Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007142.1 Hibiscus syriacus cultivar Beakdansim tig00018679_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: 102699
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:4526 original size:20 final size:20
Alignment explanation
Indices: 4501--4539 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
4491 TAGTTTTTTT
4501 TTTTTTTTTC-TTTCTCTGTA
1 TTTTTTTTTCGTTT-TCTGTA
4521 TTTTTTTTTCGTTTTCTGT
1 TTTTTTTTTCGTTTTCTGT
4540 TTCTGTCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.03, C:0.13, G:0.08, T:0.77
Consensus pattern (20 bp):
TTTTTTTTTCGTTTTCTGTA
Found at i:4535 original size:26 final size:26
Alignment explanation
Indices: 4495--4545 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
4485 TGGTACTAGT
**
4495 TTTTTTTTTTTTTTTCT-TTCTCTGTA
1 TTTTTTTTTCGTTTTCTGTT-TCTGTA
4521 TTTTTTTTTCGTTTTCTGTTTCTGT
1 TTTTTTTTTCGTTTTCTGTTTCTGT
4546 CTCTTCTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.02, C:0.12, G:0.08, T:0.78
Consensus pattern (26 bp):
TTTTTTTTTCGTTTTCTGTTTCTGTA
Found at i:5048 original size:13 final size:13
Alignment explanation
Indices: 5032--5097 Score: 60
Period size: 13 Copynumber: 4.8 Consensus size: 13
5022 TAATATATTT
*
5032 AATAATAGTAAAA
1 AATAATAATAAAA
*
5045 AATAATAATAAAT
1 AATAATAATAAAA
*
5058 AATAAAAATAATAA
1 AATAATAATAA-AA
* *
5072 TAATATTAATATAAT
1 -AATAATAATA-AAA
5087 AATAATAATAA
1 AATAATAATAA
5098 TATGGATAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
13 22 0.52
14 10 0.24
15 9 0.21
16 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (13 bp):
AATAATAATAAAA
Found at i:5051 original size:3 final size:3
Alignment explanation
Indices: 5031--5099 Score: 81
Period size: 3 Copynumber: 23.7 Consensus size: 3
5021 TTAATATATT
* *
5031 TAA TAA TAG TAA -AA -AA TAA TAA TAAA TAA TAA AAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
*
5075 TAT TAA T-A TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
5100 TGGATAAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
2 6 0.11
3 48 0.84
4 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:5700 original size:112 final size:112
Alignment explanation
Indices: 5385--6041 Score: 974
Period size: 112 Copynumber: 5.9 Consensus size: 112
5375 AGATAATATC
* * *
5385 AAACAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTTT
1 AAACAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
*
5450 CATTCA--AA-CTTCTCTGGCAATGTTGATCCATCAAATGATGAA-TT
66 CATT-ATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
5494 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAAC--CTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAAC-AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
*
5557 TCATTACGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
65 TCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
* *
5605 AAACAAAAGTTGAACAAGTTCTTCTTATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AAACAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
5670 CATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
66 CATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
5717 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAA---CTTCTTCCTTCTTCAGATGAG-TCTTC
1 AAAC-AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * * * * * *
5778 TCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTC
65 TCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
*** *
5826 AGGTAAAAGGTTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT
1 AAACAAAA-G-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT
* *
5891 CTCATTATGAACTTTCTCTGGTAATGTTGATCCACCAAATGATGAATTT
64 CTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
*
5940 AAACAAAAGTTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AAACAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * *
6005 CATTATGAACTTTCTCTGGCAATGAATGATCCATCAA
66 CATTATGAACCTTCTCTGGTAATG-TTGATCCATCAA
6042 GTGGATTTGA
Statistics
Matches: 502, Mismatches: 31, Indels: 26
0.90 0.06 0.05
Matches are distributed among these distances:
107 1 0.00
108 35 0.07
109 54 0.11
110 137 0.27
111 6 0.01
112 155 0.31
113 61 0.12
114 53 0.11
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (112 bp):
AAACAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
CATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
Found at i:5852 original size:223 final size:224
Alignment explanation
Indices: 5383--6037 Score: 1013
Period size: 223 Copynumber: 2.9 Consensus size: 224
5373 TCAGATAATA
*
5383 TCAAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* *
5447 TTTCATTCA--AA-CTTCTCTGGCAATGTTGATCCATCAAATGATGAA-TTAAACAAAAAGTTGA
66 TCTCATT-ATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGA
* *
5508 ACAAGTTCTTCTCATTATGAACCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTACGAACCTTCT
