Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008000.1 Hibiscus syriacus cultivar Beakdansim tig00110457_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: 1646480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 9
Found at i:289289 original size:42 final size:43
Alignment explanation
Indices: 289196--289294 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
289186 ATTTATGTGT
* *
289196 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
289237 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
289279 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
289295 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:289484 original size:7 final size:7
Alignment explanation
Indices: 289435--289481 Score: 76
Period size: 7 Copynumber: 6.7 Consensus size: 7
289425 CGATTTTCTC
289435 AATTGTA
1 AATTGTA
289442 AATTGTA
1 AATTGTA
289449 AATTGTA
1 AATTGTA
289456 AATTGTA
1 AATTGTA
*
289463 AATTGCA
1 AATTGTA
*
289470 AATTGCA
1 AATTGTA
289477 AATTG
1 AATTG
289482 CAATCTTCAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.38
Consensus pattern (7 bp):
AATTGTA
Found at i:291322 original size:2 final size:2
Alignment explanation
Indices: 291315--291344 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
291305 AAGCTATTTC
291315 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
291345 CTTGGGCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:303870 original size:32 final size:32
Alignment explanation
Indices: 303834--303903 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
303824 AGTTTGGATC
* * *
303834 AATATCATATTGGTT-GACTTTTGGGTCGGGTT
1 AATATCATATCGGTTAGA-TTTCGAGTCGGGTT
*
303866 AATATCATATCGGTTAGATTTCGAGTTGGGTT
1 AATATCATATCGGTTAGATTTCGAGTCGGGTT
303898 AATATC
1 AATATC
303904 GGATTGATAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 31 0.94
33 2 0.06
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.41
Consensus pattern (32 bp):
AATATCATATCGGTTAGATTTCGAGTCGGGTT
Found at i:313222 original size:35 final size:35
Alignment explanation
Indices: 313181--313273 Score: 114
Period size: 35 Copynumber: 2.7 Consensus size: 35
313171 ACAATTGTCG
* *
313181 ATTACATTTTAAACCCCAAATTCCAAAATATTTCA
1 ATTACATTCTAAACCCCAAATTCCAAAATACTTCA
* *
313216 ATTACATTCTAAATCTCAAATTCCAAAATACTTCA
1 ATTACATTCTAAACCCCAAATTCCAAAATACTTCA
* * **
313251 ATTATATGCCCAACCCCAAATTC
1 ATTACATTCTAAACCCCAAATTC
313274 ATAATTCATT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.41, C:0.26, G:0.01, T:0.32
Consensus pattern (35 bp):
ATTACATTCTAAACCCCAAATTCCAAAATACTTCA
Found at i:313918 original size:21 final size:21
Alignment explanation
Indices: 313881--313920 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
313871 AAGATGCATC
*
313881 TTAAAAAAATTATAATTTTTT
1 TTAAAAAAATTACAATTTTTT
313902 TTAAAAAAGA-TACAATTTT
1 TTAAAAAA-ATTACAATTTT
313921 AAAAAATCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (21 bp):
TTAAAAAAATTACAATTTTTT
Found at i:316080 original size:22 final size:22
Alignment explanation
Indices: 316055--316135 Score: 108
Period size: 22 Copynumber: 3.7 Consensus size: 22
316045 CTTTTGTACC
* *
316055 AGTGTTGAGGTACTTTAGTATT
1 AGTGCTGAGGAACTTTAGTATT
316077 AGTGCTGAGGAACTTTAGTATT
1 AGTGCTGAGGAACTTTAGTATT
* *
316099 AGTACTGAGGCACTTTAGTATT
1 AGTGCTGAGGAACTTTAGTATT
* *
316121 AGTGCTAAGGCACTT
1 AGTGCTGAGGAACTT
316136 CCGTTATTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (22 bp):
AGTGCTGAGGAACTTTAGTATT
Found at i:316092 original size:44 final size:44
Alignment explanation
Indices: 316044--316135 Score: 112
Period size: 44 Copynumber: 2.1 Consensus size: 44
316034 GTGCGAATGC
* ** * *
316044 ACTTTTGTACCAGTGTTGAGGTACTTTAGTATTAGTGCTGAGGA
1 ACTTTAGTACCAGTACTGAGGCACTTTAGTATTAGTGCTAAGGA
** *
316088 ACTTTAGTATTAGTACTGAGGCACTTTAGTATTAGTGCTAAGGC
1 ACTTTAGTACCAGTACTGAGGCACTTTAGTATTAGTGCTAAGGA
316132 ACTT
1 ACTT
316136 CCGTTATTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (44 bp):
ACTTTAGTACCAGTACTGAGGCACTTTAGTATTAGTGCTAAGGA
Found at i:323005 original size:22 final size:22
Alignment explanation
Indices: 322980--323029 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
322970 AATGTAAATG
*
322980 CACTTTTGTAAAAGTGCTAAGA
1 CACTTTAGTAAAAGTGCTAAGA
** *
323002 CACTTTAGTATTAGTGCTAAGG
1 CACTTTAGTAAAAGTGCTAAGA
323024 CACTTT
1 CACTTT
323030 CATGATTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (22 bp):
CACTTTAGTAAAAGTGCTAAGA
Found at i:338844 original size:35 final size:37
Alignment explanation
Indices: 338774--338873 Score: 114
Period size: 35 Copynumber: 2.8 Consensus size: 37
338764 GTGCTTGTGG
* * * * *
338774 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTATTTTTAAGAGTTTGAATCCTAGCAAAATTCT
*
338811 ATCCTA-TTTTAAGAG-TTGAATCCTAGCAGAATTCT
1 ATCCTATTTTTAAGAGTTTGAATCCTAGCAAAATTCT
* *
338846 ATCTTATTTTTGAGAGTTTGAATCCTAG
1 ATCCTATTTTTAAGAGTTTGAATCCTAG
338874 TAGGACGAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
35 21 0.40
36 15 0.28
37 17 0.32
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTTAAGAGTTTGAATCCTAGCAAAATTCT
Found at i:339638 original size:106 final size:104
Alignment explanation
Indices: 339334--340106 Score: 773
Period size: 109 Copynumber: 7.4 Consensus size: 104
339324 AATATTGTTC
* * * *
339334 CGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAATTGGAAATT-TTTGTTGACA
** * * * *
339399 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
64 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * *
339440 CGAGTCTAATATCCTTCGCTGTGAAGATGAAATTGACTCTG-AA--CGAAA-TCTTGTTGACAAT
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAATTTTTGTTGACAAC
*
339501 CAGCCGTCCCTTCGTTTTGAAGTTGAACTTGTGTTGTCT
66 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
339540 CGAGTCCAATATCCTTCGCTGCGAAGTTGAAATTGGCTCTGAAATTTGAAAAATATTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA-TTG-GAAATTTTTGTTGACA
*
