Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008526.1 Hibiscus syriacus cultivar Beakdansim tig00111398_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: 3043201
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 12
Found at i:2685691 original size:2 final size:2
Alignment explanation
Indices: 2685684--2685717 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2685674 AGTATTGGCA
2685684 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
2685718 TTACAGTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2687590 original size:13 final size:13
Alignment explanation
Indices: 2687574--2687607 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
2687564 GTAAAAGGGA
2687574 AAAATAAATAAAT
1 AAAATAAATAAAT
2687587 AAAATAAATAAAT
1 AAAATAAATAAAT
*
2687600 AAGATAAA
1 AAAATAAA
2687608 GGAAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:2687868 original size:2 final size:2
Alignment explanation
Indices: 2687863--2687889 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2687853 AACGAAAATA
2687863 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2687890 AGTTATAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2688070 original size:2 final size:2
Alignment explanation
Indices: 2688063--2688091 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2688053 TATTAAAGAA
2688063 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2688092 ATAATAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2689426 original size:105 final size:105
Alignment explanation
Indices: 2689119--2690191 Score: 1516
Period size: 105 Copynumber: 10.3 Consensus size: 105
2689109 CATTGTTCCA
* * ** *
2689119 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTATTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAATT-GTTGTTGACAA
* * * * *
2689183 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
2689225 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAGC
2689285 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * *
2689325 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTCGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAGC
*
2689390 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
2689430 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAGC
* *
2689490 AGCGATCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
2689530 AGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAGATT-GGAAAGTTGTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAA-TTGTTGTTGACAAG
* *
2689594 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTTTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
2689635 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAGC
2689695 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
2689735 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATT-GGAAAGTTGTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAA-TTGTTGTTGACAAG
*
2689799 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
2689840 AGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAGC
2689905 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
2689945 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTATTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGG-AAATT-GTTGTTGACAA
* *
2690010 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
64 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
2690052 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTG-TTGTTGACAAG
* * * * *
2690117 CAGCCGTCCCTTTGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
2690158 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
2690192 CGCGGATGGC
Statistics
Matches: 883, Mismatches: 61, Indels: 43
0.89 0.06 0.04
Matches are distributed among these distances:
100 257 0.29
101 10 0.01
102 13 0.01
103 10 0.01
104 11 0.01
105 365 0.41
106 96 0.11
107 99 0.11
109 22 0.02
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:2689472 original size:205 final size:205
Alignment explanation
Indices: 2689119--2690191 Score: 1572
Period size: 205 Copynumber: 5.2 Consensus size: 205
2689109 CATTGTTCCA
* * ** * *
2689119 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTATTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTT-GTTGTTGACAA
* * ** *
2689183 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAA
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAA
**
2689248 GTTGAAATTGAATCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACT
129 GTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACT
2689313 TGCGTTGTCTGG
194 TGCGTTGTCTGG
* * * *
2689325 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTCGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
*
2689390 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
* *
2689455 TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGATCCCTTCGTCGTGAAGTTGAACTTA
131 TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
2689520 CGTTGTCTGG
196 CGTTGTCTGG
* * *
2689530 AGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
* *
2689595 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTTTCTGGAGTCCAATATCCTTCGCTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
2689660 TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
131 TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
2689725 CGTTGTCTGG
196 CGTTGTCTGG
* *
2689735 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
*
2689800 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTTGTTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
* *
2689865 TGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
131 TGAAATTGGCTCTGA-A-T--GAAATT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
2689930 ACTTGCGTTGTCTGG
191 ACTTGCGTTGTCTGG
* * * *
2689945 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTATTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGG-AAGTT-GTTGTTGACAA
* *
2690010 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* * * *
2690075 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTTGTTGTGAAGT
129 GTTGAAATTGGCTCTG-AA-TGA-AA--T-TTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGT
* *
2690140 TGAACTTGTGTTGTCTCG
188 TGAACTTGCGTTGTCTGG
* * *
2690158 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
2690192 CGCGGATGGC
Statistics
Matches: 799, Mismatches: 52, Indels: 22
0.92 0.06 0.03
Matches are distributed among these distances:
205 477 0.60
206 45 0.06
207 2 0.00
209 5 0.01
210 98 0.12
211 5 0.01
212 89 0.11
213 52 0.07
214 4 0.01
216 22 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (205 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
CGTTGTCTGG
Found at i:2691097 original size:67 final size:67
Alignment explanation
Indices: 2691025--2691183 Score: 207
Period size: 67 Copynumber: 2.4 Consensus size: 67
2691015 GAAACGAAAT
* *
2691025 TTTGTTTTAAGGGAGATA-AAT-TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCGTA-GGAGA
1 TTTGTTTCAAGGGA-A-ACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTC-AAGGGAGA
2691087 CAAAA
63 CAAAA
* * *
2691092 TTTGTTTCGAGGGAAACAATCTCAAAGGTTTTGTGTTTTAAGAGAAACTGTCTCAAGGGAGACAA
1 TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAA
2691157 AA
66 AA
**
2691159 TTTGTTTCAAGGGAAATTATCTCAA
1 TTTGTTTCAAGGGAAACAATCTCAA
2691184 GAGAGACGAA
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
65 1 0.01
66 5 0.06
67 75 0.93
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.33
Consensus pattern (67 bp):
TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAA
AA
Found at i:2691182 original size:36 final size:36
Alignment explanation
Indices: 2691058--2691534 Score: 248
Period size: 36 Copynumber: 13.9 Consensus size: 36
2691048 AAAGATTTTG
* *
2691058 TGTTTCAAGAGAAACTGTCTCGTAG-GAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTC-AAGAGAGACAAAATT
* ** **
2691094 TGTTTCGAGGGAAACAATCTCAA-AG-G----TTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * *
2691124 GTGTTTTAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * *
2691161 TGTTTCAAGGGAAATTATCTCAAGAGAGACGAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * * *
2691197 CATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT
*
2691225 ATGTTTC-AGGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGG-GAAACTGTCTCAAGAGAGACAAAA-TT
*
2691263 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * * * *
2691299 CATTTCAAGGGAAA-TGTTTCCA-A-TG-----TTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * *
2691327 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
* *
2691365 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * * * *
2691401 CATTTCAA-GGAAAATGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT
* * *
2691429 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
*
2691467 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
2691503 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
2691535 TGGTGAGCAC
Statistics
Matches: 322, Mismatches: 75, Indels: 88
0.66 0.15 0.18
Matches are distributed among these distances:
28 8 0.02
29 31 0.10
30 18 0.06
31 18 0.06
32 4 0.01
33 4 0.01
34 4 0.01
35 16 0.05
36 120 0.37
37 90 0.28
38 9 0.03
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:2691277 original size:37 final size:37
Alignment explanation
Indices: 2691226--2691534 Score: 232
Period size: 37 Copynumber: 8.9 Consensus size: 37