130 ACAAGTTCTTCTCATTATGAACCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
* * *
5573 CTGGTAATGTTGATCCATCAAATGATGAAT
195 CTGGAAATGATGATCCACCAAATGATGAAT
* * *
5603 TTAAACAAAA-GTTGAACAAGTTCTTCTTATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
5667 TCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAA
66 TCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAA
5732 CAAGTTCTTCTCATTATGAA-CTTCTTCCTTCTTCAGATGAG-TCTTCTCATTATGAACTTTCTC
131 CAAGTTCTTCTCATTATGAACCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* *
5795 TGGAAAAGATGATCCACCAAATGATGGAT
196 TGGAAATGATGATCCACCAAATGATGAAT
*** *
5824 TCAGGTAAAAGGTTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
1 TCAAACAAAAGG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
* *
5889 TTCTCATTATGAACTTTCTCTGGTAATGTTGATCCACCAAATGATGAATTTAAAC-AAAAGTTGA
65 TTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGA
*
5953 ATAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT
130 ACAAGTTCTTCTCATTATGAAC--CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT
*
6018 CTCTGGCAATGAATGATCCA
193 CTCTGGAAATG-ATGATCCA
6038 TCAAGTGGAT
Statistics
Matches: 398, Mismatches: 25, Indels: 17
0.90 0.06 0.04
Matches are distributed among these distances:
219 1 0.00
220 62 0.16
221 55 0.14
222 84 0.21
223 139 0.35
225 21 0.05
226 28 0.07
227 8 0.02
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (224 bp):
TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
TCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAA
CAAGTTCTTCTCATTATGAACCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
TGGAAATGATGATCCACCAAATGATGAAT
Found at i:6001 original size:335 final size:331
Alignment explanation
Indices: 5385--6041 Score: 998
Period size: 335 Copynumber: 2.0 Consensus size: 331
5375 AGATAATATC
* *
5385 AAACAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTTT
1 AAACAAAAGTTGAACAAGCTCTTCTCATTATGAA--TCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * * *
5450 CATTCAAACTTCTCTGGCAATGTTGATCCATCAAATGATGAATTAAACAAAAAGTTGAACAAGTT
64 CATTCAAACTTCTCTGGAAAAGATGATCCACCAAATGATGAATTAAACAAAAAGTTGAACAAATT
5515 CTTCTCATTATGAACCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTACGAACCTTCTCTGGTAA
129 CTTCTCATTATGAACCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTACGAACCTTCTCTGGTAA
* *
5580 TGTTGATCCATCAAATGATGAATTTAAACAAAAGTTGAACAAGTTCTTCTTATTATGAACCTCTT
194 TGTTGATCCACCAAATGATGAATTTAAACAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTT
* *
5645 CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATG-TTGATCCATCAAATG
259 CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATGAATGATCCATCAAATG
5709 ATGAATTT
324 ATGAATTT
*
5717 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAA-CTTCTTCCTTCTTCAGATGAG-TCTTCTC
1 AAAC-AAAAGTTGAACAAGCTCTTCTCATTATGAATCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *** *
5780 ATT-ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTTGAACA
65 ATTCA--AAC-TTCTCTGGAAAAGATGATCCACCAAATGATGAATT-AAACAAAAAG-TTGAACA
* *
5844 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
125 AATTCTTCTCATTATGAAC--CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTACGAACCTTCTC
*
5909 TGGTAATGTTGATCCACCAAATGATGAATTTAAACAAAAGTTGAATAAGTTCTTCTCATTATGAA
188 TGGTAATGTTGATCCACCAAATGATGAATTTAAACAAAAGTTGAACAAGTTCTTCTCATTATGAA
* *
5974 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAATGAATGATCCAT
253 CCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATGAATGATCCAT
6039 CAA
318 CAA
6042 GTGGATTTGA
Statistics
Matches: 294, Mismatches: 22, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
328 1 0.00
329 9 0.03
330 24 0.08
331 30 0.10
332 10 0.03
333 53 0.18
335 156 0.53
336 11 0.04
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (331 bp):
AAACAAAAGTTGAACAAGCTCTTCTCATTATGAATCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTCAAACTTCTCTGGAAAAGATGATCCACCAAATGATGAATTAAACAAAAAGTTGAACAAATTCT
TCTCATTATGAACCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTACGAACCTTCTCTGGTAATG
TTGATCCACCAAATGATGAATTTAAACAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCT
TCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATGAATGATCCATCAAATGAT
GAATTT
Found at i:7065 original size:81 final size:83
Alignment explanation
Indices: 6659--7247 Score: 914
Period size: 81 Copynumber: 7.2 Consensus size: 83
6649 ACTATGAGCC
* * *
6659 AATTTATCTTCCAAATTCAATGATTG-TTCTGTCCAACCAAATCAGATAACTCAAAGAACACTTC
1 AATTCATCTTCCAAATTCAATGATTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
6723 CAGAAGATGCTATTGGCA
66 CAGAAGATGCTATTGGCA
* * * * *
6741 AATTCATCTT-CTAATTCGATGATTG-TTCTG-CTAAACCAGGTC--ATAACTCAAAGAAC-CTT
1 AATTCATCTTCCAAATTCAATGATTGATTCTGTC-CAATCAGATCAGATAACTCAAAGAACACTT
6800 CCAGAAGATGCTATTGGCA
65 CCAGAAGATGCTATTGGCA
* * * * *