339605 ACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
64 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * ** * * *
339646 CGAGTGGCACGATATCCTCCG-TCGTGGAGTT-AAAATCGCGGATGAAACTGAAAAGTTGTTCGT
1 CGAGT--C-CAATATCCTTCGCT-GTGAAGTTGAAATTGGC-TCTGAAATTGGAAA-TT-TTTGT
339709 TGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
59 TGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * *
339755 CGGGTAGCACGATATCC-TCTG-TCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATTGTTTGT
1 CGAGT--C-CAATATCCTTC-GCT-GTGAAGTTGAAATTGGCTCTGAAATT-GGAAATT-TTTGT
*
339818 TGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
59 TGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * **
339864 CGAGTCCAATATCATTCGCTGTGAAGTTGAGATTGGCTCCGAAATT-G-----CTTGTCGACAGT
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAATTTTTGTTGACAAC
* * * *
339923 CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
66 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * *
339962 TGGGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGAAACTAGGAAATTATTGTTGACAA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA-TTGGAAATTTTTGTTGACAA
340027 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
340067 CGAGTCCAATATCCTTCTCTGTGAAGTCGAAATTGACTCT
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT
340107 AGCTAAAACC
Statistics
Matches: 556, Mismatches: 86, Indels: 51
0.80 0.12 0.07
Matches are distributed among these distances:
98 82 0.15
99 1 0.00
100 82 0.15
101 3 0.01
102 4 0.01
104 2 0.00
105 81 0.15
106 115 0.21
107 8 0.01
108 12 0.02
109 157 0.28
110 9 0.02
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (104 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAATTTTTGTTGACAAC
CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:339892 original size:324 final size:312
Alignment explanation
Indices: 339490--340068 Score: 759
Period size: 324 Copynumber: 1.8 Consensus size: 312
339480 GAACGAAATC
* * * *
339490 TTGTTGACAATCAGCCGTCCCTTCGTTTTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCT
1 TTGTTGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCAT
* * * *
339555 TCGCTGCGAAGTTGAAATTGGCTCTGAAATTTGAAAAATATTTGTTGACAACCAGCCATCCCTTC
66 TCGCTGCGAAGTTGAAATTGGCTCCGAAA-TTG-------CTTGTCGACAACCAGCCACCCCTTC
* * * *
339620 GTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGCACGATATCCTCCG-TCGTGGAGTTAAAATC-
123 GCTGTGAAGTTGAACTTGTGCTGTCTCG-G-GGC-CAATATCCTCCGCT-GTGAAGTTAAAATCG
* *
339683 GCGGATGAAACT-GAAAAGTTGTTCGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTG
184 GC-CATGAAACTAGAAAA-TTATT-GTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTG
339747 TGTTGTCTCGGGTAGCACGATATCCTCTGTCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATT
246 TGTTGTCTCGGGTAGCACGATATCCTCTGTCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATT
339812 GT
311 GT
339814 TTGTTGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCAT
1 TTGTTGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCAT
* * ** *
339879 TCGCTGTGAAGTTGAGATTGGCTCCGAAATTGCTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAA
66 TCGCTGCGAAGTTGAAATTGGCTCCGAAATTGCTTGTCGACAACCAGCCACCCCTTCGCTGTGAA
* * * * * * *
339944 GTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGAAACTA
131 GTTGAACTTGTGCTGTCTCGGGGCCAATATCCTCCGCTGTGAAGTTAAAATCGGCCATGAAACTA
*
340009 GGAAATTATTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
196 GAAAATTATTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
340069 AGTCCAATAT
Statistics
Matches: 225, Mismatches: 27, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
312 50 0.22
313 32 0.14
314 9 0.04
315 1 0.00
316 43 0.19
323 3 0.01
324 87 0.39
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (312 bp):
TTGTTGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCAT
TCGCTGCGAAGTTGAAATTGGCTCCGAAATTGCTTGTCGACAACCAGCCACCCCTTCGCTGTGAA
GTTGAACTTGTGCTGTCTCGGGGCCAATATCCTCCGCTGTGAAGTTAAAATCGGCCATGAAACTA
GAAAATTATTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAG
CACGATATCCTCTGTCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATTGT
Found at i:339980 original size:98 final size:98
Alignment explanation
Indices: 339806--340101 Score: 369
Period size: 98 Copynumber: 2.9 Consensus size: 98
339796 CTGGAATTGG
*
339806 GAAATTGTTTGTTGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCC
1 GAAATTGATTGTTGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCC
* *
339871 AATATCATTCGCTGTGAAGTTGAGATTGGCTCC-
66 AATATCCTTCGCTGTGAAGTTGAAATTGGC-CCT
* * ** * * * * *
339904 GAAATTGCTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCC
1 GAAATTGATTGTTGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCC
339969 AATATCCTTCGCTGTGAAGTTGAAATTGGCCCT
66 AATATCCTTCGCTGTGAAGTTGAAATTGGCCCT
* *
340002 GAAACTAGGAAATTATTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
1 GAAA-T------TGATTGTTGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
* *
340067 CGAGTCCAATATCCTTCTCTGTGAAGTCGAAATTG
59 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
340102 ACTCTAGCTA
Statistics
Matches: 166, Mismatches: 24, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
97 2 0.01
98 88 0.53
99 1 0.01
105 75 0.45
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.33
Consensus pattern (98 bp):
GAAATTGATTGTTGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCC
AATATCCTTCGCTGTGAAGTTGAAATTGGCCCT
Found at i:340735 original size:65 final size:65
Alignment explanation
Indices: 340631--340811 Score: 299
Period size: 65 Copynumber: 2.8 Consensus size: 65
340621 GACAAAATTT
340631 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
340696 TGTTTCAAGAGAAACTATCTCAAGAGAGACGAAATTCATTTAAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* * **
340761 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA-TTCATTTCAAGGGAAA
340812 CTATCTCAAG
Statistics