2691216 TCAATGTTTA
*
2691226 TGTTTC-AGGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGG-GAAACTGTCTCAAGAGAGACAAAATTT
*
2691263 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * **
2691299 CATTTCAAGGGAAA-TGTTTC--------CAATGTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * *
2691327 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
2691365 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-CT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * * *
2691401 CATTTCAA-GGAAAATGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* * *
2691429 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
2691467 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
2691503 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
2691535 TGGTGAGCAC
Statistics
Matches: 208, Mismatches: 38, Indels: 52
0.70 0.13 0.17
Matches are distributed among these distances:
27 3 0.01
28 3 0.01
29 20 0.10
30 12 0.06
32 1 0.00
33 1 0.00
34 1 0.00
35 11 0.05
36 59 0.28
37 86 0.41
38 11 0.05
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:2691298 original size:102 final size:102
Alignment explanation
Indices: 2691125--2691516 Score: 660
Period size: 102 Copynumber: 3.9 Consensus size: 102
2691115 AAAGGTTTTG
* * *
2691125 TGTTTTAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAATTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
2691189 ACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
2691226 TGTTTCAGGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
2691291 ACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
2691328 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* *
2691393 ACAAAACTCATTTCAAGGAAAATGTTTTCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
2691430 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* **
2691495 ACAAAGTTTGTTTCAAGGGAAA
66 ACAAAATTCATTTCAAGGGAAA
2691517 CTGTCTCAAG
Statistics
Matches: 274, Mismatches: 16, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
101 32 0.12
102 242 0.88
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (102 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:2692423 original size:22 final size:22
Alignment explanation
Indices: 2692397--2692471 Score: 132
Period size: 22 Copynumber: 3.4 Consensus size: 22
2692387 ATGTTTGGTT
2692397 AAAGGTTTGGCATTTGATGCTC
1 AAAGGTTTGGCATTTGATGCTC
2692419 AAAGGTTTGGCATTTGATGCTC
1 AAAGGTTTGGCATTTGATGCTC
*
2692441 ATAGGTTTGGCATTTGATGCTC
1 AAAGGTTTGGCATTTGATGCTC
*
2692463 AACGGTTTG
1 AAAGGTTTG
2692472 ATGGGGTAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.21, C:0.13, G:0.28, T:0.37
Consensus pattern (22 bp):
AAAGGTTTGGCATTTGATGCTC
Found at i:2693104 original size:20 final size:21
Alignment explanation
Indices: 2693080--2693128 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
2693070 TTTTTTGTTC
*
2693080 CCTTTTTTATTTTTGTTCTTT
1 CCTTTTTTATTCTTGTTCTTT
* *
2693101 -CTTTTTTGTTCTTGTTTTTT
1 CCTTTTTTATTCTTGTTCTTT
2693121 CCTTTTTT
1 CCTTTTTT
2693129 TGCTTCTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.02, C:0.14, G:0.06, T:0.78
Consensus pattern (21 bp):
CCTTTTTTATTCTTGTTCTTT
Found at i:2693147 original size:21 final size:22
Alignment explanation
Indices: 2693092--2693152 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
2693082 TTTTTTATTT
*
2693092 TTGTTCTTTC-TTTTTTG-TTC
1 TTGTTTTTTCTTTTTTTGCTTC
2693112 TTGTTTTTTCCTTTTTTTGCTTC
1 TTGTTTTTT-CTTTTTTTGCTTC
2693135 TT-TTCTTTT-TTTTTTTGC
1 TTGTT-TTTTCTTTTTTTGC
2693153 CCTTTTTGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
20 8 0.22
21 10 0.28
22 9 0.25
23 9 0.25
ACGTcount: A:0.00, C:0.15, G:0.08, T:0.77
Consensus pattern (22 bp):
TTGTTTTTTCTTTTTTTGCTTC
Found at i:2696200 original size:9 final size:9
Alignment explanation
Indices: 2696186--2696219 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
2696176 TAAAAGGGAA
2696186 AAATAAAAT
1 AAATAAAAT
2696195 AAATAAAAT
1 AAATAAAAT
2696204 AAAT-AAAT
1 AAATAAAAT
2696212 AAGATAAA
1 AA-ATAAA
2696220 GGAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 15 0.65
10 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:2696207 original size:13 final size:13
Alignment explanation
Indices: 2696185--2696219 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
2696175 GTAAAAGGGA
2696185 AAAATAAAATAAAT
1 AAAAT-AAATAAAT
2696199 AAAATAAATAAAT
1 AAAATAAATAAAT
*
2696212 AAGATAAA
1 AAAATAAA
2696220 GGAAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:2696538 original size:2 final size:2
Alignment explanation
Indices: 2696491--2696521 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2696481 AACGAAAATA
2696491 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2696522 AAGTTATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2707862 original size:19 final size:22
Alignment explanation
Indices: 2707833--2707874 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
2707823 AAAAAAAATT
2707833 AAATATAAAAAT-TATAC-TAA
1 AAATATAAAAATATATACATAA
2707853 AAAT-TAAAAATATATACATAA
1 AAATATAAAAATATATACATAA
2707874 A
1 A
2707875 CCAGAGTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 9 0.45
21 4 0.20
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (22 bp):
AAATATAAAAATATATACATAA
Found at i:2718561 original size:2 final size:2
Alignment explanation
Indices: 2718554--2718582 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2718544 ATTCGTAATG
2718554 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2718583 GTACTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2719559 original size:10 final size:10
Alignment explanation
Indices: 2719546--2719573 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
2719536 TAAATAAATT
2719546 TTTATAATAG
1 TTTATAATAG
2719556 TTTATAATAG
1 TTTATAATAG
2719566 TTTATAAT
1 TTTATAAT
2719574 TAATATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (10 bp):
TTTATAATAG
Found at i:2719932 original size:19 final size:20
Alignment explanation
Indices: 2719896--2719935 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2719886 TGATTAAAGA
2719896 TTTTCAGTTAAAAATAAAAT
1 TTTTCAGTTAAAAATAAAAT
* *
2719916 TTTTCA-TTAGAAGTAAAAT
1 TTTTCAGTTAAAAATAAAAT
2719935 T
1 T
2719936 CTCAGTATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (20 bp):
TTTTCAGTTAAAAATAAAAT
Found at i:2721637 original size:22 final size:22
Alignment explanation
Indices: 2721575--2721747 Score: 125
Period size: 22 Copynumber: 8.3 Consensus size: 22
2721565 CGGTTTTTCA
2721575 TTGCGATAGTCTACAA-TGTCG
1 TTGCGATAGTCTACAATTGTCG
* * *
2721596 TTGCGAT--TTTCCAAAT-TCG
1 TTGCGATAGTCTACAATTGTCG
*
2721615 TTGTGATAGTCTACAATTGTCG
1 TTGCGATAGTCTACAATTGTCG
* *
2721637 TTGCGAAAGTCTACAGTTGTCG
1 TTGCGATAGTCTACAATTGTCG
* * *
2721659 TTGCGAT--TTTCCATTTCG-CG
1 TTGCGATAGTCTACAATT-GTCG
2721679 TTGCGATAGTCTACAA-TGTCG
1 TTGCGATAGTCTACAATTGTCG
* * *
2721700 TTGCGAT--TTTCCAAAT-TCG
1 TTGCGATAGTCTACAATTGTCG
* *
2721719 TTGCGATAGTCTACAGTTGTTG
1 TTGCGATAGTCTACAATTGTCG
*
2721741 TTACGAT
1 TTGCGAT
2721748 TTTCCAAATT
Statistics
Matches: 116, Mismatches: 24, Indels: 23
0.71 0.15 0.14
Matches are distributed among these distances:
19 29 0.25
20 18 0.16
21 29 0.25
22 40 0.34
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (22 bp):
TTGCGATAGTCTACAATTGTCG
Found at i:2721699 original size:63 final size:62
Alignment explanation
Indices: 2721575--2721705 Score: 185
Period size: 63 Copynumber: 2.1 Consensus size: 62
2721565 CGGTTTTTCA
* *
2721575 TTGCGATAGTCTACAATGTCGTTGCGATTTTCCAAATTCGTTGTGATAGTCTACAATTGTCG
1 TTGCGAAAGTCTACAATGTCGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAATTGTCG
* *
2721637 TTGCGAAAGTCTACAGTTGTCGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTACAA-TGTCG
1 TTGCGAAAGTCTACA-ATGTCGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAATTGTCG
2721700 TTGCGA
1 TTGCGA
2721706 TTTTCCAAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
62 17 0.27
63 28 0.45
64 17 0.27
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (62 bp):
TTGCGAAAGTCTACAATGTCGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAATTGTCG
Found at i:2721710 original size:41 final size:41
Alignment explanation
Indices: 2721634--2721769 Score: 195
Period size: 41 Copynumber: 3.3 Consensus size: 41
2721624 TCTACAATTG
* *
2721634 TCGTTGCGAAAGTCTACAGTTGTCGTTGCGATTTTCC-ATT
1 TCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAAT
*
2721674 TCGCGTTGCGATAGTCTACA-ATGTCGTTGCGATTTTCCAAAT
1 T--CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAAT
* *
2721716 TCGTTGCGATAGTCTACAGTTGTTGTTACGATTTTCCAAAT
1 TCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAAT
2721757 TCGTTGCGATAGT
1 TCGTTGCGATAGT
2721770 TAAAAAAAAA
Statistics
Matches: 86, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
40 18 0.21
41 49 0.57
42 19 0.22
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (41 bp):
TCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAAT
Found at i:2722363 original size:6 final size:6
Alignment explanation
Indices: 2722352--2722385 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
2722342 GCCACCGTCC
2722352 GTCGGG GTCGGG GTCGGG GTCGGG GTCGGG GTCG
1 GTCGGG GTCGGG GTCGGG GTCGGG GTCGGG GTCG
2722386 TGGTAATACG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.18, G:0.65, T:0.18
Consensus pattern (6 bp):