6819 AATTCATCTTCCAAATTCAATGCTTGGTTCTGTCAAACCAGGTCAGATAACTCAAAGAACACTTC
1 AATTCATCTTCCAAATTCAATGATTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
*
6884 CAGAAGATGCTATTGGTA
66 CAGAAGATGCTATTGGCA
*
6902 AATTCATCTTCTAAATTCAATGATTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
1 AATTCATCTTCCAAATTCAATGATTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
6967 CAGAAGATGCTATTGGCA
66 CAGAAGATGCTATTGGCA
*
6985 AATTCATCTTCCAAATTC-ATGCTTGATTCTGTCC-ATCAGATCAGATAACTCAAAGAACACTTC
1 AATTCATCTTCCAAATTCAATGATTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
7048 CAGAAGATGCTATTGGCA
66 CAGAAGATGCTATTGGCA
* *
7066 AATTCATCTTCTAAATTC-ATGATTGATTCTGTCCAATCAGATCATATAACTCAAAGAACACTTC
1 AATTCATCTTCCAAATTCAATGATTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
7130 CAGAAGATGCTATTGGCA
66 CAGAAGATGCTATTGGCA
*
7148 AATTCATC-T-CTAATTCAATGATTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
1 AATTCATCTTCCAAATTCAATGATTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
7211 CAGAAGATGCTATTGGCA
66 CAGAAGATGCTATTGGCA
7229 AATTCATCTTCCAAATTCA
1 AATTCATCTTCCAAATTCA
7248 TGCTTGAACT
Statistics
Matches: 470, Mismatches: 26, Indels: 21
0.91 0.05 0.04
Matches are distributed among these distances:
78 32 0.07
79 26 0.06
80 21 0.04
81 177 0.38
82 93 0.20
83 121 0.26
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (83 bp):
AATTCATCTTCCAAATTCAATGATTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
CAGAAGATGCTATTGGCA
Found at i:7143 original size:163 final size:165
Alignment explanation
Indices: 6659--7247 Score: 930
Period size: 163 Copynumber: 3.6 Consensus size: 165
6649 ACTATGAGCC
* *
6659 AATTTATCTTCCAAATTCAATGATTG-TTCTGTCCAACCAAATCAGATAACTCAAAGAACACTTC
1 AATTCATCTTCCAAATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTC
* * * *
6723 CAGAAGATGCTATTGGCAAATTCATCTTCT-AATTCGATGATTG-TTCTG-CTAAACCAGGTC-A
66 CAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATGATTGATTCTGTC-CAATCAGATCAA
6784 TAACTCAAAGAAC-CTTCCAGAAGATGCTATTGGCA
130 TAACTCAAAGAACACTTCCAGAAGATGCTATTGGCA
* * * *
6819 AATTCATCTTCCAAATTCAATGCTTGGTTCTGTCAAACCAGGTCAGATAACTCAAAGAACACTTC
1 AATTCATCTTCCAAATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTC
*
6884 CAGAAGATGCTATTGGTAAATTCATCTTCTAAATTCAATGATTGATTCTGTCCAATCAGATCAGA
66 CAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATGATTGATTCTGTCCAATCAGATCA-A
6949 TAACTCAAAGAACACTTCCAGAAGATGCTATTGGCA
130 TAACTCAAAGAACACTTCCAGAAGATGCTATTGGCA
* *
6985 AATTCATCTTCCAAATTC-ATGCTTGATTCTGTCC-ATCAGATCAGATAACTCAAAGAACACTTC
1 AATTCATCTTCCAAATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTC
7048 CAGAAGATGCTATTGGCAAATTCATCTTCTAAATTC-ATGATTGATTCTGTCCAATCAGATCATA
66 CAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATGATTGATTCTGTCCAATCAGATCA-A
7112 TAACTCAAAGAACACTTCCAGAAGATGCTATTGGCA
130 TAACTCAAAGAACACTTCCAGAAGATGCTATTGGCA
* *
7148 AATTCATC-T-CTAATTCAATGATTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
1 AATTCATCTTCCAAATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTC
*
7211 CAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCA
66 CAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCA
7248 TGCTTGAACT
Statistics
Matches: 400, Mismatches: 19, Indels: 16
0.92 0.04 0.04
Matches are distributed among these distances:
160 24 0.06
161 70 0.17
162 28 0.07
163 147 0.37
164 63 0.16
165 28 0.07
166 40 0.10
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (165 bp):
AATTCATCTTCCAAATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTC
CAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATGATTGATTCTGTCCAATCAGATCAAT
AACTCAAAGAACACTTCCAGAAGATGCTATTGGCA
Found at i:7165 original size:244 final size:245
Alignment explanation
Indices: 6659--7254 Score: 945
Period size: 244 Copynumber: 2.4 Consensus size: 245
6649 ACTATGAGCC
* * * *
6659 AATTTATCTTCCAAATTCAATGATTG-TTCTGTCCAACCAAATCAGATAACTCAAAGAACACTTC
1 AATTCATCTTCTAAATTCAATGATTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
* * *
6723 CAGAAGATGCTATTGGCAAATTCATCTT-CTAATTCGATGATTG-TTCTGCTAAACCAGGTCATA
66 CAGAAGATGCTATTGGCAAATTCATCTTCCAAATTC-ATGCTTGATTCTGCTAAACCAGATCATA
* *
6786 ACTCAAAGAACCTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGCTTGGTTCTG
130 ACTCAAAGAACCTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGATTGATTCTG
* *
6851 TCAAACCAGGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGTA
195 TCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCA
6902 AATTCATCTTCTAAATTCAATGATTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
1 AATTCATCTTCTAAATTCAATGATTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
** *
6967 CAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCATGCTTGATTCTG-TCCATCAGATCAGAT
66 CAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCATGCTTGATTCTGCTAAACCAGATC--AT
*