Matches: 107, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
65 94 0.88
66 13 0.12
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:340802 original size:102 final size:102
Alignment explanation
Indices: 340696--341153 Score: 790
Period size: 102 Copynumber: 4.5 Consensus size: 102
340686 TCAATGTTTA
* * *
340696 TGTTTCAAGAGAAACTATCTCAAGAGAGACGAAATTCATTTAAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
340761 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
340798 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
340863 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
340900 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* * *
340965 TGTTTCAAGAGAAACTGTCTCAATGGTGACGAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
341002 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
341067 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAAATT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* * **
341104 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTTTGTTTCAAGGGAAA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
341154 CTGTCTCAAG
Statistics
Matches: 337, Mismatches: 19, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 337 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (102 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:340812 original size:37 final size:37
Alignment explanation
Indices: 340761--341171 Score: 269
Period size: 37 Copynumber: 11.9 Consensus size: 37
340751 TCAATGTTTA
* *
340761 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
340798 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * *
340834 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* *
340862 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
340900 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * **
340936 CATTTCAAGGGAAA-TGTTTC--------CAATGTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * *
340964 ATGTTTCAAGAGAAACTGTCTCAATG-GTGACGAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAA-GAGAGACAAAATTT
* *
341002 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-CT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * *
341038 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* * * *
341066 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAAATT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
341104 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
341140 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
341172 TGGTGAGCAC
Statistics
Matches: 283, Mismatches: 52, Indels: 78
0.69 0.13 0.19
Matches are distributed among these distances:
27 3 0.01
28 5 0.02
29 39 0.14
30 11 0.04
32 2 0.01
33 2 0.01
34 2 0.01
35 8 0.03
36 83 0.29
37 118 0.42
38 10 0.04
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:340886 original size:167 final size:168
Alignment explanation
Indices: 340596--340898 Score: 545
Period size: 167 Copynumber: 1.8 Consensus size: 168
340586 AAGATGATGC
*
340596 TTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
1 TTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
*
340661 GAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
66 AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
*
340726 GAAATTCATTTAAAGGGAAATGTTTTCAATGTTTATGT
131 AAAATTCATTTAAAGGGAAATGTTTTCAATGTTTATGT
*
340764 TTCAAGAG-AAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGAC
1 TTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
* *
340828 AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAC
66 AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
340893 AAAATT
131 AAAATT
340899 TTGTTTCAAG
Statistics
Matches: 129, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
167 121 0.94
168 8 0.06
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.30
Consensus pattern (168 bp):
TTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
AAAATTCATTTAAAGGGAAATGTTTTCAATGTTTATGT
Found at i:341149 original size:36 final size:36
Alignment explanation
Indices: 341067--341171 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 36
341057 TCAATGTTTA
* * *
341067 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAG-ACAAAATT
*
341104 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
341140 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
341172 TGGTGAGCAC
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
36 38 0.59
37 26 0.41
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:341989 original size:22 final size:22
Alignment explanation
Indices: 341964--342014 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
341954 TTGTGTTTGG
341964 TCAAAGGTTTGGAATTTGATGC
1 TCAAAGGTTTGGAATTTGATGC
*
341986 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGAATTTGATGC
342008 TCAAAGG
1 TCAAAGG
342015 ATTGATGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.27, C:0.10, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGAATTTGATGC
Found at i:342649 original size:20 final size:21
Alignment explanation
Indices: 342623--342684 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
342613 CTTTTTGTTC
*
342623 CCTTTTTTATTTTTGTTCTTT
1 CCTTTTTTATTCTTGTTCTTT
* *
342644 -CTTTTTTGTTCTTGTTTTTT
1 CCTTTTTTATTCTTGTTCTTT
*
342664 CCTTTTTTGCTTCTT-TTCTTT
1 CCTTTTTT-ATTCTTGTTCTTT
342685 TTTCTTTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 12 0.35
22 5 0.15
ACGTcount: A:0.02, C:0.16, G:0.06, T:0.76
Consensus pattern (21 bp):
CCTTTTTTATTCTTGTTCTTT
Found at i:342695 original size:22 final size:22
Alignment explanation
Indices: 342641--342693 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
342631 ATTTTTGTTC
342641 TTTCTTTTTTG-TTCTTGTTTT
1 TTTCTTTTTTGCTTCTTGTTTT
* *
342662 TTCCTTTTTTGCTTCTTTTCTTT
1 TTTCTTTTTTGCTTCTTGT-TTT
342685 TTTCTTTTT
1 TTTCTTTTT
342694 GCCCTTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 10 0.37
22 6 0.22
23 11 0.41