GTCGGG
Found at i:2722515 original size:21 final size:21
Alignment explanation
Indices: 2722489--2722540 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
2722479 AATTTGGAAA
2722489 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGATTTCCAACT
* *
2722510 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGATTTCCAACT
2722531 ATCGCAACGC
1 ATCGCAACGC
2722541 AAAATGCAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.31, G:0.15, T:0.25
Consensus pattern (21 bp):
ATCGCAACGCGATTTCCAACT
Found at i:2723454 original size:2 final size:2
Alignment explanation
Indices: 2723447--2723481 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2723437 TTCACATAAC
2723447 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2723482 AATGAGGTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2724887 original size:49 final size:50
Alignment explanation
Indices: 2724792--2724888 Score: 160
Period size: 49 Copynumber: 2.0 Consensus size: 50
2724782 TTCATAATTG
2724792 TAAATTAAAAACATAATTAAGATTTTTTTATATAACTATTAAGATAATCA
1 TAAATTAAAAACATAATTAAGATTTTTTTATATAACTATTAAGATAATCA
* * *
2724842 TAAATTAAATATATAATTAAGA-TTTTTTATATAATTATTAAGATAAT
1 TAAATTAAAAACATAATTAAGATTTTTTTATATAACTATTAAGATAAT
2724889 AAACTAGTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 24 0.55
50 20 0.45
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.43
Consensus pattern (50 bp):
TAAATTAAAAACATAATTAAGATTTTTTTATATAACTATTAAGATAATCA
Found at i:2725820 original size:22 final size:20
Alignment explanation
Indices: 2725795--2725843 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
2725785 TTGTTGTCGG
*
2725795 TATTTTTTTAATGTTTTTTCAT
1 TATTTTTTT-AT-TTTTTTAAT
2725817 TATTTCTTTTATTTTTTTAAT
1 TATTT-TTTTATTTTTTTAAT
*
2725838 AATTTT
1 TATTTT
2725844 GTTTTTATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 1 0.04
21 12 0.50
22 7 0.29
23 4 0.17
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (20 bp):
TATTTTTTTATTTTTTTAAT
Found at i:2726976 original size:29 final size:29
Alignment explanation
Indices: 2726930--2727115 Score: 178
Period size: 29 Copynumber: 6.4 Consensus size: 29
2726920 ACCGTTGACC
* *
2726930 GGGTGATATTTTGGGAATTAATTCGAAAT
1 GGGTGCTATTTTGGGAATTAATTCGAAAA
* *
2726959 GGGTGTTATTTTGAGAATTAATTCGAAAA
1 GGGTGCTATTTTGGGAATTAATTCGAAAA
* *
2726988 GGGTGCTATTTTAGGAATTTATTCAGAAAA
1 GGGTGCTATTTTGGGAATTAATTC-GAAAA
**
2727018 AAGTGCTATTTTGGGAATTTAATTCGAAAA
1 GGGTGCTATTTTGGGAA-TTAATTCGAAAA
* *
2727048 -AGTGTTATTTTGGGAATTTAATTCGAAAA
1 GGGTGCTATTTTGGGAA-TTAATTCGAAAA
* * ** * **
2727077 -GGTGCAAGTTTGATAATTATTTTAAAAA
1 GGGTGCTATTTTGGGAATTAATTCGAAAA
2727105 GGGTGCTATTT
1 GGGTGCTATTT
2727116 CTGTAAAATG
Statistics
Matches: 131, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
28 9 0.07
29 92 0.70
30 24 0.18
31 6 0.05
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.39
Consensus pattern (29 bp):
GGGTGCTATTTTGGGAATTAATTCGAAAA
Found at i:2727057 original size:59 final size:59
Alignment explanation
Indices: 2726936--2727076 Score: 162
Period size: 59 Copynumber: 2.4 Consensus size: 59
2726926 GACCGGGTGA
* *** * *
2726936 TATTTTGGGAA-TTAATTCGAAATGGGTGTTATTTTGAGAATTAATTCGAAAAGGGTGC
1 TATTTTAGGAATTTAATTCGAAAAAAGTGCTATTTTGAGAATTAATTCGAAAAGAGTGC
* *
2726994 TATTTTAGGAATTT-ATTCAGAAAAAAGTGCTATTTTGGGAATTTAATTCGAAAA-AGTGT
1 TATTTTAGGAATTTAATTC-GAAAAAAGTGCTATTTTGAGAA-TTAATTCGAAAAGAGTGC
*
2727053 TATTTTGGGAATTTAATTCGAAAA
1 TATTTTAGGAATTTAATTCGAAAA
2727077 GGTGCAAGTT
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
58 14 0.20
59 40 0.57
60 16 0.23
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.39
Consensus pattern (59 bp):
TATTTTAGGAATTTAATTCGAAAAAAGTGCTATTTTGAGAATTAATTCGAAAAGAGTGC
Found at i:2734288 original size:29 final size:29
Alignment explanation
Indices: 2734250--2734396 Score: 163
Period size: 29 Copynumber: 5.0 Consensus size: 29
2734240 ACCGTTGACC
* * * *
2734250 GGGTGATATTTTGAGAATTAATTTGAAAT
1 GGGTGCTATTTTGGGAATTAATTCGAAAA
2734279 GGGTGCTATTTTGGGAATTAATTCGAAAA
1 GGGTGCTATTTTGGGAATTAATTCGAAAA
* *
2734308 GTGTGCTATTTTGGGAATTTATTCGGAAAA
1 GGGTGCTATTTTGGGAATTAATTC-GAAAA
*
2734338 AGGTGCTATTTTGGGAATTTAATTCGAAAA
1 GGGTGCTATTTTGGGAA-TTAATTCGAAAA
* * *
2734368 --TTGCTATTTTGGCAATTTAATTTGAAAA
1 GGGTGCTATTTTGGGAA-TTAATTCGAAAA
2734396 G
1 G
2734397 ATGCTAGATT
Statistics
Matches: 103, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
28 25 0.24
29 47 0.46
30 25 0.24
31 6 0.06
ACGTcount: A:0.31, C:0.05, G:0.24, T:0.39
Consensus pattern (29 bp):
GGGTGCTATTTTGGGAATTAATTCGAAAA
Found at i:2736210 original size:13 final size:13
Alignment explanation
Indices: 2736180--2736241 Score: 56
Period size: 14 Copynumber: 4.7 Consensus size: 13
2736170 ATATCAATCT
* *
2736180 TAAATTAATTTCTT
1 TAAAATAATTT-TA
2736194 TAAAATAATTTTA
1 TAAAATAATTTTA
2736207 TAAAATAA-TTTA
1 TAAAATAATTTTA
2736219 -AAAATATATTTTA
1 TAAAATA-ATTTTA
*
2736232 AAAAAGTAAT
1 TAAAA-TAAT
2736242 ACCAAACTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
11 6 0.14
12 5 0.12
13 13 0.31
14 16 0.38
15 2 0.05
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (13 bp):
TAAAATAATTTTA
Found at i:2736229 original size:12 final size:12
Alignment explanation
Indices: 2736154--2736235 Score: 60
Period size: 13 Copynumber: 6.4 Consensus size: 12
2736144 TTTTCTCGTC
2736154 AAAAATAATTTT
1 AAAAATAATTTT
*
2736166 AATAATATCAATCTT
1 AA-AA-AT-AATTTT
*
2736181 -AAATTAATTTCTT
1 AAAAATAA-TT-TT
*
2736194 TAAAATAATTTT
1 AAAAATAATTTT
2736206 ATAAAATAA-TTT
1 A-AAAATAATTTT
2736218 AAAAATATATTTT
1 AAAAATA-ATTTT
2736231 AAAAA
1 AAAAA
2736236 AGTAATACCA
Statistics
Matches: 56, Mismatches: 5, Indels: 17
0.72 0.06 0.22
Matches are distributed among these distances:
11 8 0.14
12 11 0.20
13 23 0.41
14 9 0.16
15 5 0.09
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (12 bp):
AAAAATAATTTT
Found at i:2738651 original size:41 final size:41
Alignment explanation
Indices: 2738606--2738736 Score: 122
Period size: 41 Copynumber: 3.2 Consensus size: 41
2738596 ACAAACGCTT
2738606 CAATAGATTATAAATTTTGCGGCGATTTAGCCAAAACGCCG
1 CAATAGATTATAAATTTTGCGGCGATTTAGCCAAAACGCCG
* ** * * * * *
2738647 CAATATAGTGGTAAA-CTGGCAGCGTTTTTA-CCACAAACGCCA
1 CAATAGA-TTATAAATTTTGCGGCG-ATTTAGCCA-AAACGCCG
* * *
2738689 CAATAGAGTATAAATTTTGCGGCGATTGAGTCAAAACGCCG
1 CAATAGATTATAAATTTTGCGGCGATTTAGCCAAAACGCCG
2738730 CAATAGA
1 CAATAGA
2738737 GCGGTAAATT
Statistics
Matches: 66, Mismatches: 19, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
41 36 0.55
42 30 0.45
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (41 bp):
CAATAGATTATAAATTTTGCGGCGATTTAGCCAAAACGCCG
Found at i:2738752 original size:41 final size:40
Alignment explanation
Indices: 2738624--2738753 Score: 118
Period size: 41 Copynumber: 3.1 Consensus size: 40
2738614 TATAAATTTT
* *
2738624 GCGGCGATTTAGCCAAAACGCCGCAATATAGTGGTAAACTG
1 GCGGCGATTTAGCCAAAACGCCGCAATAGAG-GGTAAATTG
* * * ** *
2738665 GCAGCGTTTTTA-CCACAAACGCCACAATAGAGTATAAATTTT
1 GCGGCG-ATTTAGCCA-AAACGCCGCAATAGAGGGTAAA-TTG
* *
2738707 GCGGCGATTGAGTCAAAACGCCGCAATAGAGCGGTAAATTG
1 GCGGCGATTTAGCCAAAACGCCGCAATAGAG-GGTAAATTG
2738748 GCGGCG
1 GCGGCG
2738754 TTTTGACAAA
Statistics
Matches: 68, Mismatches: 16, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
41 38 0.56
42 30 0.44
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.21
Consensus pattern (40 bp):
GCGGCGATTTAGCCAAAACGCCGCAATAGAGGGTAAATTG
Found at i:2738757 original size:83 final size:83
Alignment explanation
Indices: 2738555--2738757 Score: 280
Period size: 83 Copynumber: 2.4 Consensus size: 83
2738545 CGGTTTTAGA
* * * * * ** *
2738555 AAAACGCCGCAATAGGGTGCTAAATTAGCGGCGTTTATATCACAAACGCTTCAATAGATTATAAA
1 AAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTTTTACCACAAACGCCACAATAGAGTATAAA
*
2738620 TTTTGCGGCGATTTAGCC
66 TTTTGCGGCGATTGAGCC
* * *
2738638 AAAACGCCGCAATATAGTGGTAAACTGGCAGCGTTTTTACCACAAACGCCACAATAGAGTATAAA
1 AAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTTTTACCACAAACGCCACAATAGAGTATAAA
*
2738703 TTTTGCGGCGATTGAGTC
66 TTTTGCGGCGATTGAGCC
*
2738721 AAAACGCCGCAATAGAGCGGTAAATTGGCGGCGTTTT
1 AAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTTT
2738758 GACAAAAAAA
Statistics
Matches: 103, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
83 103 1.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (83 bp):
AAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTTTTACCACAAACGCCACAATAGAGTATAAA
TTTTGCGGCGATTGAGCC
Found at i:2739543 original size:23 final size:21
Alignment explanation
Indices: 2739496--2739535 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2739486 CGAACAATTA
2739496 GTTTTTTACTGAACACGAAAT
1 GTTTTTTACTGAACACGAAAT
2739517 GTTTTTTACTGAACACGAA
1 GTTTTTTACTGAACACGAA
2739536 TGATGTTTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (21 bp):
GTTTTTTACTGAACACGAAAT
Found at i:2740784 original size:12 final size:12
Alignment explanation
Indices: 2740767--2740792 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2740757 TTTAGTTCAT
2740767 CATTTCATCACC
1 CATTTCATCACC
2740779 CATTTCATCACC
1 CATTTCATCACC
2740791 CA
1 CA
2740793 CTAAAACTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.42, G:0.00, T:0.31
Consensus pattern (12 bp):
CATTTCATCACC
Found at i:2742336 original size:13 final size:16
Alignment explanation
