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCATGAATTCA
TCATCGAGGGATCAGCATCACCACAAC
Found at i:51141 original size:19 final size:19
Alignment explanation
Indices: 51117--51153 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
51107 ATAACCAACA
*
51117 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
*
51136 AAATCGTAACGCGATCTC
1 AAATCGCAACGCGATCTC
51154 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:51208 original size:20 final size:20
Alignment explanation
Indices: 51183--51221 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
51173 CCAGATTCGC
*
51183 AACGCGATTTTGACTATCGT
1 AACGCGATTCTGACTATCGT
51203 AACGCGATTCTGACTATCG
1 AACGCGATTCTGACTATCG
51222 CAACACTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (20 bp):
AACGCGATTCTGACTATCGT
Found at i:51394 original size:17 final size:17
Alignment explanation
Indices: 51372--51409 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
51362 CGATATCCGT
51372 TCCTATATCCAACGACA
1 TCCTATATCCAACGACA
51389 TCCTATATCCAACGACA
1 TCCTATATCCAACGACA
51406 TCCT
1 TCCT
51410 TCCCCATCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.32, C:0.37, G:0.05, T:0.26
Consensus pattern (17 bp):
TCCTATATCCAACGACA
Found at i:52334 original size:14 final size:14
Alignment explanation
Indices: 52305--52341 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
52295 AGAAAAAGAA
52305 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
52320 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
52334 GAAGAAAA
1 GAAGAAAA
52342 TGCCACAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:54346 original size:18 final size:18
Alignment explanation
Indices: 54323--54357 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
54313 AGCAAAAGGC
*
54323 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
54341 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
54358 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:54553 original size:20 final size:20
Alignment explanation
Indices: 54528--54644 Score: 171
Period size: 20 Copynumber: 5.8 Consensus size: 20
54518 TTACACATTC
*
54528 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
54548 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
*
54568 ATTTGACTATCGCAACGCAA
1 ATTTGACTATCGCAACGCGA
**
54588 ATTTGACTATCGCAACATGA
1 ATTTGACTATCGCAACGCGA
* *
54608 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
54628 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
54645 AGAAAATCGC
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 86 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:54583 original size:40 final size:40
Alignment explanation
Indices: 54528--54644 Score: 189
Period size: 40 Copynumber: 2.9 Consensus size: 40
54518 TTACACATTC
54528 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACGTGA
1 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACGTGA
* * *
54568 ATTTGACTATCGCAACGCAAATTTGACTATCGCAACATGA
1 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACGTGA
* *
54608 ATTTGATTATCGCAACGGGAATTTGACTATCGCAACG
1 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACG
54645 AGAAAATCGC
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 70 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (40 bp):
ATTTGAATATCGCAACGCGAATTTGACTATCGCAACGTGA
Found at i:54621 original size:60 final size:60
Alignment explanation
Indices: 54528--54644 Score: 189
Period size: 60 Copynumber: 1.9 Consensus size: 60
54518 TTACACATTC
* *
54528 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACGTGAATTTGACTATCGCAACGCAA
1 ATTTGAATATCGCAACACGAATTTGACTATCGCAACGGGAATTTGACTATCGCAACGCAA
* * *
54588 ATTTGACTATCGCAACATGAATTTGATTATCGCAACGGGAATTTGACTATCGCAACG
1 ATTTGAATATCGCAACACGAATTTGACTATCGCAACGGGAATTTGACTATCGCAACG
54645 AGAAAATCGC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (60 bp):