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (22 bp):
TTTCTTTTTTGCTTCTTGTTTT
Found at i:346318 original size:11 final size:11
Alignment explanation
Indices: 346238--346319 Score: 53
Period size: 11 Copynumber: 7.3 Consensus size: 11
346228 TTATATACGT
*
346238 TAATAGTAAAA
1 TAATATTAAAA
*
346249 TAATAATAAATA
1 TAATATTAAA-A
346261 TAATAGTTATAAA
1 TAATA-TTA-AAA
*
346274 T-ATATATATAA
1 TAATAT-TAAAA
346285 TAACT-TTAAAA
1 TAA-TATTAAAA
*
346296 -AACATTAAAA
1 TAATATTAAAA
*
346306 TAATATTAGAA
1 TAATATTAAAA
346317 TAA
1 TAA
346320 AAATAATTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
10 8 0.14
11 28 0.50
12 13 0.23
13 5 0.09
14 2 0.04
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (11 bp):
TAATATTAAAA
Found at i:346837 original size:35 final size:37
Alignment explanation
Indices: 346767--346866 Score: 114
Period size: 35 Copynumber: 2.8 Consensus size: 37
346757 ATGCTTGTGG
* * * * *
346767 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTATTTTTAAGAGTTTGAATCCTAGCAAAATTCT
*
346804 ATCCTA-TTTTAAGAG-TTGAATCCTAGCAGAATTCT
1 ATCCTATTTTTAAGAGTTTGAATCCTAGCAAAATTCT
* *
346839 ATCTTATTTTTGAGAGTTTGAATCCTAG
1 ATCCTATTTTTAAGAGTTTGAATCCTAG
346867 TAGGACGAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
35 21 0.40
36 15 0.28
37 17 0.32
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTTAAGAGTTTGAATCCTAGCAAAATTCT
Found at i:347523 original size:117 final size:117
Alignment explanation
Indices: 347308--347523 Score: 285
Period size: 117 Copynumber: 1.8 Consensus size: 117
347298 AAATCGAAAT
347308 TTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAGATTTCATTT
1 TTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAGATTTCATTT
* *
347373 TGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAATTTGTTTAATTTAAAAA
66 TGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAATTTGTTTAATTTAAAAA
* * * * * *
347425 TTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACTCATT-TCTCAATATTTCAT
1 TTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCT-TCAAGATTTCAT
* * *
347488 TTTGATTTTCCAAGTCTATTTTAGCTTTC-AAAAGAA
64 TTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAA
347524 GATCATTTTA
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
116 2 0.02
117 79 0.93
118 4 0.05
ACGTcount: A:0.29, C:0.15, G:0.07, T:0.49
Consensus pattern (117 bp):
TTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAGATTTCATTT
TGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAATTTGTTTAATTTAAAAA
Found at i:350264 original size:15 final size:15
Alignment explanation
Indices: 350244--350273 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
350234 ACATACTAAC
350244 AACCACTAACGTCCT
1 AACCACTAACGTCCT
350259 AACCACTAACGTCCT
1 AACCACTAACGTCCT
350274 TAGTTGATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.40, G:0.07, T:0.20
Consensus pattern (15 bp):
AACCACTAACGTCCT
Found at i:352510 original size:21 final size:21
Alignment explanation
Indices: 352486--352530 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
352476 AAAAGAATGA
*
352486 TATTGGTACTGATTTATGAGG
1 TATTGGTACTGATTTAAGAGG
*
352507 TATTGGTATTGATTTAAGAGG
1 TATTGGTACTGATTTAAGAGG
352528 TAT
1 TAT
352531 CGATACTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.02, G:0.27, T:0.44
Consensus pattern (21 bp):
TATTGGTACTGATTTAAGAGG
Found at i:352635 original size:22 final size:20
Alignment explanation
Indices: 352585--352636 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
352575 ACAGAATGCC
*
352585 AAGAGGGTATCGGTACCAAG
1 AAGAGGGTATCGATACCAAG
*
352605 TAGA-GGTATCGATACCATAG
1 AAGAGGGTATCGATACCA-AG
352625 AAGAGTGGTATC
1 AAGAG-GGTATC
352637 AGTACTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 12 0.46
20 8 0.31
22 6 0.23
ACGTcount: A:0.35, C:0.13, G:0.31, T:0.21
Consensus pattern (20 bp):
AAGAGGGTATCGATACCAAG
Found at i:353419 original size:56 final size:56
Alignment explanation
Indices: 353359--353476 Score: 136
Period size: 57 Copynumber: 2.1 Consensus size: 56
353349 AATGCATTTC
*
353359 ATGCA-CCGATGCA-CATACTATGCATCGATGCACTCAGAG-T-TTTATGAAAACATCGA
1 ATGCATCCGATGCACCA-ACCATGCATCGATGCACTCAG-GCTATTT-TG-AAACATCGA
** *
353415 ATGCATTTGATGCACCAGCCATGCATCGATGCACTCAGGCTATTTTGAAACATCGA
1 ATGCATCCGATGCACCAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGA
353471 ATGCAT
1 ATGCAT
353477 TTTATGCATC
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
56 21 0.39
57 28 0.52
58 5 0.09
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (56 bp):
ATGCATCCGATGCACCAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGA
Found at i:353464 original size:57 final size:56
Alignment explanation
Indices: 353378--353484 Score: 164
Period size: 56 Copynumber: 1.9 Consensus size: 56
353368 TGCACATACT
353378 ATGCATCGATGCACTCAGAGTTTTATGAAAACATCGAATGCATTTGATGCACCAGCC
1 ATGCATCGATGCACTCAGAGTTTTATG-AAACATCGAATGCATTTGATGCACCAGCC
*
353435 ATGCATCGATGCACTCAG-GCTATTT-TGAAACATCGAATGCATTTTATGCA
1 ATGCATCGATGCACTCAGAG-T-TTTATGAAACATCGAATGCATTTGATGCA
353485 TCGATGCCCT
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
56 23 0.49
57 21 0.45
58 3 0.06
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (56 bp):
ATGCATCGATGCACTCAGAGTTTTATGAAACATCGAATGCATTTGATGCACCAGCC
Found at i:359380 original size:20 final size:20
Alignment explanation
Indices: 359355--359395 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
359345 GATACACTTA
*
359355 ACAAGGTCGTGCATCGATGC
1 ACAAGGTCATGCATCGATGC
359375 ACAAGGTCATGCATCGATGC
1 ACAAGGTCATGCATCGATGC
359395 A
1 A
359396 TCCGTCGGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (20 bp):
ACAAGGTCATGCATCGATGC
Found at i:361590 original size:2 final size:2
Alignment explanation
Indices: 361583--361613 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
361573 CAGCTTAAGC
361583 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