Indices: 2742306--2742337 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
2742296 AGCCAAAATC
2742306 TTCTTCTCTATTCTTT
1 TTCTTCTCTATTCTTT
2742322 TTCTT-TCT-TTCTTT
1 TTCTTCTCTATTCTTT
2742336 TT
1 TT
2742338 GATATCTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (16 bp):
TTCTTCTCTATTCTTT
Found at i:2744258 original size:37 final size:36
Alignment explanation
Indices: 2744164--2744280 Score: 150
Period size: 34 Copynumber: 3.3 Consensus size: 36
2744154 GGTAATCAAT
* *
2744164 TTTGAAAAAATAGTTTTCAAAGATTGGTAAAT-ATTC
1 TTTG-AAAAATAGTTTTCAAAGTTTGGTAAATGTTTC
*
2744200 TTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTTC
1 TTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTTC
*
2744235 TTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT-
1 TTTGAAAAATAG-TTTTCAAAGTTTGGTAAATGTTTC
*
2744271 GTTGAAAAAT
1 TTTGAAAAAT
2744281 GATAATGGGA
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
34 24 0.33
35 7 0.10
36 19 0.26
37 22 0.31
ACGTcount: A:0.35, C:0.04, G:0.18, T:0.43
Consensus pattern (36 bp):
TTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTTC
Found at i:2748803 original size:21 final size:21
Alignment explanation
Indices: 2748779--2748839 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
2748769 AACCTTGAAA
2748779 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
2748800 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
2748814 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
2748835 AAATG
1 AAATG
2748840 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:2748890 original size:36 final size:36
Alignment explanation
Indices: 2748777--2748889 Score: 176
Period size: 35 Copynumber: 3.2 Consensus size: 36
2748767 CCAACCTTGA
2748777 AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
2748813 -AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
* * *
2748848 AAAAATAGTTTTTCAAAGTTTGGTAGATGTTT-GTTG
1 AAAAAT-GGTTTTCAAAGTTTGGTAAATGTTTCTTTG
2748884 AAAAAT
1 AAAAAT
2748890 AATAATGGGA
Statistics
Matches: 72, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
35 35 0.49
36 14 0.19
37 23 0.32
ACGTcount: A:0.33, C:0.04, G:0.19, T:0.43
Consensus pattern (36 bp):
AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
Found at i:2751236 original size:20 final size:20
Alignment explanation
Indices: 2751211--2751252 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2751201 TTATCATTAT
2751211 TAAAATATAAAAAT-AAATAA
1 TAAAATA-AAAAATAAAATAA
*
2751231 TAAAATAAATAATAAAATAA
1 TAAAATAAAAAATAAAATAA
2751251 TA
1 TA
2751253 TTTTTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAAATAAAAAATAAAATAA
Found at i:2751248 original size:12 final size:12
Alignment explanation
Indices: 2751220--2751250 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
2751210 TTAAAATATA
2751220 AAAATAAATAAT
1 AAAATAAATAAT
2751232 AAAATAAATAAT
1 AAAATAAATAAT
2751244 AAAATAA
1 AAAATAA
2751251 TATTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAATAAATAAT
Found at i:2751542 original size:20 final size:20
Alignment explanation
Indices: 2751517--2751558 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2751507 CAAATAAAAT
2751517 GGAGGTCGGATTCGAACTTA
1 GGAGGTCGGATTCGAACTTA
2751537 GGAGGTCGGATTCGAACTTA
1 GGAGGTCGGATTCGAACTTA
2751557 GG
1 GG
2751559 GGGCCGAGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.14, G:0.38, T:0.24
Consensus pattern (20 bp):
GGAGGTCGGATTCGAACTTA
Found at i:2767649 original size:20 final size:20
Alignment explanation
Indices: 2767624--2767662 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2767614 CTATTTTAGA
*
2767624 AAATCGCAATGCGAATATGT
1 AAATCGCAACGCGAATATGT
*
2767644 AAATCGCAACGCGATTATG
1 AAATCGCAACGCGAATATG
2767663 ACTATCGCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (20 bp):
AAATCGCAACGCGAATATGT
Found at i:2767692 original size:21 final size:21
Alignment explanation
Indices: 2767645--2767710 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
2767635 CGAATATGTA
* *
2767645 AATCGCAACGCGATTATGAC-T
1 AATCGCAACGAGATAAT-ACAT
2767666 -ATCGCAACGAGATAATACAT
1 AATCGCAACGAGATAATACAT
* *
2767686 AATCGCAATGAGATAATACAA
1 AATCGCAACGAGATAATACAT
2767707 AATC
1 AATC
2767711 ACAATGCGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 2 0.05
20 15 0.38
21 22 0.56
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.21
Consensus pattern (21 bp):
AATCGCAACGAGATAATACAT
Found at i:2767715 original size:21 final size:21
Alignment explanation
Indices: 2767674--2767716 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2767664 CTATCGCAAC
* *
2767674 GAGATAATACATAATCGCAAT
1 GAGATAATACAAAATCACAAT
2767695 GAGATAATACAAAATCACAAT
1 GAGATAATACAAAATCACAAT
2767716 G
1 G
2767717 CGATTTTCAA
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:0.51, C:0.14, G:0.14, T:0.21
Consensus pattern (21 bp):
GAGATAATACAAAATCACAAT
Found at i:2767894 original size:22 final size:22
Alignment explanation
Indices: 2767869--2767911 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2767859 GGCGACATCC
* *
2767869 GTCCTCATCTCCGACGAAATCT
1 GTCCCCATATCCGACGAAATCT
*
2767891 GTCCCCATATCCGGCGAAATC
1 GTCCCCATATCCGACGAAATC
2767912 CGTCTATCTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.37, G:0.16, T:0.23
Consensus pattern (22 bp):
GTCCCCATATCCGACGAAATCT
Found at i:2768387 original size:20 final size:20
Alignment explanation
Indices: 2768358--2768406 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
2768348 GCGATTATCT
*
2768358 CGTTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
2768378 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
2768398 TGTTGCGAT
1 CGTTGCGAT
2768407 TTTCATTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:2768412 original size:20 final size:20
Alignment explanation
Indices: 2768374--2768429 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
2768364 GATAGTCAAA
* **
2768374 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
2768394 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
2768414 TTCGTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
2768430 AAGTTTTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:2770368 original size:34 final size:34
Alignment explanation
Indices: 2770269--2770371 Score: 118
Period size: 34 Copynumber: 3.1 Consensus size: 34
2770259 ACGAAACTTA
* * ** *
2770269 AAAATCACAACGCGAATTTGACTATCGCAACGGG
1 AAAATCGCAATGCGAAAATGACTATCGCAACGTG
* * **
2770303 ATAATCGCAATGCG-AAATAAAAATCGCAACGTG
1 AAAATCGCAATGCGAAAATGACTATCGCAACGTG
2770336 AAAATCGCAATGCGAAAATGACTATCGCAACGTG
1 AAAATCGCAATGCGAAAATGACTATCGCAACGTG
2770370 AA
1 AA
2770372 TTTAGTTTCG
Statistics
Matches: 55, Mismatches: 13, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
33 26 0.47
34 29 0.53
ACGTcount: A:0.43, C:0.20, G:0.19, T:0.17
Consensus pattern (34 bp):
AAAATCGCAATGCGAAAATGACTATCGCAACGTG
Found at i:2770421 original size:20 final size:20
Alignment explanation
Indices: 2770396--2770464 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
2770386 GCGATTATCC
*
2770396 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
*
2770416 CGTTGCGATATTC-ATTTCCG
1 CGTTGCGATAGTCAATTT-CG
* * *
2770436 CTTTGCGATAGTCATTTTCA
1 CGTTGCGATAGTCAATTTCG
2770456 CGTTGCGAT
1 CGTTGCGAT
2770465 TTAAGTTTCG
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 3 0.08
20 34 0.85
21 3 0.08
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:2771040 original size:42 final size:42
Alignment explanation
Indices: 2770993--2771086 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
2770983 CCTCTCCTAT
*
2770993 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCTTCCCAC
1 CGTTCAAGAGGCCCCTATCATCACTCAAGAGGTCCC-TCCCAC
* * * *
2771035 CGTTCAAGAGGCCCTTGTCATCATTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCCCTATCATCACTCAAGAGGTCCCTCCCAC
*
2771077 CATTCAAGAG
1 CGTTCAAGAG
2771087 CCTGATTCAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 40 0.89
43 5 0.11
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.22
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTATCATCACTCAAGAGGTCCCTCCCAC
Found at i:2771041 original size:21 final size:21
Alignment explanation
Indices: 2771017--2771086 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
2771007 CTATCATCCC
*
2771017 TCAAGAGTCCCTTCCCACCGT
1 TCAAGAGTCCCTTCCCACCAT
* ** *
2771038 TCAAGAGGCCCTTGTCATCAT
1 TCAAGAGTCCCTTCCCACCAT
*
2771059 TGAAGAGGTCCC-TCCCACCAT
1 TCAAGA-GTCCCTTCCCACCAT
2771080 TCAAGAG
1 TCAAGAG
2771087 CCTGATTCAT
Statistics
Matches: 37, Mismatches: 11, Indels: 3
0.73 0.22 0.06
Matches are distributed among these distances:
20 1 0.03
21 32 0.86
22 4 0.11
ACGTcount: A:0.24, C:0.34, G:0.19, T:0.23
Consensus pattern (21 bp):
TCAAGAGTCCCTTCCCACCAT
Found at i:2772447 original size:14 final size:14
Alignment explanation
Indices: 2772410--2772471 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
2772400 TTACTTGTTT
*
2772410 AATTGATTTATAAA
1 AATTGATTTGTAAA
2772424 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
2772438 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
2772453 TATTGATGTGTAAA
1 AATTGATTTGTAAA
2772467 TAATT
1 -AATT
2772472 CTTATTTGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:2772547 original size:63 final size:65
Alignment explanation
Indices: 2772424--2772581 Score: 230