ATTTGAATATCGCAACACGAATTTGACTATCGCAACGGGAATTTGACTATCGCAACGCAA
Found at i:54670 original size:34 final size:33
Alignment explanation
Indices: 54616--54707 Score: 87
Period size: 34 Copynumber: 2.7 Consensus size: 33
54606 GAATTTGATT
* *
54616 ATCGCAACGGGAATTTGACTATCGCAACG-AGAAA
1 ATCGCAAAGCGAA-TTGACTATCGCAACGCA-AAA
* * *
54650 ATCGCAAAGCGTATTAGACTATTGCAATGCAAAA
1 ATCGCAAAGCGAATT-GACTATCGCAACGCAAAA
* *
54684 ATCGCAATGCGAATTGACTTTCGC
1 ATCGCAAAGCGAATTGACTATCGC
54708 GTTGCGATTT
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
33 9 0.19
34 37 0.79
35 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (33 bp):
ATCGCAAAGCGAATTGACTATCGCAACGCAAAA
Found at i:54726 original size:20 final size:20
Alignment explanation
Indices: 54701--54759 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
54691 TGCGAATTGA
*
54701 CTTTCGCGTTGCGATTTTGG
1 CTTTCGCATTGCGATTTTGG
54721 CTTTCGCATTGCGATTTTGG
1 CTTTCGCATTGCGATTTTGG
54741 CTTTCGCATTGCGATTTTG
1 CTTTCGCATTGCGATTTTG
54760 AGTTTAGAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.08, C:0.20, G:0.25, T:0.46
Consensus pattern (20 bp):
CTTTCGCATTGCGATTTTGG
Found at i:54913 original size:14 final size:14
Alignment explanation
Indices: 54894--54932 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
54884 CATCAATTAA
54894 ACAAATCAATTTTT
1 ACAAATCAATTTTT
*
54908 ACAAATCAACTTTT
1 ACAAATCAATTTTT
54922 ACAAATCAATT
1 ACAAATCAATT
54933 AAACAAGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (14 bp):
ACAAATCAATTTTT
Found at i:56946 original size:20 final size:20
Alignment explanation
Indices: 56909--56946 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
56899 AATAGTTTTT
**
56909 GAAACTTAAAATTGCAACAC
1 GAAACTTAAAATCACAACAC
56929 GAAACTTAAAATCACAAC
1 GAAACTTAAAATCACAAC
56947 GTGAAAATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.21, G:0.08, T:0.18
Consensus pattern (20 bp):
GAAACTTAAAATCACAACAC
Found at i:56952 original size:20 final size:20
Alignment explanation
Indices: 56908--56952 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
56898 GAATAGTTTT
**
56908 TGAAACTTAAAATTGCAACA
1 TGAAACTTAAAATCACAACA
* *
56928 CGAAACTTAAAATCACAACG
1 TGAAACTTAAAATCACAACA
56948 TGAAA
1 TGAAA
56953 ATGACTATCG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.51, C:0.18, G:0.11, T:0.20
Consensus pattern (20 bp):
TGAAACTTAAAATCACAACA
Found at i:57069 original size:19 final size:20
Alignment explanation
Indices: 57026--57078 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
57016 TGAAACTAAA
*
57026 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCATT
*
57046 TTCGCATTGCGATTTTTA-T
1 TTCGCATTGCGATTTTCATT
57065 TTCGCATTGCGATT
1 TTCGCATTGCGATT
57079 ATCCCGTTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.49
Consensus pattern (20 bp):
TTCGCATTGCGATTTTCATT
Found at i:57108 original size:20 final size:20
Alignment explanation
Indices: 57083--57151 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
57073 GCGATTATCC
*
57083 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
57103 CGTTGCGATAGTC-ATTTCCG
1 CGTTGCGATAGTCAATTT-CG
* * *
57123 TGTTGCGATAGTTATTTTCG
1 CGTTGCGATAGTCAATTTCG
57143 CGTTGCGAT
1 CGTTGCGAT
57152 TTTAAGTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 3 0.07
20 36 0.86
21 3 0.07
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:57165 original size:40 final size:40
Alignment explanation
Indices: 57084--57168 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
57074 CGATTATCCC
*
57084 GTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTCCGT
1 GTTGCGATAGTCAAATTCGCGTTGCGATAGTAATTTCCGT
* ** **
57124 GTTGCGATAGTTATTTTCGCGTTGCGATTTTAAGTTT-CGT
1 GTTGCGATAGTCAAATTCGCGTTGCGATAGTAA-TTTCCGT
57164 GTTGC
1 GTTGC
57169 AACTATTCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 35 0.92
41 3 0.08
ACGTcount: A:0.16, C:0.16, G:0.26, T:0.41