361614 TTAATCAATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:362161 original size:65 final size:64
Alignment explanation
Indices: 362083--362242 Score: 200
Period size: 65 Copynumber: 2.5 Consensus size: 64
362073 GGAATAAATT
* *
362083 AAACATCGAATGCATTTCATGCACCGATGCA-CATACTATGCATCGATGCACTCAGAG-T-TTTA
1 AAACATCGAATGCATTTCATGCATCGATGCACCAGAC-ATGCATCGATGCACTCAG-GCTATTT-
362145 TAA
63 T-A
* * * *
362148 AAACATAGAATGCATTTGATGCATTGATGCACCAGACATGCATTGATGCACTCAGGCTATTTTA
1 AAACATCGAATGCATTTCATGCATCGATGCACCAGACATGCATCGATGCACTCAGGCTATTTTA
*
362212 AAACATCGAATGCATTTTATGCATCGATGCA
1 AAACATCGAATGCATTTCATGCATCGATGCA
362243 TTCTTAGTGC
Statistics
Matches: 83, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
64 30 0.36
65 46 0.55
66 7 0.08
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.29
Consensus pattern (64 bp):
AAACATCGAATGCATTTCATGCATCGATGCACCAGACATGCATCGATGCACTCAGGCTATTTTA
Found at i:362258 original size:19 final size:17
Alignment explanation
Indices: 362221--362261 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
362211 AAAACATCGA
*
362221 ATGCATTTTATGCATCG
1 ATGCATTTTATGCACCG
362238 ATGCATTCTTAGTGCACCG
1 ATGCATT-TTA-TGCACCG
362257 ATGCA
1 ATGCA
362262 CTAAGGGTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 3 0.14
19 11 0.52
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (17 bp):
ATGCATTTTATGCACCG
Found at i:363185 original size:2 final size:2
Alignment explanation
Indices: 363178--363227 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
363168 TAAGTTATGA
363178 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
363220 AT AT AT AT
1 AT AT AT AT
363228 GTTTAGGTGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:369020 original size:13 final size:13
Alignment explanation
Indices: 369002--369027 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
368992 CAAACAAAAA
369002 AAAATAAGAAAGT
1 AAAATAAGAAAGT
369015 AAAATAAGAAAGT
1 AAAATAAGAAAGT
369028 TGATTAGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
AAAATAAGAAAGT
Found at i:370998 original size:18 final size:16
Alignment explanation
Indices: 370975--371008 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
370965 AATTTGTAAT
370975 TTTTAAATATAAATAACG
1 TTTTAAA-ATAAA-AACG
370993 TTTTAAAATAAAAACG
1 TTTTAAAATAAAAACG
371009 AGCAGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 5 0.31
18 7 0.44
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (16 bp):
TTTTAAAATAAAAACG
Found at i:375589 original size:26 final size:26
Alignment explanation
Indices: 375553--375613 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
375543 CAGTCATAAT
375553 ATTTTTCAAACCCCATTCAATCAAAC
1 ATTTTTCAAACCCCATTCAATCAAAC
375579 ATTTTTCAAACCCCATTCAATCAAAC
1 ATTTTTCAAACCCCATTCAATCAAAC
375605 ATTTTTCAA
1 ATTTTTCAA
375614 CAGTTCTTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.34
Consensus pattern (26 bp):
ATTTTTCAAACCCCATTCAATCAAAC
Found at i:378289 original size:9 final size:9
Alignment explanation
Indices: 378275--378304 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
378265 AGAATTAACT
378275 TTAATCTAA
1 TTAATCTAA
378284 TTAATCTAA
1 TTAATCTAA
378293 TCTAATCTAA
1 T-TAATCTAA
378303 TT
1 TT
378305 GAAATGTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (9 bp):
TTAATCTAA
Found at i:378352 original size:53 final size:48
Alignment explanation
Indices: 378292--378383 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 48
378282 AATTAATCTA
** * *
378292 ATCTAATCTAATTGAAATGTAACCAATTCGATTAATTTCTTTTTACGG
1 ATCTAATCTAATCAAAATGAAACCAATTCGATTAATTTATTTTTACGG
* *
378340 ATCTAATTTAATCAAAATGAAACTAATTCGATTAATTTATTTTT
1 ATCTAATCTAATCAAAATGAAACCAATTCGATTAATTTATTTTT
378384 TGGAATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (48 bp):
ATCTAATCTAATCAAAATGAAACCAATTCGATTAATTTATTTTTACGG
Found at i:387435 original size:83 final size:83
Alignment explanation
Indices: 387331--387671 Score: 375
Period size: 83 Copynumber: 4.1 Consensus size: 83
387321 AAATAGCCTA
* * ** *
387331 AAGGACTTATCACTCTTCTTGAAAATCTTACAGAGGACCCGGAGGATTTAATCATCATGCTCGAA
1 AAGGACTTATCACTCTGCTTGAAAAACTTACAGAGGACCCAAAAGATTTAATCATCATGCTCGAA
* *
387396 AGACTTACTGATGGACCG
66 AGACTTACTGATAGCCCG
* ** * **
387414 AATGACTTATCACTCTGCTTG---AGGTTACAGAGAACCTTAAAGATTTAATCATCATGCTCGAA
1 AAGGACTTATCACTCTGCTTGAAAAACTTACAGAGGACCCAAAAGATTTAATCATCATGCTCGAA
* *
387476 AGACTTACTAATGGCCCG
66 AGACTTACTGATAGCCCG
* * * * * * *
387494 AAGGACTTATCACTCTG-GTCAAAAGACTTACAAAAGACTCAAAAAATTTAATTATCATGCTCGA
1 AAGGACTTATCACTCTGCTTGAAAA-ACTTACAGAGGACCCAAAAGATTTAATCATCATGCTCGA
* *
387558 AAGAATTACCGATAGCCCG
65 AAGACTTACTGATAGCCCG
* * *
387577 AAGGACTTATCATTCTACTTGAAAAACTTACAGAGGACCCAAAGGATTTAATCATCATGCTCGAA
1 AAGGACTTATCACTCTGCTTGAAAAACTTACAGAGGACCCAAAAGATTTAATCATCATGCTCGAA
* * *
387642 GGACATACTGATAGCCAG
66 AGACTTACTGATAGCCCG
387660 AAGGACTTATCA
1 AAGGACTTATCA
387672 AGTAATAAAC
Statistics
Matches: 210, Mismatches: 43, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
79 1 0.00
80 66 0.31
82 1 0.00
83 137 0.65
84 5 0.02
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.26
Consensus pattern (83 bp):
AAGGACTTATCACTCTGCTTGAAAAACTTACAGAGGACCCAAAAGATTTAATCATCATGCTCGAA
AGACTTACTGATAGCCCG
Found at i:387784 original size:13 final size:13
Alignment explanation
Indices: 387766--387798 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
387756 TTCTCATTTT
387766 TCATATAAAAATA
1 TCATATAAAAATA
*
387779 TCATATCAAAATA
1 TCATATAAAAATA
387792 TCATATA
1 TCATATA
387799 TCGGGTAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (13 bp):
TCATATAAAAATA
Found at i:401391 original size:42 final size:41
Alignment explanation
Indices: 401300--401550 Score: 326
Period size: 42 Copynumber: 5.9 Consensus size: 41
401290 CTATACACCA
* * *
401300 GTAAGGCTTAACCTGTGCACAAAGCAGA-GGAGCCTAGGAAAACT
1 GTAAGGCTT-ACCT-TGCACACAGCAAAGGGA-CCT-GGTAAACT
* * *