7031 AACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTC-ATGATTGATTC
129 AACTCAAAGAAC-CTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGATTGATTC
* * *
7095 TGTCCAATCAGATCATATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCA
193 TGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCA
7148 AATTCATC-TCT-AATTCAATGATTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
1 AATTCATCTTCTAAATTCAATGATTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
7211 CAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCATGCTTGA
66 CAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCATGCTTGA
7255 ACTGGGATAT
Statistics
Matches: 329, Mismatches: 18, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
243 24 0.07
244 173 0.53
245 14 0.04
246 79 0.24
247 39 0.12
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (245 bp):
AATTCATCTTCTAAATTCAATGATTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
CAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCATGCTTGATTCTGCTAAACCAGATCATAA
CTCAAAGAACCTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGATTGATTCTGT
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCA
Found at i:8006 original size:19 final size:16
Alignment explanation
Indices: 7984--8029 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 16
7974 AATAGAAAAG
7984 AATAAATTGAATTTCCAAA
1 AATAAATTGAATTT-C--A
*
8003 AATAAATTGACTTTCA
1 AATAAATTGAATTTCA
8019 AATAAATTGAA
1 AATAAATTGAA
8030 CTTGAAATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 11 0.44
18 1 0.04
19 13 0.52
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.33
Consensus pattern (16 bp):
AATAAATTGAATTTCA
Found at i:18989 original size:13 final size:15
Alignment explanation
Indices: 18967--19003 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
18957 TTTGACATAA
18967 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
18979 AAATAAAATACTTGC
1 AAATAAAATACTTGC
18994 AAATAAAATA
1 AAATAAAATA
19004 AAACATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:19042 original size:18 final size:17
Alignment explanation
Indices: 18994--19044 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
18984 AAATACTTGC
*
18994 AAATAAAATAAAACATAT
1 AAAT-AAATAAAAAATAT
*
19012 AAAT-ATTATAAAAATAAT
1 AAATAAATA-AAAAAT-AT
19030 AAATAAATAAAAAAT
1 AAATAAATAAAAAAT
19045 TTGAAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 3 0.11
17 5 0.19
18 16 0.59
19 3 0.11
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATAAATAAAAAATAT
Found at i:20693 original size:20 final size:20
Alignment explanation
Indices: 20668--20706 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
20658 GTACTAGTTT
20668 TTTTTTTTTC-TTTCTCTGTA
1 TTTTTTTTTCGTTT-TCTGTA
20688 TTTTTTTTTCGTTTTCTGT
1 TTTTTTTTTCGTTTTCTGT
20707 TTCTGTCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.03, C:0.13, G:0.08, T:0.77
Consensus pattern (20 bp):
TTTTTTTTTCGTTTTCTGTA
Found at i:20702 original size:26 final size:24
Alignment explanation
Indices: 20665--20712 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 24
20655 TTGGTACTAG
20665 TTTTTTTTTTTTCT-TTCTCTGTAT
1 TTTTTTTTTTTTCTGTT-TCTGTAT
20689 TTTTTTTTCGTTTTCTGTTTCTGT
1 TTTTTTTT--TTTTCTGTTTCTGT
20713 CTCTTCTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
26 11 0.52
27 2 0.10
ACGTcount: A:0.02, C:0.12, G:0.08, T:0.77
Consensus pattern (24 bp):
TTTTTTTTTTTTCTGTTTCTGTAT
Found at i:21209 original size:3 final size:3
Alignment explanation
Indices: 21201--21285 Score: 136
Period size: 3 Copynumber: 28.7 Consensus size: 3
21191 TTAATATATT
* *
21201 TAA TAA TAA TAG TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
21248 TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
21286 TGGATAAAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
2 2 0.03
3 73 0.97
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:25691 original size:7 final size:7
Alignment explanation
Indices: 25679--25710 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
25669 TAGGGATTAA
25679 ATTAATT
1 ATTAATT
25686 ATTAATT
1 ATTAATT
*
25693 ATTATTT
1 ATTAATT
25700 ATTAATT
1 ATTAATT
25707 ATTA
1 ATTA
25711 TTTTTTAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
ATTAATT
Found at i:25711 original size:14 final size:14
Alignment explanation
Indices: 25679--25718 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
25669 TAGGGATTAA
*
25679 ATTAATTATTAATT
1 ATTATTTATTAATT
25693 ATTATTTATTAATT
1 ATTATTTATTAATT
*
25707 ATTATTTTTTAA
1 ATTATTTATTAA
25719 CAACAGTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTATTTATTAATT
Found at i:25888 original size:11 final size:10
Alignment explanation
Indices: 25840--25902 Score: 72
Period size: 10 Copynumber: 6.1 Consensus size: 10
25830 TTAGCTTTAC
25840 ATTCTATTTTT
1 ATTC-ATTTTT
* *
25851 ATTGAATTTT