Consensus pattern (40 bp):
GTTGCGATAGTCAAATTCGCGTTGCGATAGTAATTTCCGT
Found at i:59111 original size:20 final size:21
Alignment explanation
Indices: 59088--59141 Score: 85
Period size: 20 Copynumber: 2.7 Consensus size: 21
59078 AAAAATGAAA
*
59088 ATCGCAACACGAAATT-GACT
1 ATCGCAACGCGAAATTCGACT
59108 ATCGCAACGCG-AATTCGACT
1 ATCGCAACGCGAAATTCGACT
59128 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
59142 CTAAAATCGC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 4 0.13
20 25 0.81
21 2 0.06
ACGTcount: A:0.37, C:0.28, G:0.19, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATTCGACT
Found at i:59549 original size:22 final size:22
Alignment explanation
Indices: 59522--59568 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
59512 GAGATAGACA
*
59522 GATTTCGTCGGAGATGGGGATG
1 GATTTCGTCGGAGATGGGGACG
59544 GATTTCGTCGGAGATGGGGACG
1 GATTTCGTCGGAGATGGGGACG
59566 GAT
1 GAT
59569 GTCGCCATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.19, C:0.11, G:0.45, T:0.26
Consensus pattern (22 bp):
GATTTCGTCGGAGATGGGGACG
Found at i:59785 original size:20 final size:20
Alignment explanation
Indices: 59760--59918 Score: 144
Period size: 20 Copynumber: 7.8 Consensus size: 20
59750 TCAGAATCGC
59760 TCAGAATCGCGTTGCGATAG
1 TCAGAATCGCGTTGCGATAG
59780 TCAGAATCGCGTTGCGATAG
1 TCAGAATCGCGTTGCGATAG
*
59800 TCAGAATCGCGTTGCGATTTTG
1 TCAGAATCGCGTTGCGA--TAG
**
59822 T-ATTATCGCGTTGCGATAG
1 TCAGAATCGCGTTGCGATAG
* **
59841 TCAGAATCGCATTGCGATTT
1 TCAGAATCGCGTTGCGATAG
*
59861 TCCA-AATTCGCGTTGCGAT-T
1 T-CAGAA-TCGCGTTGCGATAG
* * **
59881 TACATATTCGCAATGCGATAG
1 T-CAGAATCGCGTTGCGATAG
*
59902 TCAAAATCGCGTTGCGA
1 TCAGAATCGCGTTGCGA
59919 ATCTGGAAAC
Statistics
Matches: 113, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.03
20 79 0.70
21 28 0.25
22 3 0.03
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (20 bp):
TCAGAATCGCGTTGCGATAG
Found at i:59842 original size:41 final size:42
Alignment explanation
Indices: 59760--59879 Score: 151
Period size: 41 Copynumber: 3.0 Consensus size: 42
59750 TCAGAATCGC
*
59760 TCAGAATCGCGTTGCGA--TAGTCAGAATCGCGTTGCGATAG
1 TCAGAATCGCGTTGCGATTTTGTCAGAATCGCGTTGCGATAG
**
59800 TCAGAATCGCGTTGCGATTTTGT-ATTATCGCGTTGCGATAG
1 TCAGAATCGCGTTGCGATTTTGTCAGAATCGCGTTGCGATAG
* *
59841 TCAGAATCGCATTGCGATTTT-CCA-AATTCGCGTTGCGAT
1 TCAGAATCGCGTTGCGATTTTGTCAGAA-TCGCGTTGCGAT
59880 TTACATATTC
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
40 18 0.26
41 49 0.70
42 3 0.04
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.32
Consensus pattern (42 bp):
TCAGAATCGCGTTGCGATTTTGTCAGAATCGCGTTGCGATAG
Found at i:59898 original size:61 final size:61
Alignment explanation
Indices: 59772--59918 Score: 174
Period size: 61 Copynumber: 2.4 Consensus size: 61
59762 AGAATCGCGT
** **
59772 TGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTTGTATTATCGCGT
1 TGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTCATATTATCGCAA
* **
59833 TGCGATAGTCAGAATCGCATTGCGATTTTCCA-AATTCGCGTTGCGATTTACATA-T-TCGCAA
1 TGCGATAGTCAGAATCGCGTTGCGATAGT-CAGAA-TCGCGTTGCGATTT-CATATTATCGCAA
*
59894 TGCGATAGTCAAAATCGCGTTGCGA
1 TGCGATAGTCAGAATCGCGTTGCGA
59919 ATCTGGAAAC
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
61 55 0.74
62 17 0.23
63 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.31
Consensus pattern (61 bp):
TGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTCATATTATCGCAA
Found at i:59968 original size:19 final size:19
Alignment explanation
Indices: 59933--59980 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
59923 GGAAACTGAT
* *
59933 TTGCGATATTGGAGATCGCG
1 TTGCGAT-TTAGAGATCGCA
59953 TTGCGATTTAGAGATCGCA
1 TTGCGATTTAGAGATCGCA
59972 TTGCGATTT
1 TTGCGATTT
59981 TGTTGGTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.21, C:0.15, G:0.29, T:0.35
Consensus pattern (19 bp):
TTGCGATTTAGAGATCGCA
Done.