Period size: 63 Copynumber: 2.4 Consensus size: 65
2772414 GATTTATAAA
* * *
2772424 AATTGATTTGTAAAAGTTGATTTGTTTAATATTGATGTGTAAATAATTCTTATTTGTGCTTGTTT
1 AATTGATTTGTAAAAGTTGATTTGTTTAATATTGATGTGCAAATAATTATTATTTGTGCTTATTT
*
2772489 AATTGATTTGTAAAAGTTGCTTTGTTT-A-ATTGATGTGCAAATAATTATTATTTGTGCTTATTT
1 AATTGATTTGTAAAAGTTGATTTGTTTAATATTGATGTGCAAATAATTATTATTTGTGCTTATTT
2772552 AATTGATTGAAATGTAAAAGTTGATTTGTT
1 AATTGATT----TGTAAAAGTTGATTTGTT
2772582 GATTTCAATT
Statistics
Matches: 84, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
63 40 0.48
64 1 0.01
65 26 0.31
67 17 0.20
ACGTcount: A:0.30, C:0.03, G:0.17, T:0.50
Consensus pattern (65 bp):
AATTGATTTGTAAAAGTTGATTTGTTTAATATTGATGTGCAAATAATTATTATTTGTGCTTATTT
Found at i:2772658 original size:20 final size:20
Alignment explanation
Indices: 2772633--2772710 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
2772623 AGGTACACTT
*
2772633 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAACTCAAAA
* *
2772653 TCGCAATGCGAAAGTCAAAA
1 TCGCAACGCGAAACTCAAAA
**
2772673 TCGCAATACGAAAGC-CAAAA
1 TCGCAACGCGAAA-CTCAAAA
*
2772693 TCGCAACGCGAAAGTCAA
1 TCGCAACGCGAAACTCAA
2772711 TTGGCGTTGT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.45, C:0.26, G:0.17, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:2772783 original size:20 final size:20
Alignment explanation
Indices: 2772760--2772879 Score: 126
Period size: 20 Copynumber: 6.3 Consensus size: 20
2772750 ATTGCAATAG
*
2772760 TCAAATTCCCGTTGCGATAA
1 TCAAATTCGCGTTGCGATAA
* *
2772780 TCAAATTCACGTTGCGATAG
1 TCAAATTCGCGTTGCGATAA
2772800 TCAAATTCGCGTTGCGAT--
1 TCAAATTCGCGTTGCGATAA
* *
2772818 T----TTTGAGTTGCGATAA
1 TCAAATTCGCGTTGCGATAA
*
2772834 TCAAATTCGCGTTGCGATAG
1 TCAAATTCGCGTTGCGATAA
* *
2772854 TCAATTTCGCGTTGCGATAT
1 TCAAATTCGCGTTGCGATAA
2772874 TCAAAT
1 TCAAAT
2772880 GAATGTGTAA
Statistics
Matches: 83, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
14 11 0.13
16 1 0.01
18 1 0.01
20 70 0.84
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (20 bp):
TCAAATTCGCGTTGCGATAA
Found at i:2773144 original size:139 final size:138
Alignment explanation
Indices: 2772850--2773131 Score: 483
Period size: 139 Copynumber: 2.0 Consensus size: 138
2772840 TCGCGTTGCG
* * * *
2772850 ATAGTCAATTTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAG-CAAATTCGCATTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGAACA
*
2772915 TATCAATGTTCAAACTCAAGTTACTAATACATGCCAACTGAAAATGTTAAAAGTTTACACATAAA
65 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCAACTGAAAATGTTAAAAGTTTACACATAAA
2772980 ATACACATA
130 ATACACATA
*
2772989 ATAGTCAAATTCGCATTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAATAGAACA
1 ATAG-CAAATTCGCATTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGAACA
2773054 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
65 TAGCAATGTTCAAACTCAAGTTACTAATACATGCC-AACTGAAAATGTTAAAAGTTTACACATAA
2773119 AATACACATA
129 AATACACATA
2773129 ATA
1 ATA
2773132 CAACGTTTGC
Statistics
Matches: 136, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
139 94 0.69
140 42 0.31
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (138 bp):
ATAGCAAATTCGCATTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGAACAT
AGCAATGTTCAAACTCAAGTTACTAATACATGCCAACTGAAAATGTTAAAAGTTTACACATAAAA
TACACATA
Found at i:2773212 original size:18 final size:18
Alignment explanation
Indices: 2773189--2773223 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2773179 AAGCTGGTTG
2773189 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
2773207 TGATTGCGATTTTGATT
1 TGATTGAGATTTTGATT
2773224 GCCTTTTTTT
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:0.20, C:0.03, G:0.23, T:0.54
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:2776369 original size:20 final size:20
Alignment explanation
Indices: 2776344--2776434 Score: 121
Period size: 20 Copynumber: 4.5 Consensus size: 20
2776334 TTGAAATTCA
*
2776344 GCGTTGCGACAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
2776364 GCGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
**
2776384 GCGTTGCGATAATGT-ATTATC
1 GCGTTGCGAT-A-GTCAGAATC
*
2776405 GCATTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
2776425 GCGTTGCGAT
1 GCGTTGCGAT
2776435 TTACATATTC
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
19 2 0.03
20 43 0.70
21 14 0.23
22 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (20 bp):
GCGTTGCGATAGTCAGAATC
Found at i:2776467 original size:61 final size:61
Alignment explanation
Indices: 2776347--2776468 Score: 138
Period size: 61 Copynumber: 2.0 Consensus size: 61
2776337 AAATTCAGCG
* * **
2776347 TTGCGACAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATAATGTATTATCGCA
1 TTGCGACAGTCAGAATCGCGTTGCGATAGTCAGAATCGCATTGCGATAATCTAAAATCGCA
* * * * **
2776408 TTGCGATAGTCAGAATCGCGTTGCGAT-TTACATATTCGCATTGCGATTTTCTAAAATCGCA
1 TTGCGACAGTCAGAATCGCGTTGCGATAGT-CAGAATCGCATTGCGATAATCTAAAATCGCA
2776469 ACGCGAATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 1 0.02
61 49 0.98
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (61 bp):
TTGCGACAGTCAGAATCGCGTTGCGATAGTCAGAATCGCATTGCGATAATCTAAAATCGCA
Found at i:2776571 original size:19 final size:19
Alignment explanation
Indices: 2776547--2776602 Score: 94
Period size: 19 Copynumber: 2.9 Consensus size: 19
2776537 TGCGATACTG
*
2776547 GAGATCGCGTTGTGATTTA
1 GAGATCGCGTTGCGATTTA
2776566 GAGATCGCGTTGCGATTTA
1 GAGATCGCGTTGCGATTTA
*
2776585 GAGATCGCATTGCGATTT
1 GAGATCGCGTTGCGATTT
2776603 TGTTGGTCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.21, C:0.14, G:0.30, T:0.34
Consensus pattern (19 bp):
GAGATCGCGTTGCGATTTA
Found at i:2780596 original size:2 final size:2
Alignment explanation
Indices: 2780584--2780615 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2780574 CGGATAGCTC
*
2780584 AT AT GT 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
2780616 TTCAGTTGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2784597 original size:21 final size:21
Alignment explanation
Indices: 2784571--2784629 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
2784561 ATTTACCGTG
2784571 ATTGCGGCCGTCGCGGGCGCT
1 ATTGCGGCCGTCGCGGGCGCT
* * *
2784592 ATTGCGGCCATCGCAGACGCT
1 ATTGCGGCCGTCGCGGGCGCT
2784613 ATTGCGGCCGTCGCGGG
1 ATTGCGGCCGTCGCGGG
2784630 TAACTCGGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.10, C:0.32, G:0.39, T:0.19
Consensus pattern (21 bp):
ATTGCGGCCGTCGCGGGCGCT
Found at i:2785721 original size:23 final size:23
Alignment explanation
Indices: 2785691--2785735 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
2785681 GCTTAGGAAT
2785691 GTTTAAGTAAAAATAAATTAAGA
1 GTTTAAGTAAAAATAAATTAAGA
2785714 GTTTAAGTAAAAATAAATTAAG
1 GTTTAAGTAAAAATAAATTAAG
2785736 TAAATTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (23 bp):
GTTTAAGTAAAAATAAATTAAGA
Found at i:2786517 original size:20 final size:20
Alignment explanation
Indices: 2786494--2786532 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2786484 TAAAAATGAA
* *
2786494 TAAACATTATTAACTAATGT
1 TAAAAATTAATAACTAATGT
*
2786514 TAAAAATTAATAATTAATG
1 TAAAAATTAATAACTAATG
2786533 AATAATAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATTAATAACTAATGT
Found at i:2794250 original size:6 final size:7
Alignment explanation
Indices: 2794233--2794264 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
2794223 ATTATGTAAT
2794233 GGAAAAA
1 GGAAAAA
2794240 GGAAAAA
1 GGAAAAA
2794247 -GAAAAA
1 GGAAAAA
2794253 GGAAAAA
1 GGAAAAA
2794260 -GAAAA
1 GGAAAA
2794265 CACACGATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 11 0.46
7 13 0.54
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (7 bp):
GGAAAAA
Found at i:2794252 original size:13 final size:13
Alignment explanation
Indices: 2794234--2794264 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
2794224 TTATGTAATG
2794234 GAAAAAGGAAAAA
1 GAAAAAGGAAAAA
2794247 GAAAAAGGAAAAA
1 GAAAAAGGAAAAA
2794260 GAAAA
1 GAAAA
2794265 CACACGATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
GAAAAAGGAAAAA
Found at i:2794864 original size:16 final size:17
Alignment explanation
Indices: 2794843--2794894 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
2794833 TTTAAAATTT
2794843 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
2794859 AATTACTCATAA-TTT--
1 AATTACTC-TAACTTTCA
*
2794874 AATCACTCTAACTTTCA
1 AATTACTCTAACTTTCA
2794891 AATT
1 AATT
2794895 TAATTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 10 0.34
16 7 0.24
17 6 0.21
18 3 0.10
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Found at i:2802630 original size:28 final size:29
Alignment explanation
Indices: 2802570--2802632 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
2802560 GGAAAAAAAT
**
2802570 ATAGTTTCCATATACAATTATTTTTTTAA
1 ATAGTTTCCATATACAATTATTTTTCCAA
*
2802599 ATAGTTTCCATGTAC-ATGT-TTTTTCCAA
1 ATAGTTTCCATATACAAT-TATTTTTCCAA
2802627 ATAGTT
1 ATAGTT
2802633 ATCATCTACG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 15 0.50
29 15 0.50
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.49
Consensus pattern (29 bp):
ATAGTTTCCATATACAATTATTTTTCCAA
Found at i:2812866 original size:27 final size:27
Alignment explanation
Indices: 2812802--2812866 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 27
2812792 GCATCTTTTA
2812802 AAAAAATTA-AA-ATTTTATATAATTT