1 ATTCATTTTT
*
25861 ATTCATTTTA
1 ATTCATTTTT
25871 ATTCATTTTT
1 ATTCATTTTT
25881 ATTACATTTTT
1 ATT-CATTTTT
*
25892 ATTTATTTTT
1 ATTCATTTTT
25902 A
1 A
25903 ATAATAATAA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
10 31 0.70
11 13 0.30
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (10 bp):
ATTCATTTTT
Found at i:25899 original size:21 final size:20
Alignment explanation
Indices: 25840--25902 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 20
25830 TTAGCTTTAC
* *
25840 ATTCTATTTTTATTGAATTTT
1 ATTC-ATTTTTATTCATTTTT
*
25861 ATTCATTTTAATTCATTTTT
1 ATTCATTTTTATTCATTTTT
*
25881 ATTACATTTTTATTTATTTTT
1 ATT-CATTTTTATTCATTTTT
25902 A
1 A
25903 ATAATAATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
20 16 0.44
21 20 0.56
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (20 bp):
ATTCATTTTTATTCATTTTT
Found at i:25900 original size:31 final size:32
Alignment explanation
Indices: 25835--25900 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 32
25825 ATTTTTTAGC
25835 TTTACATTCTATTTTTATTGAATTTTATTCAT
1 TTTACATTCTATTTTTATTGAATTTTATTCAT
*
25867 TTTA-ATTC-ATTTTTATT-ACATTTTTATTTAT
1 TTTACATTCTATTTTTATTGA-A-TTTTATTCAT
25898 TTT
1 TTT
25901 TAATAATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
29 1 0.03
30 10 0.32
31 16 0.52
32 4 0.13
ACGTcount: A:0.24, C:0.08, G:0.02, T:0.67
Consensus pattern (32 bp):
TTTACATTCTATTTTTATTGAATTTTATTCAT
Found at i:37653 original size:21 final size:22
Alignment explanation
Indices: 37629--37669 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
37619 ATTGTGTCTC
* *
37629 GCTAA-CAACTTCGTTGATACA
1 GCTAACCAACCTCCTTGATACA
37650 GCTAACCAACCTCCTTGATA
1 GCTAACCAACCTCCTTGATA
37670 AAACTCGTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.27
Consensus pattern (22 bp):
GCTAACCAACCTCCTTGATACA
Found at i:38564 original size:19 final size:20
Alignment explanation
Indices: 38526--38568 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
38516 GAAACCCCTT
*
38526 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
38546 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
38565 TGAA
1 TGAA
38569 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:43337 original size:12 final size:12
Alignment explanation
Indices: 43320--43424 Score: 90
Period size: 12 Copynumber: 8.8 Consensus size: 12
43310 ATTGTCCCAC
43320 GCATAGTGCTCT
1 GCATAGTGCTCT
* *
43332 GTATAGTGCTCC
1 GCATAGTGCTCT
43344 GCATAGTGC-CAT
1 GCATAGTGCTC-T
*
43356 GCATAATGCTCCT
1 GCATAGTGCT-CT
*
43369 -CATAGTGCTCC
1 GCATAGTGCTCT
* *
43380 GTATAGTGC-CAC
1 GCATAGTGCTC-T
43392 GCATAGTGCTCT
1 GCATAGTGCTCT
*
43404 GCATAGTGCTCC
1 GCATAGTGCTCT
*
43416 ACATAGTGC
1 GCATAGTGC
43425 CACACATTAA
Statistics
Matches: 75, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
11 3 0.04
12 69 0.92
13 2 0.03
14 1 0.01
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.29
Consensus pattern (12 bp):
GCATAGTGCTCT
Found at i:43351 original size:24 final size:24
Alignment explanation
Indices: 43319--43424 Score: 126
Period size: 24 Copynumber: 4.4 Consensus size: 24
43309 CATTGTCCCA
*
43319 CGCATAGTGCTCTGTATAGTGCTC
1 CGCATAGTGCTCTGCATAGTGCTC
*
43343 CGCATAGTGC-CATGCATAATGCTC
1 CGCATAGTGCTC-TGCATAGTGCTC
* * *
43367 CTCATAGTGCTCCGTATAGTGC-C
1 CGCATAGTGCTCTGCATAGTGCTC
43390 ACGCATAGTGCTCTGCATAGTGCTC
1 -CGCATAGTGCTCTGCATAGTGCTC
*
43415 CACATAGTGC
1 CGCATAGTGC
43425 CACACATTAA
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
23 2 0.03
24 64 0.94
25 2 0.03
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (24 bp):
CGCATAGTGCTCTGCATAGTGCTC
Found at i:43360 original size:36 final size:36
Alignment explanation
Indices: 43316--43427 Score: 163
Period size: 36 Copynumber: 3.1 Consensus size: 36
43306 ATGCATTGTC
*
43316 CCACGCATAGTGCTCTGTATAGTGCTCCGCATAGTG
1 CCACGCATAGTGCTCTGCATAGTGCTCCGCATAGTG
* * *
43352 CCATGCATAATGCTCCT-CATAGTGCTCCGTATAGTG
1 CCACGCATAGTGCT-CTGCATAGTGCTCCGCATAGTG
*
43388 CCACGCATAGTGCTCTGCATAGTGCTCCACATAGTG
1 CCACGCATAGTGCTCTGCATAGTGCTCCGCATAGTG
43424 CCAC
1 CCAC
43428 ACATTAATAC
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
35 2 0.03
36 62 0.94
37 2 0.03
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.27
Consensus pattern (36 bp):
CCACGCATAGTGCTCTGCATAGTGCTCCGCATAGTG
Found at i:43610 original size:45 final size:45
Alignment explanation
Indices: 43560--43654 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 45
43550 TGATAATGCA
* **
43560 CTTGGGACCACACCTATTGGAGCTATGCCCGACCATGATGATGTG
1 CTTGGGACCACACCTATTGGAGCTATGCCCGACCACGACAATGTG
*** *
43605 CTTGGGACCATGGCTATTGGAGCTATGGCCGACCACGACAATGTG
1 CTTGGGACCACACCTATTGGAGCTATGCCCGACCACGACAATGTG
43650 CTTGG
1 CTTGG
43655 AGCCACGCCT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.21, C:0.25, G:0.29, T:0.24
Consensus pattern (45 bp):