401344 ATAAGGTTTATCCTTGCACACAACAAAGGGACCTGAG-AAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTG-GTAAACT
401386 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGTAAACT
*
401428 GTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGTAAACT
401470 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGTAAACT
*
401512 ATAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGTAA
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGTAA
401551 TACTTCCTTC
Statistics
Matches: 188, Mismatches: 12, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
41 9 0.05
42 147 0.78
43 19 0.10
44 13 0.07
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.18
Consensus pattern (41 bp):
GTAAGGCTTACCTTGCACACAGCAAAGGGACCTGGTAAACT
Found at i:401547 original size:84 final size:84
Alignment explanation
Indices: 401300--401547 Score: 374
Period size: 84 Copynumber: 2.9 Consensus size: 84
401290 CTATACACCA
* * * * *
401300 GTAAGGCTTAACCTGTGCACAAAGCAGA-GGAGCCTAGGAAAACTATAAGGTTTATCCTT-GCAC
1 GTAAGGCTTACCCT-TGCACACAGCAAAGGGA-CCT-GGTAAACTATAAGGCTTA-CCTTCGCAC
* *
401363 ACAACAAAGGGACCTGAGAAACT
62 ACAGCAAAGGGACCTGGGAAACT
*
401386 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTATAAGGCTTACCTTCGCACACAG
401451 CAAAGGGACCTGGGAAACT
66 CAAAGGGACCTGGGAAACT
401470 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTATAAGGCTTACCTTCGCACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTATAAGGCTTACCTTCGCACACAG
401535 CAAAGGGACCTGG
66 CAAAGGGACCTGG
401548 TAATACTTCC
Statistics
Matches: 151, Mismatches: 9, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
83 4 0.03
84 117 0.77
85 14 0.09
86 16 0.11
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.18
Consensus pattern (84 bp):
GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTATAAGGCTTACCTTCGCACACAG
CAAAGGGACCTGGGAAACT
Found at i:402546 original size:29 final size:29
Alignment explanation
Indices: 402483--402580 Score: 90
Period size: 29 Copynumber: 3.3 Consensus size: 29
402473 CATTTTACAG
**
402483 AAATAGCACCCCTTTTCGAATTAATTACC-A
1 AAATAGCACCAATTTT-GAATTAATT-CCTA
*
402513 AAATAGCACCTATTTTGAATTAATTCCTA
1 AAATAGCACCAATTTTGAATTAATTCCTA
* ** *
402542 TAATAGCACCAAAATCGAATTAATTCCTA
1 AAATAGCACCAATTTTGAATTAATTCCTA
* *
402571 GAATAACACC
1 AAATAGCACC
402581 GGTCAACGGT
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.03
29 42 0.72
30 14 0.24
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (29 bp):
AAATAGCACCAATTTTGAATTAATTCCTA
Found at i:402618 original size:18 final size:18
Alignment explanation
Indices: 402588--402640 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
402578 ACCGGTCAAC
402588 GGTCAAC-GGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
402605 GGTCAACGGGTCGGGTTG
1 GGTCAACGGGTCGGGTCG
*
402623 GGTCAACGGGTCGAGTCG
1 GGTCAACGGGTCGGGTCG
402641 TGACCGGTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
17 7 0.22
18 25 0.78
ACGTcount: A:0.13, C:0.21, G:0.47, T:0.19
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:408925 original size:84 final size:84
Alignment explanation
Indices: 408778--409021 Score: 375
Period size: 84 Copynumber: 2.9 Consensus size: 84
408768 CTATACACCA
* * * * *
408778 GTAAGGCTTAACCTGTGCACAAAGCAGA-GGAGCCTAGGAAAACTGTAAGGTTTATCCTT-GCAC
1 GTAAGGCTTACCCT-TGCACACAGCAAAGGGA-CCTA-GTAAACTGTAAGGCTTA-CCTTCGCAC
408841 ACAGCAAAGGGACCTGGGAAACT
62 ACAGCAAAGGGACCTGGGAAACT
408864 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTAGTAAACTGTAAGGCTTACCTTCGCACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTAGTAAACTGTAAGGCTTACCTTCGCACACAG
408929 CAAAGGGACCTGGGAAACT
66 CAAAGGGACCTGGGAAACT
*
408948 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTAGTAAACTGTAAGGCTTACCTTCGCACACAG
*
409013 TAAAGGGAC
66 CAAAGGGAC
409022 ATGGTAATAC
Statistics
Matches: 149, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
83 4 0.03
84 114 0.77
85 15 0.10
86 16 0.11
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.18
Consensus pattern (84 bp):
GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTAGTAAACTGTAAGGCTTACCTTCGCACACAG
CAAAGGGACCTGGGAAACT
Found at i:409027 original size:42 final size:42
Alignment explanation
Indices: 408778--409028 Score: 337
Period size: 42 Copynumber: 5.9 Consensus size: 42
408768 CTATACACCA
* * * *
408778 GTAAGGCTTAACCTGTGCACAAAGCAGA-GGAGCCTAGGAAAACT
1 GTAAGGCTTACCCT-TGCACACAGCAAAGGGA-CCT-GGTAAACT
* * *
408822 GTAAGGTTTATCCTTGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
*
408864 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTAGTAAACT
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
*
408906 GTAAGGCTTA-CCTTCGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCCTT-GCACACAGCAAAGGGACCTGGTAAACT
408948 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
* *
408990 GTAAGGCTTA-CCTTCGCACACAGTAAAGGGACATGGTAA
1 GTAAGGCTTACCCTT-GCACACAGCAAAGGGACCTGGTAA
409029 TACTTCCTTC
Statistics
Matches: 189, Mismatches: 14, Indels: 10
0.89 0.07 0.05
Matches are distributed among these distances:
41 8 0.04
42 148 0.78
43 18 0.10
44 15 0.08
ACGTcount: A:0.33, C:0.24, G:0.25, T:0.19
Consensus pattern (42 bp):
GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
Found at i:410013 original size:29 final size:28
Alignment explanation
Indices: 409951--410047 Score: 86
Period size: 29 Copynumber: 3.3 Consensus size: 28
409941 ATTTTACAGA
* *
409951 AATAGCACCCCTTTTCGAATTAATTACCAA
1 AATAGCACCCATTTT-GAATTAATT-CCAT
409981 AATAGCACCCATTTTGAATTAATTCCTAT
1 AATAGCACCCATTTTGAATTAATTCC-AT
* * ** * *
410010 AATATCACCAAAATCGAATTAATTCCCGT
1 AATAGCACCCATTTTGAATTAATT-CCAT
410039 AATAGCACC
1 AATAGCACC
410048 GGTCAACGGT
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
28 2 0.04
29 38 0.68
30 16 0.29
ACGTcount: A:0.38, C:0.25, G:0.07, T:0.30
Consensus pattern (28 bp):
AATAGCACCCATTTTGAATTAATTCCAT
Found at i:410089 original size:18 final size:18