1 AAAAAATTATAATATTTTATATAATTT
** * * **
2812827 AAGTATTTTTAATATTTTATATTCTTT
1 AAAAAATTATAATATTTTATATAATTT
2812854 AAAAAATTATAAT
1 AAAAAATTATAAT
2812867 TTCTCATCTT
Statistics
Matches: 28, Mismatches: 10, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
25 5 0.18
26 2 0.07
27 21 0.75
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (27 bp):
AAAAAATTATAATATTTTATATAATTT
Found at i:2818666 original size:31 final size:31
Alignment explanation
Indices: 2818625--2818684 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
2818615 TCGATTGAGT
* *
2818625 ATTTTTTTACAAATCGATAACGTTTATGAAA
1 ATTTTGTTACAAATCGATAACGTTAATGAAA
*
2818656 ATTTTGTTACAAATCGATAATGTTAATGA
1 ATTTTGTTACAAATCGATAACGTTAATGA
2818685 CTTTTTTGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (31 bp):
ATTTTGTTACAAATCGATAACGTTAATGAAA
Found at i:2818692 original size:31 final size:31
Alignment explanation
Indices: 2818625--2818693 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
2818615 TCGATTGAGT
*
2818625 ATTTTT-TTACAAATCGATAACGTTTATGAA
1 ATTTTTGTTACAAATCGATAACGTTAATGAA
* * *
2818655 AATTTTGTTACAAATCGATAATGTTAATGAC
1 ATTTTTGTTACAAATCGATAACGTTAATGAA
*
2818686 TTTTTTGT
1 ATTTTTGT
2818694 AATTTTTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (31 bp):
ATTTTTGTTACAAATCGATAACGTTAATGAA
Found at i:2820992 original size:5 final size:5
Alignment explanation
Indices: 2820982--2821010 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
2820972 CGGCATCCAG
2820982 GTTCT GTTCT GTTCT GTTCT GTTCT GTTC
1 GTTCT GTTCT GTTCT GTTCT GTTCT GTTC
2821011 CTTTCCAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.21, G:0.21, T:0.59
Consensus pattern (5 bp):
GTTCT
Found at i:2822454 original size:2 final size:2
Alignment explanation
Indices: 2822447--2822483 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2822437 ACAAATGTGT
*
2822447 TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2822484 GTTTGATACG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2830598 original size:2 final size:2
Alignment explanation
Indices: 2830591--2830634 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2830581 CGATAAATAA
2830591 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
2830633 AT
1 AT
2830635 CGTTAGAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2833523 original size:118 final size:119
Alignment explanation
Indices: 2833315--2833552 Score: 424
Period size: 118 Copynumber: 2.0 Consensus size: 119
2833305 TCAATGTTTT
2833315 ATATCAAGGTAAAAAATCATTTTGTTGATGAAAAGTGTTAGTCAACAAATGGTAAATGCTCTTAA
1 ATATCAAGGTAAAAAATCATTTTGTTGATGAAAAGTGTTAGTCAACAAATGGTAAATGCTCTTAA
* * *
2833380 ACATGAGTCTTTTTGTCTTAAAATGAATCGTTAATAATTAAAATGCT-AAAAAA
66 ACATAAGTCTTTTTATCTTAAAATGAATAGTTAATAATTAAAATGCTCAAAAAA
* *
2833433 ATATCGAGGTAAAAAATCATTTTGTTGATGAAAAGTGTTAGTCAACATATGGTAAATGCTCTTAA
1 ATATCAAGGTAAAAAATCATTTTGTTGATGAAAAGTGTTAGTCAACAAATGGTAAATGCTCTTAA
2833498 ACATAAGTCTTTTTATCTTAAAATGAATAGTTAATAATTAAAATGCTCAAAAAA
66 ACATAAGTCTTTTTATCTTAAAATGAATAGTTAATAATTAAAATGCTCAAAAAA
2833552 A
1 A
2833553 AAACTAAAAT
Statistics
Matches: 114, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
118 107 0.94
119 7 0.06
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (119 bp):
ATATCAAGGTAAAAAATCATTTTGTTGATGAAAAGTGTTAGTCAACAAATGGTAAATGCTCTTAA
ACATAAGTCTTTTTATCTTAAAATGAATAGTTAATAATTAAAATGCTCAAAAAA
Found at i:2833880 original size:21 final size:21
Alignment explanation
Indices: 2833854--2833906 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
2833844 GTTTCCAGAT
2833854 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
* *
2833875 TCGCAACGCAAACTTCGACTA
1 TCGCAACGCGAACATCGACTA
*
2833896 TCGCAATGCGA
1 TCGCAACGCGA
2833907 TTTTCCAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:2834004 original size:18 final size:18
Alignment explanation
Indices: 2833961--2834025 Score: 103
Period size: 18 Copynumber: 3.6 Consensus size: 18
2833951 TTCCAAATTC
*
2833961 GCGTTGCGATAGTCCAAG
1 GCGTTGCGATAGTCGAAG
*
2833979 TTCGTTGCGATAGTCGAAG
1 -GCGTTGCGATAGTCGAAG
2833998 GCGTTGCGATAGTCGAAG
1 GCGTTGCGATAGTCGAAG
2834016 GCGTTGCGAT
1 GCGTTGCGAT
2834026 TTATTCCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
18 27 0.63
19 16 0.37
ACGTcount: A:0.20, C:0.18, G:0.35, T:0.26
Consensus pattern (18 bp):
GCGTTGCGATAGTCGAAG
Found at i:2834050 original size:78 final size:79
Alignment explanation
Indices: 2833918--2834155 Score: 275
Period size: 78 Copynumber: 2.9 Consensus size: 79
2833908 TTTCCAAATT
*
2833918 CGTTGCGATAGTCTAAGTTCGCGTTGCGATTTATTCCAAATTCGCGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCGAAG-T-GCGTTGCGATTTATTCCAAATTCGCGTTGCGATAGTCCAAGTTCG
2833983 TTGCGATAGTCGAAGG
64 TTGCGATAGTCGAAGG
2833999 CGTTGCGATAGTCGAAG-GCGTTGCGATTTATTCCAAATTCGCGTTGCGATAGTCCAAGTTCGTT
1 CGTTGCGATAGTCGAAGTGCGTTGCGATTTATTCCAAATTCGCGTTGCGATAGTCCAAGTTCGTT
*
2834063 GCGATAGTCCAAGTTCG
66 GCGATAGTCGAAG---G
* * * * * * * *
2834080 CGTTGCGATTTATTCCAAGTTCGTTGCGA--TAGTCGAAGTTCGCGTTGCGATTTATTCAAAGTT
1 CGTTGCGA--TAGTCGAAGTGCGTTGCGATTTATTCCAAATTCGCGTTGCGA--TAGTCCAAGTT
*
2834143 CGTTGTGATAGTC
62 CGTTGCGATAGTC
2834156 CAAAATTGCA
Statistics
Matches: 138, Mismatches: 11, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
78 59 0.43
81 25 0.18
82 18 0.13
83 7 0.05
84 29 0.21
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (79 bp):
CGTTGCGATAGTCGAAGTGCGTTGCGATTTATTCCAAATTCGCGTTGCGATAGTCCAAGTTCGTT
GCGATAGTCGAAGG
Found at i:2834097 original size:42 final size:40
Alignment explanation
Indices: 2833918--2834158 Score: 247
Period size: 42 Copynumber: 5.9 Consensus size: 40
2833908 TTTCCAAATT
* * *
2833918 CGTTGCGATAGTCTAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 CGTTGCGATAGTCCAAGTT--CGTTGCGA--TAGTCCAAGTTCG
*
2833962 CGTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAG---G
1 CGTTGCGATAGTCCAAGTTCGTTGCGATAGTCCAAGTTCG
* * * *
2833999 CGTTGCGATAGTCGAAG-GCGTTGCGATTTATTCCAAATTCG
1 CGTTGCGATAGTCCAAGTTCGTTGCGA--TAGTCCAAGTTCG
2834040 CGTTGCGATAGTCCAAGTTCGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCGTTGCGATAGTCCAAGTTCG
* *
2834080 CGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGA--TAGTCCAAGTTCGTTGCGATAGTCCAAGTTCG
* * *
2834122 CGTTGCGATTTATTCAAAGTTCGTTGTGATAGTCCAA
1 CGTTGCGA--TAGTCCAAGTTCGTTGCGATAGTCCAA
2834159 AATTGCAACT
Statistics
Matches: 171, Mismatches: 18, Indels: 18
0.83 0.09 0.09
Matches are distributed among these distances:
36 8 0.05
37 17 0.10
38 6 0.04
40 25 0.15
41 17 0.10
42 80 0.47
44 18 0.11
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (40 bp):
CGTTGCGATAGTCCAAGTTCGTTGCGATAGTCCAAGTTCG
Found at i:2834146 original size:21 final size:20
Alignment explanation
Indices: 2833918--2834158 Score: 183
Period size: 21 Copynumber: 11.8 Consensus size: 20
2833908 TTTCCAAATT
*
2833918 CGTTGCGATAGTCTAAGTTC
1 CGTTGCGATAGTCCAAGTTC
* *
2833938 GCGTTGCGATTTATTCCAAATTC
1 -CGTTGCGA--TAGTCCAAGTTC
2833961 GCGTTGCGATAGTCCAAGTT-
1 -CGTTGCGATAGTCCAAGTTC
* *
2833981 CGTTGCGATAGTCGAAG--G
1 CGTTGCGATAGTCCAAGTTC
* *
2833999 CGTTGCGATAGTCGAAG--G
1 CGTTGCGATAGTCCAAGTTC
* *
2834017 CGTTGCGATTTATTCCAAATTC
1 CGTTGCGA--TAGTCCAAGTTC
2834039 GCGTTGCGATAGTCCAAGTT-
1 -CGTTGCGATAGTCCAAGTTC
2834059 CGTTGCGATAGTCCAAGTTC
1 CGTTGCGATAGTCCAAGTTC
*
2834079 GCGTTGCGATTTATTCCAAGTT-
1 -CGTTGCGA--TAGTCCAAGTTC
*
2834101 CGTTGCGATAGTCGAAGTTC
1 CGTTGCGATAGTCCAAGTTC
* *
2834121 GCGTTGCGATTTATTCAAAGTT-
1 -CGTTGCGA--TAGTCCAAGTTC
*
2834143 CGTTGTGATAGTCCAA
1 CGTTGCGATAGTCCAA
2834159 AATTGCAACT
Statistics
Matches: 184, Mismatches: 20, Indels: 34
0.77 0.08 0.14
Matches are distributed among these distances:
18 26 0.14
19 50 0.27
20 6 0.03
21 57 0.31
23 45 0.24
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCCAAGTTC
Found at i:2834147 original size:63 final size:60
Alignment explanation
Indices: 2833902--2834147 Score: 222
Period size: 63 Copynumber: 4.0 Consensus size: 60
2833892 ACTATCGCAA
* *
2833902 TGCGATT-TTCCAAATTCGTTGCGATAGTCTAAGTTCGCGTTGCGATTTATTCCAAA-TTCGCGT
1 TGCGATTATTCCAAATTCGTTGCGATAGTCGAAGTT-GCGTTGCGA--TAGT-CAAAGTTC-CGT
* * * *
2833965 TGCGA-TAGTCCAAGTTCGTTGCGATAGTCGAAG--GCGTTGCGATAGTCGAAG--GCGT
1 TGCGATTATTCCAAATTCGTTGCGATAGTCGAAGTTGCGTTGCGATAGTCAAAGTTCCGT
* *
2834020 TGCGATTTATTCCAAATTCGCGTTGCGATAGTCCAAGTT-CGTTGCGATAGTCCAAGTTCGCGT
1 TGCGA-TTATTCCAAATT--CGTTGCGATAGTCGAAGTTGCGTTGCGATAGTCAAAGTTC-CGT
* *
2834083 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCAAAGTT-CGT
1 TGCGA-TTATTCCAAATTCGTTGCGATAGTCGAAGTT-GCGTTGCGA--TAGTCAAAGTTCCGT
2834146 TG
1 TG
2834148 TGATAGTCCA
Statistics
Matches: 153, Mismatches: 15, Indels: 30
0.77 0.08 0.15
Matches are distributed among these distances:
55 8 0.05
57 12 0.08
58 3 0.02
59 16 0.10
60 25 0.16
61 18 0.12
62 1 0.01
63 61 0.40
65 9 0.06
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.34
Consensus pattern (60 bp):
TGCGATTATTCCAAATTCGTTGCGATAGTCGAAGTTGCGTTGCGATAGTCAAAGTTCCGT
Found at i:2835072 original size:21 final size:21
Alignment explanation
Indices: 2835010--2835098 Score: 110
Period size: 21 Copynumber: 4.2 Consensus size: 21
2835000 TGGACTATCA
2835010 CAACGAACTTGGAATAAATCG
1 CAACGAACTTGGAATAAATCG
* * *
2835031 TAACGCGAACTTCGACT--ATCG
1 CAA--CGAACTTGGAATAAATCG
2835052 CAACGAACTTGGAATAAATCG
1 CAACGAACTTGGAATAAATCG
*
2835073 CAACGAATTTGGAATAAATCG