CTTGGGACCACACCTATTGGAGCTATGCCCGACCACGACAATGTG
Found at i:48783 original size:15 final size:15
Alignment explanation
Indices: 48760--48798 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
48750 AAGAAGAAGA
* *
48760 ATTATTTAAAATTAT
1 ATTAATTAAAATAAT
48775 ATTAATTAAAATAAT
1 ATTAATTAAAATAAT
*
48790 ATAAATTAA
1 ATTAATTAA
48799 TTAAATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTAATTAAAATAAT
Found at i:63742 original size:18 final size:18
Alignment explanation
Indices: 63710--63749 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
63700 ACCAAAAGGC
**
63710 AATCAAAATTGCAATCAA
1 AATCAAAATCCCAATCAA
*
63728 AATCAAAATCCCAATCAT
1 AATCAAAATCCCAATCAA
63746 AATC
1 AATC
63750 GGCTTCACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.23, G:0.03, T:0.23
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:63940 original size:20 final size:20
Alignment explanation
Indices: 63915--64055 Score: 169
Period size: 20 Copynumber: 7.0 Consensus size: 20
63905 TTACACATTC
* *
63915 ATTTGAATATCGTAACGAGA
1 ATTTGACTATCGCAACGAGA
*
63935 ATTTGACTATCGCAAC-ACAA
1 ATTTGACTATCGCAACGA-GA
63955 ATTTGACTATCGCAACGCA-A
1 ATTTGACTATCGCAACG-AGA
*
63975 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGAGA
* *
63995 ATTTGACTATCGCAATGTGA
1 ATTTGACTATCGCAACGAGA
* *
64015 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGAGA
*
64035 ATTTGACTATCACAACGAGA
1 ATTTGACTATCGCAACGAGA
64055 A
1 A
64056 AATCGCAACG
Statistics
Matches: 105, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
19 1 0.01
20 103 0.98
22 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (20 bp):
ATTTGACTATCGCAACGAGA
Found at i:64195 original size:20 final size:20
Alignment explanation
Indices: 64170--64218 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
64160 AATTAAACAA
*
64170 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAACTTGACT
* *
64190 ATCGCAACGTGAACTTGATT
1 ATCGCAACGCGAACTTGACT
64210 ATCGCAACG
1 ATCGCAACG
64219 GGTGATGGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGAACTTGACT
Found at i:65673 original size:20 final size:20
Alignment explanation
Indices: 65615--65665 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
65605 TCTGAAACTT
*
65615 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
65635 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
**
65655 ACTATCGCAAC
1 AAAATCGCAAC
65666 GAGAAAATCG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.51, C:0.22, G:0.14, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:66106 original size:22 final size:22
Alignment explanation
Indices: 66069--66131 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 22
66059 TCTGAGAGAT
66069 GGAGAT-A-GACGGATTTCGCC
1 GGAGATGAGGACGGATTTCGCC
* *
66089 GGAGATGAGGACGTATTTCGTC
1 GGAGATGAGGACGGATTTCGCC
* * *
66111 AGAGATGGGGACGGATGTCGC
1 GGAGATGAGGACGGATTTCGC
66132 TGTAGAGAGT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 6 0.18
21 1 0.03
22 27 0.79
ACGTcount: A:0.24, C:0.16, G:0.40, T:0.21
Consensus pattern (22 bp):
GGAGATGAGGACGGATTTCGCC
Found at i:66365 original size:39 final size:39
Alignment explanation
Indices: 66317--66429 Score: 111
Period size: 39 Copynumber: 2.8 Consensus size: 39
66307 GATTTTGTAT
*
66317 TATCGTGTTGCGATAGTTAGATTCGCGTTGCGAACTTGGA
1 TATCGTGTTGCGATAGTCAGA-TCGCGTTGCGAACTTGGA
* * * ** *
66357 -ATTGTGTTGCGATACTGGAGATCGCGTTGCGATTTTGTA
1 TATCGTGTTGCGATAGT-CAGATCGCGTTGCGAACTTGGA
*
66396 TTATCGCGTTGCGATAGTCAGAATCGCGTTGCGA
1 -TATCGTGTTGCGATAGTCAG-ATCGCGTTGCGA
66430 TTTACATATT
Statistics
Matches: 59, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
39 29 0.49
40 5 0.08
41 25 0.42
ACGTcount: A:0.19, C:0.16, G:0.30, T:0.35
Consensus pattern (39 bp):
TATCGTGTTGCGATAGTCAGATCGCGTTGCGAACTTGGA
Found at i:66375 original size:19 final size:21
Alignment explanation
Indices: 66318--66430 Score: 69
Period size: 20 Copynumber: 5.6 Consensus size: 21
66308 ATTTTGTATT
* *
66318 ATCGTGTTGCGATAGTT--AG
1 ATCGCGTTGCGATACTTGGAG
66337 ATTCGCGTTGCGA-ACTTGGA-
1 A-TCGCGTTGCGATACTTGGAG
* *
66357 ATTGTGTTGCGATAC-TGGAG
1 ATCGCGTTGCGATACTTGGAG
* * *
66377 ATCGCGTTGCGAT-TTTGTATT
1 ATCGCGTTGCGATACTTGGA-G
* **
66398 ATCGCGTTGCGATAGTCAGA-
1 ATCGCGTTGCGATACTTGGAG
66418 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
66431 TTACATATTC
Statistics
Matches: 73, Mismatches: 13, Indels: 15
0.72 0.13 0.15
Matches are distributed among these distances:
19 17 0.23
20 40 0.55
21 14 0.19
22 2 0.03
ACGTcount: A:0.19, C:0.16, G:0.30, T:0.35
Consensus pattern (21 bp):
ATCGCGTTGCGATACTTGGAG
Found at i:66422 original size:41 final size:40
Alignment explanation
Indices: 66303--66432 Score: 147
Period size: 41 Copynumber: 3.2 Consensus size: 40
66293 GAAAATCTCA
*
66303 TTGCGATTTTGTATTATCGTGTTGCGATAGTTAGATTCGCG
1 TTGCGATTTTGTATTATCGTGTTGCGATAG-TAGAATCGCG