Alignment explanation
Indices: 410055--410107 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
410045 ACCGGTCAAC
410055 GGTCAAC-GGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
410072 GGTCAACGGGTAGGGTCG
1 GGTCAACGGGTCGGGTCG
410090 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
410108 TGATCGGTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
17 7 0.21
18 26 0.79
ACGTcount: A:0.13, C:0.21, G:0.49, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:412634 original size:24 final size:24
Alignment explanation
Indices: 412607--412657 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
412597 ACCCAATCAA
* *
412607 CATGGACTAGATGACGTCTGAAGT
1 CATGGACTAGATGACATATGAAGT
412631 CATGGACTAGATGACATATGAAGT
1 CATGGACTAGATGACATATGAAGT
412655 CAT
1 CAT
412658 CTGTTGGGCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (24 bp):
CATGGACTAGATGACATATGAAGT
Found at i:413536 original size:16 final size:15
Alignment explanation
Indices: 413496--413530 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
413486 TAAAAAAGTG
*
413496 AAAAAAAATGAAAAGA
1 AAAAAAAAAGAAAA-A
413512 AAAAAAAAAGAAAAA
1 AAAAAAAAAGAAAAA
413527 AAAA
1 AAAA
413531 GGAAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.89, C:0.00, G:0.09, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAGAAAAA
Found at i:420093 original size:29 final size:30
Alignment explanation
Indices: 420039--420105 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 30
420029 ATTCAGGTAC
420039 GTTTCTTCCTCTTTTTTAGTCTTTAATCTA
1 GTTTCTTCCTCTTTTTTAGTCTTTAATCTA
420069 GTTTCTTCCTC-TTTTTAGTCTTTAATCTA
1 GTTTCTTCCTCTTTTTTAGTCTTTAATCTA
*
420098 GTCTCTTC
1 GTTTCTTC
420106 TTTAATCTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 25 0.69
30 11 0.31
ACGTcount: A:0.12, C:0.22, G:0.07, T:0.58
Consensus pattern (30 bp):
GTTTCTTCCTCTTTTTTAGTCTTTAATCTA
Found at i:421747 original size:19 final size:19
Alignment explanation
Indices: 421723--421760 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
421713 GCGCTAAGTC
421723 ACCATGAACTCGATGCGCA
1 ACCATGAACTCGATGCGCA
421742 ACCATGAACTCGATGCGCA
1 ACCATGAACTCGATGCGCA
421761 CAAGTTTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.16
Consensus pattern (19 bp):
ACCATGAACTCGATGCGCA
Found at i:421861 original size:17 final size:17
Alignment explanation
Indices: 421839--421872 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
421829 CATGGGACAA
*
421839 AATAATGGCGTGAATAG
1 AATAATGGCATGAATAG
421856 AATAATGGCATGAATAG
1 AATAATGGCATGAATAG
421873 GACTGTGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.26, T:0.24
Consensus pattern (17 bp):
AATAATGGCATGAATAG
Found at i:422275 original size:2 final size:2
Alignment explanation
Indices: 422270--422302 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
422260 TGACACACAC
422270 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 A
422303 AAATAAGGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:424444 original size:31 final size:31
Alignment explanation
Indices: 424403--424468 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
424393 TGCATCATAT
* * *
424403 GTCCCCAAACTATGACCCTTATTTTAAATTG
1 GTCCCCAAACTATGACCCTAATTCTAAATTA
* *
424434 GTCCCTAAACTATGACTCTAATTCTAAATTA
1 GTCCCCAAACTATGACCCTAATTCTAAATTA
424465 GTCC
1 GTCC
424469 GTAACTTTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (31 bp):
GTCCCCAAACTATGACCCTAATTCTAAATTA
Found at i:425332 original size:2 final size:2
Alignment explanation
Indices: 425325--425354 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
425315 ATAAACTTTA
425325 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
425355 TAAAAACTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:425980 original size:21 final size:21
Alignment explanation
Indices: 425910--425988 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
425900 TCCCTTCCCA
*
425910 AAAAGGATCGATCCCTTTGGT
1 AAAAGGATCGATCCCTTTGAT
* * **
425931 ATAACGG-TCGAACTATTTGA-
1 A-AAAGGATCGATCCCTTTGAT
*
425951 AAAATGATCGATCCCTTTGAT
1 AAAAGGATCGATCCCTTTGAT
425972 AAAAGGATCGATCCCTT
1 AAAAGGATCGATCCCTT
425989 ATGCCTTGTT
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
19 3 0.07
20 11 0.25
21 26 0.59
22 4 0.09
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (21 bp):
AAAAGGATCGATCCCTTTGAT
Found at i:426689 original size:70 final size:70
Alignment explanation
Indices: 426605--426744 Score: 235
Period size: 70 Copynumber: 2.0 Consensus size: 70
426595 ATGTTAAAGC
* * *
426605 TATGCATATTTTGTTTTGTGCATTAGGCCCGGATGAATATGGAAGAGTCTCATATTATTCAAATG
1 TATGCACATTTTGTTTTATGCATTAGGCCCAGATGAATATGGAAGAGTCTCATATTATTCAAATG
426670 CCAAG
66 CCAAG
* *
426675 TATGCACATTTTGTTTTATGCATTAGGCCCAGATGAATATGGAAGAGTCTCCTATTGTTCAAATG
1 TATGCACATTTTGTTTTATGCATTAGGCCCAGATGAATATGGAAGAGTCTCATATTATTCAAATG
426740 CCAAG
66 CCAAG
426745 GAGATTTGGG
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.35
Consensus pattern (70 bp):
TATGCACATTTTGTTTTATGCATTAGGCCCAGATGAATATGGAAGAGTCTCATATTATTCAAATG
CCAAG
Found at i:427183 original size:170 final size:169
Alignment explanation
Indices: 426901--427240 Score: 626
Period size: 170 Copynumber: 2.0 Consensus size: 169
426891 CAGTGGTCTC
426901 AAGGGATATGGAGAGATCATCCCTAATGAGAAGCTTGTTAAGAAGATTATATATTCTCTTCCAAA
1 AAGGGATATGGAGAGATCATCCCTAATGAGAAGCTTGTTAAGAAGATTATATATTCTCTTCCAAA
* *
426966 ATCTTGGTAATTGAAGAAGATGATGATCATTGAAGTGAAGAACTTAAAAACTCTATCGCTTGATG
66 ATCTTGGTAATTGAAGAAGACGACGATCATTGAAGTGAAGAACTTAAAAACTCTATCGCTTGATG
*
427031 AACTTATTGGCTCCCTTCTCACTCATGAGATGATGGAAAA
131 AAATTATTGGCTCCCTTCTCACTCATGAGATGAT-GAAAA
*
427071 AAGGGATATGGAGTGATCATCCCTAATGAGAAGCTTGTTAAGAAGATTATATATTCTCTTCCAAA
1 AAGGGATATGGAGAGATCATCCCTAATGAGAAGCTTGTTAAGAAGATTATATATTCTCTTCCAAA
*
427136 ATCTTGGTAATTGAAGAAGACGACGATCATTGAAGTGGAGAACTTAAAAACTCTATCGCTTGATG
66 ATCTTGGTAATTGAAGAAGACGACGATCATTGAAGTGAAGAACTTAAAAACTCTATCGCTTGATG