1 CAACGAACTTGGAATAAATCG
2835094 CAACG
1 CAACG
2835099 CGAACTTCGA
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
19 10 0.18
21 37 0.65
23 10 0.18
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.20
Consensus pattern (21 bp):
CAACGAACTTGGAATAAATCG
Found at i:2835109 original size:63 final size:63
Alignment explanation
Indices: 2835010--2835201 Score: 221
Period size: 63 Copynumber: 3.1 Consensus size: 63
2835000 TGGACTATCA
* *
2835010 CAACGAACTTGGAATAAATCGTAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCG
1 CAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCG
* * * * *
2835073 CAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATTGCAACAAATTTAGAATAAATCA
1 CAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCG
* * * * *
2835136 CAACGCGAACTTCGACT--ATAGCAA--CGAACTTAGACTATCGCAACGAATTTGTAATAAATCG
1 CAA--CGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCG
*
2835197 TAACG
1 CAACG
2835202 CGAACTTCGA
Statistics
Matches: 109, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
59 2 0.02
61 33 0.30
63 65 0.60
65 9 0.08
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (63 bp):
CAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCG
Found at i:2835118 original size:42 final size:42
Alignment explanation
Indices: 2835072--2835169 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
2835062 GGAATAAATC
* * *
2835072 GCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATT
1 GCAACGAATTTAGAATAAATCACAACGCGAACTTCGACTATA
*
2835114 GCAACAAATTTAGAATAAATCACAACGCGAACTTCGACTATA
1 GCAACGAATTTAGAATAAATCACAACGCGAACTTCGACTATA
*
2835156 GCAACGAACTTAGA
1 GCAACGAATTTAGA
2835170 CTATCGCAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.21
Consensus pattern (42 bp):
GCAACGAATTTAGAATAAATCACAACGCGAACTTCGACTATA
Found at i:2835185 original size:61 final size:61
Alignment explanation
Indices: 2835027--2835220 Score: 205
Period size: 61 Copynumber: 3.1 Consensus size: 61
2835017 CTTGGAATAA
* * * * *
2835027 ATCGTAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAA--CGAATTTGGAAT
1 ATCGCAAC-CGAACTTCGACTATCGCAACGAA-TTTGAATAAATCGCAACGCGAACTTCGACT
* * *
2835088 AAATCGCAACGCGAACTTCGACTATTGCAACAAATTTAGAATAAATCACAACGCGAACTTCGACT
1 --ATCGCAAC-CGAACTTCGACTATCGCAACGAATTT-GAATAAATCGCAACGCGAACTTCGACT
* * *
2835153 ATAGCAA-CGAACTTAGACTATCGCAACGAATTTGTAATAAATCGTAACGCGAACTTCGACT
1 ATCGCAACCGAACTTCGACTATCGCAACGAATTTG-AATAAATCGCAACGCGAACTTCGACT
2835214 ATCGCAA
1 ATCGCAA
2835221 ATCAGTTTCC
Statistics
Matches: 112, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
60 1 0.01
61 53 0.47
62 2 0.02
63 47 0.42
65 9 0.08
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (61 bp):
ATCGCAACCGAACTTCGACTATCGCAACGAATTTGAATAAATCGCAACGCGAACTTCGACT
Found at i:2846300 original size:22 final size:21
Alignment explanation
Indices: 2846275--2846315 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2846265 TAAAAACTTA
*
2846275 TATAATTAATAATAATTTTAGT
1 TATAATTAAGAAT-ATTTTAGT
2846297 TATAATTAAGAATATTTTA
1 TATAATTAAGAATATTTTA
2846316 ACGATAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
TATAATTAAGAATATTTTAGT
Found at i:2849219 original size:3 final size:3
Alignment explanation
Indices: 2849211--2849252 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
2849201 TATATGCTCC
* *
2849211 TGA TGA TGA TGA TGA TGA TGA CGA TGA TCA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
2849253 GAGTGAGGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.05, G:0.31, T:0.31
Consensus pattern (3 bp):
TGA
Found at i:2851878 original size:60 final size:60
Alignment explanation
Indices: 2851777--2851892 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
2851767 CTCCACGCTG
* * * * * *
2851777 TCGACATTTAGGTCGAACAAGTTGGTAGTTGCATTCATTCCCCTT-GAACTTGAAGCCATC
1 TCGACATTGAGGTCGAAAAAGCTCGTAGTTGAATGCATT-CCCTTGGAACTTGAAGCCATC
* *
2851837 TCGACATTGAGGTCGAAAAAGCTCGTAGTTGAATGCCTTCCCTTGGAGCTTGAAGC
1 TCGACATTGAGGTCGAAAAAGCTCGTAGTTGAATGCATTCCCTTGGAACTTGAAGC
2851893 GTCGTGCCAA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
59 5 0.11
60 42 0.89
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.29
Consensus pattern (60 bp):
TCGACATTGAGGTCGAAAAAGCTCGTAGTTGAATGCATTCCCTTGGAACTTGAAGCCATC
Found at i:2856077 original size:24 final size:25
Alignment explanation
Indices: 2856050--2856103 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
2856040 TAATTAAAAA
2856050 TATATTT-AATATATCTTAAAATTT
1 TATATTTCAATATATCTTAAAATTT
** *
2856074 TATAATTTCGTTATCTCTTAAAATTT
1 TAT-ATTTCAATATATCTTAAAATTT
2856100 TATA
1 TATA
2856104 AATTTATTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 3 0.12
25 5 0.20
26 17 0.68
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (25 bp):
TATATTTCAATATATCTTAAAATTT
Found at i:2857817 original size:24 final size:23
Alignment explanation
Indices: 2857762--2857843 Score: 65
Period size: 23 Copynumber: 3.5 Consensus size: 23
2857752 TATTTATGTC
2857762 GTTCGTTTAACGTTTGCGAACAT
1 GTTCGTTTAACGTTTGCGAACAT
* * * * *
2857785 GCTCATTTATATGTTTGCGAGCTT
1 GTTCGTTTA-ACGTTTGCGAACAT
* ***
2857809 GTTCGTTTAGCGTTCATGAACAT
1 GTTCGTTTAACGTTTGCGAACAT
*
2857832 GTTTGTTTAACG
1 GTTCGTTTAACG
2857844 GTCATTTATA
Statistics
Matches: 42, Mismatches: 16, Indels: 2
0.70 0.27 0.03
Matches are distributed among these distances:
23 24 0.57
24 18 0.43
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.43
Consensus pattern (23 bp):
GTTCGTTTAACGTTTGCGAACAT
Found at i:2858066 original size:38 final size:38
Alignment explanation
Indices: 2858022--2858102 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 38
2858012 AATGAGCTTC
*
2858022 TAAACGAACTTGTTAATGACCATAAATGAACGAGTCGA
1 TAAACGAACTTGTTAATGACCATAAACGAACGAGTCGA
* * * * *
2858060 TAAACGAGCTTGTTCATGAGCATAAACGAATGAGTCTA
1 TAAACGAACTTGTTAATGACCATAAACGAACGAGTCGA
2858098 TAAAC
1 TAAAC
2858103 AAGCTCGCTC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.25
Consensus pattern (38 bp):
TAAACGAACTTGTTAATGACCATAAACGAACGAGTCGA
Found at i:2858115 original size:38 final size:38
Alignment explanation
Indices: 2858037--2858116 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
2858027 GAACTTGTTA
* * * *
2858037 ATGACCATAAATGAACGAGTCGATAAACGAGCTTGTTC
1 ATGACCATAAACGAACGAGTCGATAAACAAGCTCGCTC
* * *
2858075 ATGAGCATAAACGAATGAGTCTATAAACAAGCTCGCTC
1 ATGACCATAAACGAACGAGTCGATAAACAAGCTCGCTC
2858113 ATGA
1 ATGA
2858117 ATATAAAAGA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.23
Consensus pattern (38 bp):
ATGACCATAAACGAACGAGTCGATAAACAAGCTCGCTC
Found at i:2858123 original size:38 final size:38
Alignment explanation
Indices: 2858037--2858128 Score: 94
Period size: 38 Copynumber: 2.4 Consensus size: 38
2858027 GAACTTGTTA
* * * * *
2858037 ATGACCATAAATGAACGAGTCGATAAACGAGCTTGTTC
1 ATGAACATAAACGAACGAGTCGATAAACAAGCTCGCTC
* * *
2858075 ATGAGCATAAACGAATGAGTCTATAAACAAGCTCGCTC
1 ATGAACATAAACGAACGAGTCGATAAACAAGCTCGCTC
* *
2858113 ATGAATATAAAAGAAC
1 ATGAACATAAACGAAC
2858129 CGAACACACA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.22
Consensus pattern (38 bp):
ATGAACATAAACGAACGAGTCGATAAACAAGCTCGCTC
Found at i:2858403 original size:19 final size:20
Alignment explanation
Indices: 2858381--2858421 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
2858371 AAAAAATAAG
2858381 AATTTAAAAA-AATATTAAA
1 AATTTAAAAATAATATTAAA
*
2858400 AATTTAAAAATATTATTAAA
1 AATTTAAAAATAATATTAAA
2858420 AA
1 AA
2858422 ATAAAAGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AATTTAAAAATAATATTAAA
Found at i:2858432 original size:20 final size:20
Alignment explanation
Indices: 2858393--2858432 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2858383 TTTAAAAAAA
*
2858393 TATTAAAAATTTAAAAATAT
1 TATTAAAAATATAAAAATAT
2858413 TATTAAAAA-ATAAAAGATAT
1 TATTAAAAATATAAAA-ATAT
2858433 CAGAAGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (20 bp):
TATTAAAAATATAAAAATAT
Found at i:2871463 original size:16 final size:17
Alignment explanation
Indices: 2871431--2871464 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2871421 AGTTCCTCTT
*
2871431 TCCTTTACTTTTTTTTA
1 TCCTTTACTTTTCTTTA
2871448 TCCTTT-CTTTTCTTTA
1 TCCTTTACTTTTCTTTA
2871464 T
1 T
2871465 AATTTTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.71
Consensus pattern (17 bp):
TCCTTTACTTTTCTTTA
Found at i:2876812 original size:15 final size:15
Alignment explanation
Indices: 2876800--2876838 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
2876790 CCCAATCCCA
2876800 ATCATCTTCATCCTC
1 ATCATCTTCATCCTC
*
2876815 TTCATCTTCATCCTC
1 ATCATCTTCATCCTC
*
2876830 TTCATCTTC
1 ATCATCTTC
2876839 TTCGATGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.15, C:0.38, G:0.00, T:0.46
Consensus pattern (15 bp):
ATCATCTTCATCCTC
Found at i:2896355 original size:94 final size:95
Alignment explanation
Indices: 2896133--2896355 Score: 403
Period size: 95 Copynumber: 2.4 Consensus size: 95
2896123 TAATCACAGC
* *
2896133 AAAGTTAGTTGCAGCTTCAACTAACCAGGAACTCGTATGAAAGCACAGTACATTTGCCACGTCTA
1 AAAGTTAGTTGCAACTTCAACTAACCAGGAACTTGTATGAAAGCACAGTACATTTGCCACGTCTA
2896198 GTTAAAAAAAATACATGATATAAGAACATT
66 GTTAAAAAAAATACATGATATAAGAACATT
2896228 AAAGTTAGTTGCAACTTCAACTAACCAGGAACTTGTATGAAAGCACAGTACATTTGCCACGTCTA
1 AAAGTTAGTTGCAACTTCAACTAACCAGGAACTTGTATGAAAGCACAGTACATTTGCCACGTCTA