** * * * *
66344 TTGCGAACTTGGA--ATTGTGTTGCGATACTGGAGATCGCG
1 TTGCGATTTTGTATTATCGTGTTGCGATAGTAGA-ATCGCG
*
66383 TTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCGCG
1 TTGCGATTTTGTATTATCGTGTTGCGATAGT-AGAATCGCG
66424 TTGCGATTT
1 TTGCGATTT
66433 ACATATTCGC
Statistics
Matches: 71, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
38 3 0.04
39 28 0.39
41 38 0.54
42 2 0.03
ACGTcount: A:0.18, C:0.15, G:0.28, T:0.38
Consensus pattern (40 bp):
TTGCGATTTTGTATTATCGTGTTGCGATAGTAGAATCGCG
Found at i:66549 original size:20 final size:20
Alignment explanation
Indices: 66526--66571 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
66516 GGAAACTGAT
* *
66526 TTGCGATACTGGAGATCGCG
1 TTGCGATACTAGAGATCGCA
*
66546 TTGCGA-ATTAGAGATCGCA
1 TTGCGATACTAGAGATCGCA
66565 TTGCGAT
1 TTGCGAT
66572 TTTGTTGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
TTGCGATACTAGAGATCGCA
Found at i:66721 original size:24 final size:23
Alignment explanation
Indices: 66694--66775 Score: 137
Period size: 23 Copynumber: 3.5 Consensus size: 23
66684 TTTTTAAATA
* *
66694 TTTTGAAAATATATAATATATAG
1 TTTTGAAAACATATATTATATAG
66717 TTTTTGAAAACATATATTATATAG
1 -TTTTGAAAACATATATTATATAG
66741 TTTTGAAAACATATATTATATAG
1 TTTTGAAAACATATATTATATAG
66764 TTTTGAAAACAT
1 TTTTGAAAACAT
66776 TTTTTAAAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
23 35 0.62
24 21 0.38
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.44
Consensus pattern (23 bp):
TTTTGAAAACATATATTATATAG
Found at i:66799 original size:37 final size:37
Alignment explanation
Indices: 66741--67068 Score: 373
Period size: 37 Copynumber: 8.9 Consensus size: 37
66731 TATTATATAG
* * * *
66741 TTTTGAAAACATATATTATATAGTTTTGAAAA-CATT
1 TTTTAAAAATATATATTATATAGTTTTGAAAATTAGT
* * * * *
66777 TTTTAAAATATATATAATATATAATTTTTAAAA-AACAT
1 TTTTAAAA-ATATATATTATATAGTTTTGAAAATTA-GT
* *
66815 TTTTGAAAAACATATGTATTATATAGTTTTAAAAATTAGT
1 TTTT--AAAA-ATATATATTATATAGTTTTGAAAATTAGT
66855 TTTTAAAAATATATATTATATAGTTTTGAAAATTAGT
1 TTTTAAAAATATATATTATATAGTTTTGAAAATTAGT
66892 TTTTAAAAATATATATTATATAGTTTTGAAAATTAGT
1 TTTTAAAAATATATATTATATAGTTTTGAAAATTAGT
*
66929 TTTTAAAAATATATATTATATAGTTTTGAAAATTAGC
1 TTTTAAAAATATATATTATATAGTTTTGAAAATTAGT
* *
66966 TTTT--AAATATATATTATAGAGTTTTG--AATT-TT
1 TTTTAAAAATATATATTATATAGTTTTGAAAATTAGT
* *
66998 TTTTAAAAAAATATATATTATATGGTTTTGAAAATTACT
1 TTTT--AAAAATATATATTATATAGTTTTGAAAATTAGT
* * *
67037 TTTTAAAAACATATATTGTATAGTTTTAAAAA
1 TTTTAAAAATATATATTATATAGTTTTGAAAA
67069 AATGTGTTTT
Statistics
Matches: 253, Mismatches: 27, Indels: 23
0.83 0.09 0.08
Matches are distributed among these distances:
32 4 0.02
33 4 0.02
35 21 0.08
36 27 0.11
37 149 0.59
38 13 0.05
39 5 0.02
40 29 0.11
41 1 0.00
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (37 bp):
TTTTAAAAATATATATTATATAGTTTTGAAAATTAGT
Found at i:67119 original size:16 final size:17
Alignment explanation
Indices: 67077--67116 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
67067 AAAATGTGTT
67077 TTTATTTATCTATTTTA
1 TTTATTTATCTATTTTA
67094 TTTCATTTATC-A-TTTA
1 TTT-ATTTATCTATTTTA
67110 TTTATTT
1 TTTATTT
67117 TATTTTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.18
16 7 0.32
17 4 0.18
18 7 0.32
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTATTTATCTATTTTA
Found at i:69897 original size:187 final size:198
Alignment explanation
Indices: 69687--70077 Score: 660
Period size: 187 Copynumber: 2.0 Consensus size: 198
69677 AGAAATCAGG
69687 TACACCGTAGTGGCAAAATTAGAGAAATAATATATGCGGGAAAAAAATTAAAAAAT-GA-GA-T-
1 TACACCGTAGTGGCAAAATTAGAGAAATAATATATGCGGGAAAAAAATTAAAAAATAGAGGATTA
69748 G-ATTA-TTTGTGATCTA-GTCATTTGTTATAGT-GCGT-AAACTCGTCATATGGAAGTGACGAA
66 GAATTATTTTGTGATCTAGGTCATTTGTTATAGTCGCGTAAAACTCGTCATATGGAAGTGACGAA
69808 TTTCTTACAATTTTGATCCATTTCATTTAAT-G-ATACTGTAATAATACTTTAGATCTCAAAATA
131 TTTCTTACAATTTTGATCCATTTCATTTAATAGCATACTGTAATAATACTTTAGATCTCAAAATA
69871 AAT
196 AAT
69874 TACACCGTAGTGGCAAAATTAGAGAAATAATATATGCGGGAAAAAAATTAAAAAATGAGAGTGAT
1 TACACCGTAGTGGCAAAATTAGAGAAATAATATATGCGGGAAAAAAATTAAAAAAT-AGAG-GAT
69939 TGAGAATTATTTTGTGATCTAGGTCATTTGTTATAGTGCGCGTAAAACTCGTCATATGGAAGTGA
64 T-AGAATTATTTTGTGATCTAGGTCATTTGTTATAGT-CGCGTAAAACTCGTCATATGGAAGTGA
70004 CGAATTTCTTACAATTTTGATCCATTTCATTTAATGAGCATACTGTAATAATACTTTAGATCTCA
127 CGAATTTCTTACAATTTTGATCCATTTCATTTAAT-AGCATACTGTAATAATACTTTAGATCTCA
70069 AAATAAAT
191 AAATAAAT
70077 T
1 T
70078 TCAAGATACC
Statistics
Matches: 188, Mismatches: 0, Indels: 16
0.92 0.00 0.08
Matches are distributed among these distances:
187 56 0.30
189 2 0.01
191 2 0.01
192 1 0.01
194 1 0.01
195 4 0.02
196 11 0.06
197 15 0.08
199 4 0.02
200 56 0.30
202 1 0.01
203 35 0.19
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (198 bp):
TACACCGTAGTGGCAAAATTAGAGAAATAATATATGCGGGAAAAAAATTAAAAAATAGAGGATTA
GAATTATTTTGTGATCTAGGTCATTTGTTATAGTCGCGTAAAACTCGTCATATGGAAGTGACGAA
TTTCTTACAATTTTGATCCATTTCATTTAATAGCATACTGTAATAATACTTTAGATCTCAAAATA
AAT
Found at i:73553 original size:2 final size:2
Alignment explanation
Indices: 73546--73591 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
73536 TATTTTGATA
73546 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
73588 AT AT
1 AT AT
73592 TTGTTTTAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82745 original size:21 final size:18
Alignment explanation
Indices: 82721--82759 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 18
82711 CGATACTCAT
82721 CTCTCGTCCTTCATCTTCTCC
1 CTCTCG-CCTTC--CTTCTCC
82742 CTCTCGCCTTCCTTCTCC
1 CTCTCGCCTTCCTTCTCC
82760 AACTGTGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
20 5 0.28
21 6 0.33
ACGTcount: A:0.03, C:0.51, G:0.05, T:0.41
Consensus pattern (18 bp):
CTCTCGCCTTCCTTCTCC
Found at i:90032 original size:8 final size:8
Alignment explanation
Indices: 90019--90110 Score: 105
Period size: 8 Copynumber: 11.2 Consensus size: 8
90009 CAGAGAAATC
90019 AGTTTGAG
1 AGTTTGAG
90027 AGTTTGAG
1 AGTTTGAG
*
90035 AATTTGAG
1 AGTTTGAG
90043 AGTTTGAG
1 AGTTTGAG
*
90051 AATTTGAG
1 AGTTTGAG
90059 AGTTTGAG
1 AGTTTGAG
**
90067 AGAATGAG
1 AGTTTGAG
90075 AGTTTGAG
1 AGTTTGAG
90083 AGAATTTGAG
1 AG--TTTGAG
*
90093 TGTTTTGAG
1 AG-TTTGAG
90102 A-TTTGAG
1 AGTTTGAG
90109 AG
1 AG
90111 CATTCTTCAT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
7 7 0.10
8 50 0.71
9 6 0.09
10 7 0.10
ACGTcount: A:0.30, C:0.00, G:0.34, T:0.36
Consensus pattern (8 bp):
AGTTTGAG
Found at i:90545 original size:170 final size:169
Alignment explanation
Indices: 90186--90705 Score: 693
Period size: 170 Copynumber: 3.1 Consensus size: 169
90176 ATTCAACCAA
* * * **
90186 TAATATGTTTGATGGGACGAGACACTATGGCATGACAAAGATTATCTGGCAAAGGTGAAAGTGCT
1 TAATATGTTTGATGGGACGAGACACTATGTCATGGCAAAGATTATCTGACAAAGGTGAAAGCACT
* *
90251 TCTTATGGGATGTGACTTCCCTTTTTGTCAGAGATTCTCTATA-TTTTCAGTTAATAATAGCCCT
66 TCTTATGGGATGCGACTT-CCTTTTTGTCAGAGATTCTCTACATTTTTCAGTTAATAATAGCCCT
* * * * *
90315 AATTGATGTTCACCATCGGGAAACTATTCATGTCAACACA
130 AATTGATGTTCCCCGTCGGGGAACTATTCACGTCAACACC
* * * * *
90355 TATTATGTTTGATGGGACGAGATAGTATGTCATGGCAGAGATTATCTGACAAAGGTAAAAGCACT
1 TAATATGTTTGATGGGACGAGACACTATGTCATGGCAAAGATTATCTGACAAAGGTGAAAGCACT
* * * *
90420 TCTTGTGGGACGCGTCTTCCATTTTTGTCAGAGATTCTCTACATTTTTCAATTAATAATAGCCCT
66 TCTTATGGGATGCGACTTCC-TTTTTGTCAGAGATTCTCTACATTTTTCAGTTAATAATAGCCCT
*
90485 AATTGATGTTCCCCGTCGGGGAACTATGCACGTCAACACC
130 AATTGATGTTCCCCGTCGGGGAACTATTCACGTCAACACC
* *
90525 TAATATGTTTGTTGGGACGAGACACTATGTCATGGAAAAGATTATCTGACAAAGGTGAAAGCACT
1 TAATATGTTTGATGGGACGAGACACTATGTCATGGCAAAGATTATCTGACAAAGGTGAAAGCACT
* * * * *
90590 TCTTATGGGATAC-ACCTTCTCTTTTCGTCATAGATTCTCTGCATTTTTTAGTTAATAATAGCCC
66 TCTTATGGGATGCGA-CTTC-CTTTTTGTCAGAGATTCTCTACATTTTTCAGTTAATAATAGCCC
* **
90654 TAATTGTTGTTCCATGTCGGGGAACTATTCACGTCAACACC
129 TAATTGATGTTCCCCGTCGGGGAACTATTCACGTCAACACC
*
90695 TATTATGTTTG
1 TAATATGTTTG
90706 TGGTCCTAAA
Statistics
Matches: 304, Mismatches: 43, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
168 2 0.01
169 90 0.30
170 211 0.69
171 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (169 bp):
TAATATGTTTGATGGGACGAGACACTATGTCATGGCAAAGATTATCTGACAAAGGTGAAAGCACT
TCTTATGGGATGCGACTTCCTTTTTGTCAGAGATTCTCTACATTTTTCAGTTAATAATAGCCCTA
ATTGATGTTCCCCGTCGGGGAACTATTCACGTCAACACC
Found at i:92302 original size:17 final size:17
Alignment explanation
Indices: 92257--92304 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
92247 AAATATATTA
92257 TAATT-ATAT-AAA-AT
1 TAATTAATATAAAATAT
*
92271 TAA-TAAAATAAAATAT
1 TAATTAATATAAAATAT
92287 TAATTAATATAAAATAT
1 TAATTAATATAAAATAT
92304 T
1 T
92305 TAATAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 1 0.04
14 6 0.21
15 3 0.11
16 5 0.18
17 13 0.46
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAATTAATATAAAATAT
Found at i:92312 original size:34 final size:34
Alignment explanation
Indices: 92234--92301 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
92224 ACAAATAATT
92234 AATTAATAAAATTAAATATATTATAATTATATAA
1 AATTAATAAAATTAAATATATTATAATTATATAA
92268 AATTAATAAAA-TAAA-ATA-T-TAATTAATATAA
1 AATTAATAAAATTAAATATATTATAATT-ATATAA
92299 AAT
1 AAT
92302 ATTTAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
30 5 0.15
31 10 0.30
32 3 0.09
33 4 0.12
34 11 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (34 bp):
AATTAATAAAATTAAATATATTATAATTATATAA
Found at i:100598 original size:22 final size:21
Alignment explanation
Indices: 100556--100595 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
100546 GAGTTTGTTT
*
100556 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
100577 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
100596 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Done.