2896293 GTT-AAAAAAATACATGATATAAGAACATT
66 GTTAAAAAAAATACATGATATAAGAACATT
* *
2896322 ACAGTTAGTTGCAACTTCAACTAACCAGCAACTT
1 AAAGTTAGTTGCAACTTCAACTAACCAGGAACTT
2896356 TTTGTGGCTC
Statistics
Matches: 124, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
94 58 0.47
95 66 0.53
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (95 bp):
AAAGTTAGTTGCAACTTCAACTAACCAGGAACTTGTATGAAAGCACAGTACATTTGCCACGTCTA
GTTAAAAAAAATACATGATATAAGAACATT
Found at i:2899361 original size:2 final size:2
Alignment explanation
Indices: 2899350--2899384 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2899340 GTCATCATGG
2899350 AT AT -T 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
2899385 GCATTTTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2903488 original size:11 final size:11
Alignment explanation
Indices: 2903472--2903496 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2903462 GATATATACA
2903472 GTTACTCCATG
1 GTTACTCCATG
2903483 GTTACTCCATG
1 GTTACTCCATG
2903494 GTT
1 GTT
2903497 GCTTACAGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (11 bp):
GTTACTCCATG
Found at i:2909051 original size:34 final size:34
Alignment explanation
Indices: 2909008--2909092 Score: 161
Period size: 34 Copynumber: 2.5 Consensus size: 34
2908998 GCCCCGCCTA
2909008 TATATATATAATATTTTTTATTTTTTATATTAAT
1 TATATATATAATATTTTTTATTTTTTATATTAAT
2909042 TATATATATAATATTTTTTATTTTTTATATTAAT
1 TATATATATAATATTTTTTATTTTTTATATTAAT
*
2909076 TATATATAAAATATTTT
1 TATATATATAATATTTT
2909093 CGGGTTCGGG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (34 bp):
TATATATATAATATTTTTTATTTTTTATATTAAT
Found at i:2922932 original size:35 final size:35
Alignment explanation
Indices: 2922886--2922958 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
2922876 TCAGTATGAA
2922886 TAACATAGAATAGCCTATTAGATTGAACAGTTTGG
1 TAACATAGAATAGCCTATTAGATTGAACAGTTTGG
*
2922921 TAACATAGAATAGCCTATTAGATTGAACATTTTGG
1 TAACATAGAATAGCCTATTAGATTGAACAGTTTGG
2922956 TAA
1 TAA
2922959 GGTTACAACT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (35 bp):
TAACATAGAATAGCCTATTAGATTGAACAGTTTGG
Found at i:2936366 original size:18 final size:18
Alignment explanation
Indices: 2936325--2936368 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
2936315 GGAGGGGATT
2936325 TTTTTATATAAAAAATGA
1 TTTTTATATAAAAAATGA
*
2936343 TATTTTA-ATAAAAAAGTTA
1 T-TTTTATATAAAAAA-TGA
2936362 TTTTTAT
1 TTTTTAT
2936369 TTTTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
TTTTTATATAAAAAATGA
Found at i:2937595 original size:50 final size:50
Alignment explanation
Indices: 2937473--2937596 Score: 144
Period size: 51 Copynumber: 2.5 Consensus size: 50
2937463 GCAGTAAAGT
* ** *
2937473 GCGC-CCCCTGCACCGCGCTACACGATGATTTGGCACCACGTGAGGTGTA
1 GCGCGCCCCTGCACCGCGCTATACGATGAGCTGGCACCACGTGAGGTATA
* * *
2937522 GCGCGCCTCCTGCACCGCACTATACGGTGAGCTGGCGCCACGTG-GGTATA
1 GCGCGCC-CCTGCACCGCGCTATACGATGAGCTGGCACCACGTGAGGTATA
*
2937572 GCGCGGCCCCTGCAGCGCGCTATAC
1 GCGC-GCCCCTGCACCGCGCTATAC
2937597 CTATATATCT
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
49 4 0.06
50 26 0.41
51 33 0.52
ACGTcount: A:0.16, C:0.36, G:0.31, T:0.17
Consensus pattern (50 bp):
GCGCGCCCCTGCACCGCGCTATACGATGAGCTGGCACCACGTGAGGTATA
Found at i:2937786 original size:13 final size:14
Alignment explanation
Indices: 2937758--2937786 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2937748 ATATTTTATA
2937758 ATATTTTTACTATT
1 ATATTTTTACTATT
2937772 ATATTTTTACT-TT
1 ATATTTTTACTATT
2937785 AT
1 AT
2937787 TTAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATTTTTACTATT
Found at i:2937994 original size:110 final size:111
Alignment explanation
Indices: 2937861--2938081 Score: 354
Period size: 110 Copynumber: 2.0 Consensus size: 111
2937851 TGAAAATCAT
*
2937861 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
* * * *
2937926 TATTTAGTT-ATTTATTTAATGCATGATTATTATATTAATAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
* * *
2937971 ATATCTCGACACTTTGTTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTATTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
*
2938036 TAATTAGTTGATTCCTTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
2938082 TTTTTGTAAT
Statistics
Matches: 101, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
110 69 0.68
111 32 0.32
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.47
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:2943474 original size:31 final size:31
Alignment explanation
Indices: 2943408--2943466 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 31
2943398 AATTTAAGGA
*
2943408 AAAATGGTTTTTGGACTTGAATTGAATTTAC
1 AAAATGGTATTTGGACTTGAATTGAATTTAC
2943439 AAAAT-GTATTTGGACTT-AATTGAATTTA
1 AAAATGGTATTTGGACTTGAATTGAATTTA
2943467 TTCAAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.41
30 11 0.41
31 5 0.19
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.42
Consensus pattern (31 bp):
AAAATGGTATTTGGACTTGAATTGAATTTAC
Found at i:2943553 original size:19 final size:19
Alignment explanation
Indices: 2943531--2943597 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
2943521 AATGTTTTTA
*
2943531 TGAATAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
2943550 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
* * *
2943569 TGAACAGTCAATAACTGTT
1 TGAACAGTAAATTACTATT
2943588 TGAACAGTAA
1 TGAACAGTAA
2943598 TCTGAGGCTA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.34
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:2943729 original size:21 final size:21
Alignment explanation
Indices: 2943703--2943743 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2943693 ATTTGAATAT
* *
2943703 TATGAAGGGGTATCGATTCCC
1 TATGAAGAGGTACCGATTCCC
2943724 TATGAAGAGGTACCGATTCC
1 TATGAAGAGGTACCGATTCC
2943744 TCCCATTCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (21 bp):
TATGAAGAGGTACCGATTCCC
Found at i:2943806 original size:21 final size:21
Alignment explanation
Indices: 2943773--2943812 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2943763 TTTTTGCAGA
*
2943773 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
2943795 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
2943813 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:2944067 original size:34 final size:32
Alignment explanation
Indices: 2944028--2944097 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
2944018 TTTTGTAAAG
*
2944028 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
2944062 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
2944094 GGGA
1 GGGA
2944098 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:2945020 original size:49 final size:51
Alignment explanation
Indices: 2944900--2945008 Score: 168
Period size: 51 Copynumber: 2.2 Consensus size: 51
2944890 ATACAAAACA
* * **
2944900 CGGTACCTACCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGTCG
1 CGGTACCTGCCACGCGCTATATAAAATTATGTCAGGAGTAAAGGTATAACG
2944951 CGGTACCTGCCACGCGCTATATAAAATTAT-T-AGGAGTAAAGGTATAACG
1 CGGTACCTGCCACGCGCTATATAAAATTATGTCAGGAGTAAAGGTATAACG
2945000 CGGTACCTG
1 CGGTACCTG
2945009 ATCCGTGCTA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
49 25 0.46
50 1 0.02
51 28 0.52
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (51 bp):
CGGTACCTGCCACGCGCTATATAAAATTATGTCAGGAGTAAAGGTATAACG
Found at i:2945135 original size:49 final size:48
Alignment explanation
Indices: 2945034--2945154 Score: 143
Period size: 49 Copynumber: 2.5 Consensus size: 48
2945024 CTACGTGGCA
* **
2945034 TATAGCGCGCTGCAGGGGCCGCGCTATACCCACGTGGCACCAGCTCACCG
1 TATAGCGCGATGCAGGGG--GCGCTATACCCACGTGGCACCAAATCACCG
* * * *
2945084 TATAGCGAGATGCAGGGGGCGTTATACCCCACGTGGCGCCAAATCATCG
1 TATAGCGCGATGCAGGGGGCGCTATA-CCCACGTGGCACCAAATCACCG
*
2945133 TATAGCGCGATGCATGGGGCGC
1 TATAGCGCGATGCAGGGGGCGC
2945155 ACTTTACTGC
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
48 7 0.12
49 37 0.62
50 16 0.27
ACGTcount: A:0.21, C:0.31, G:0.32, T:0.17
Consensus pattern (48 bp):
TATAGCGCGATGCAGGGGGCGCTATACCCACGTGGCACCAAATCACCG
Found at i:2947555 original size:2 final size:2
Alignment explanation
Indices: 2947548--2947579 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2947538 TCATGGCAAC
2947548 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
2947580 TAACAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2956057 original size:19 final size:19
Alignment explanation
Indices: 2956033--2956071 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2956023 TTTTAGTTCC
*
2956033 GTTACTTGTGTATAAATAT
1 GTTACTGGTGTATAAATAT
2956052 GTTACTGGTGTATAAATAT
1 GTTACTGGTGTATAAATAT
2956071 G
1 G
2956072 ATACAACACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.44
Consensus pattern (19 bp):
GTTACTGGTGTATAAATAT
Found at i:2957629 original size:29 final size:33
Alignment explanation
Indices: 2957586--2957654 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 33
2957576 TATTATTATT
**
2957586 AAAATATTATTTCTA-TAGTTT-TA-T-AAATA
1 AAAATATTAACTCTAGTAGTTTCTATTAAAATA
*
2957615 AAAATATTAACTCTAGTATTTTCTATTAAAATA
1 AAAATATTAACTCTAGTAGTTTCTATTAAAATA
2957648 AAAATAT
1 AAAATAT
2957655 GATAAATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 13 0.39
30 5 0.15
31 2 0.06
32 1 0.03
33 12 0.36
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (33 bp):
AAAATATTAACTCTAGTAGTTTCTATTAAAATA
Done.