427201 AAATTATTGGCTCCCTTCTCACTCATGAGATGATGAAAA
131 AAATTATTGGCTCCCTTCTCACTCATGAGATGATGAAAA
427240 A
1 A
427241 TGAGGAAGAA
Statistics
Matches: 165, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
169 6 0.04
170 159 0.96
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (169 bp):
AAGGGATATGGAGAGATCATCCCTAATGAGAAGCTTGTTAAGAAGATTATATATTCTCTTCCAAA
ATCTTGGTAATTGAAGAAGACGACGATCATTGAAGTGAAGAACTTAAAAACTCTATCGCTTGATG
AAATTATTGGCTCCCTTCTCACTCATGAGATGATGAAAA
Found at i:429104 original size:21 final size:21
Alignment explanation
Indices: 429067--429113 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
429057 TTTTAAATGT
* *
429067 TTTTC-AAACTTAGTCGAACC
1 TTTTCAAAACATACTCGAACC
* *
429087 TTTTCAAAACATACTCGATCG
1 TTTTCAAAACATACTCGAACC
429108 TTTTCA
1 TTTTCA
429114 CACTTTATAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.38
Consensus pattern (21 bp):
TTTTCAAAACATACTCGAACC
Found at i:429228 original size:50 final size:50
Alignment explanation
Indices: 429152--429262 Score: 152
Period size: 50 Copynumber: 2.2 Consensus size: 50
429142 ATGGCTTAAA
* * * *
429152 GGATCGATCCCTTTGACCAAAGGATCAATCCTTTGGATAGA-AGTGAGTTTG
1 GGATCGAT-CCTTTGACAAAAGGATCAATCCATTGGACA-ACAGTGAATTTG
*
429203 GGATCGATCCTTTTACAAAAGGATCAATCCATTGGACAACAGTGAATTTG
1 GGATCGATCCTTTGACAAAAGGATCAATCCATTGGACAACAGTGAATTTG
429253 GGATCGATCC
1 GGATCGATCC
429263 CTCGAGGAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
49 1 0.02
50 45 0.83
51 8 0.15
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (50 bp):
GGATCGATCCTTTGACAAAAGGATCAATCCATTGGACAACAGTGAATTTG
Found at i:429350 original size:20 final size:21
Alignment explanation
Indices: 429327--429369 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
429317 GGTCGAAATA
* *
429327 TTTGA-AAAATGATTGATCCC
1 TTTGATAAAACGATCGATCCC
429347 TTTGATAAAACGATCGATCCC
1 TTTGATAAAACGATCGATCCC
429368 TT
1 TT
429370 GTGCCTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
TTTGATAAAACGATCGATCCC
Found at i:431448 original size:18 final size:18
Alignment explanation
Indices: 431425--431463 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
431415 AGGGGCCTTG
*
431425 AGTGCAACACTTTAAACC
1 AGTGCAACACCTTAAACC
431443 AGTGCAACACCTTAAACC
1 AGTGCAACACCTTAAACC
431461 AGT
1 AGT
431464 ACGACACACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.28, G:0.13, T:0.21
Consensus pattern (18 bp):
AGTGCAACACCTTAAACC
Found at i:431470 original size:18 final size:18
Alignment explanation
Indices: 431429--431470 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
431419 GCCTTGAGTG
* *
431429 CAACACTTTAAACCAGTG
1 CAACACCTTAAACCAGTA
431447 CAACACCTTAAACCAGTA
1 CAACACCTTAAACCAGTA
*
431465 CGACAC
1 CAACAC
431471 ACAGTTGACC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.33, G:0.10, T:0.17
Consensus pattern (18 bp):
CAACACCTTAAACCAGTA
Found at i:447996 original size:182 final size:181
Alignment explanation
Indices: 447690--448544 Score: 1232
Period size: 182 Copynumber: 4.7 Consensus size: 181
447680 TGTCGGTTTA
* *
447690 TGTCGATACTTTATAAAACTGTATCGATCCACATCAATATAACAAG-AAAAATATGACAAAACCG
1 TGTCGATACTTTATAAAA-TGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACCG
* * * **
447754 GTCACGAAAAGACAAAACCGGTAAAGCGCTATTGGATATATTGAAAGTGTCGATACTTTAATATA
65 GTCTCTAAAAGACAAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATA
*
447819 AGTATCGACACTTTGTGAATTTAAAAGAAAAGCAGTTTTAGCGCCTATAAAG
130 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
* * *
447871 TGTCGATACTTTATTAAAATGTATCGATCCATAACGATATAACAAGAAAAAATATGACAAAATCG
1 TGTCGATACTTTA-TAAAATGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACCG
* * * *
447936 GTCTCTAAAGGACAAAACCGGTAAAGGGCTACTGGATATATTGAAAGTCTCGATACTTTAATATA
65 GTCTCTAAAAGACAAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATA
*
448001 AGTATCGACACTTTGTGAATTTAAAAGAGAATCAGTTTTAGCGCCTATAAAG
130 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
* *
448053 TGTTGATACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
1 TGTCGATACTTTATAA-AATGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACCG
* * * * *
448118 GTCTCTAAATGACAAAACCGGTATAGAACGACCGAATATATTGAAAGTGTCGATACTTTAATATA
65 GTCTCTAAAAGACAAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATA
*
448183 AGTATCGTCACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
130 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
* * * * *
448235 TGTCAATATTTTATAACAATGTATCGATCTACAACGATATAACATGTAAAAATATGAGAAAACCG
1 TGTCGATACTTTATAA-AATGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACCG
* * **
448300 GTCTCTAAAAGACAAAACCGGTATAGAGCGACCAAATATATTGAAAGTGTCGATACTTTAATATA
65 GTCTCTAAAAGACAAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATA
*
448365 AGTATCGACACTTAT-TGAATTTAAATGAGAAGCAGTTTTAGCGCCTATAAAG
130 AGTATCGACACTT-TGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
* * *
448417 TGTCGATACTTTATAAAAATGTATCGATCCATAACGATATAACAGGTAAAAATATGACAAAATCG
1 TGTCGATACTTTAT-AAAATGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACCG
* * * * *
448482 ATCTCGAAATGACAAAACCGGTAAA-ATGTTACCGGATATATTGAAAGTG-CTGATATTTTAATA
65 GTCTCTAAAAGACAAAACCGGTAAAGA-GCTACCGGATATATTGAAAGTGTC-GATACTTTAATA
448545 AGTACGCGTA
Statistics
Matches: 613, Mismatches: 54, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
181 42 0.07
182 568 0.93
183 3 0.00
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (181 bp):
TGTCGATACTTTATAAAATGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACCGG
TCTCTAAAAGACAAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAA
GTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
Found at i:453371 original size:199 final size:198
Alignment explanation
Indices: 452922--453621 Score: 869
Period size: 199 Copynumber: 3.5 Consensus size: 198
452912 TAAATATATT
* *
452922 TCGATACATTT-TCTAAAAGTATCGA-CCCAAAAAACATCGAAACCAATAATTATAATGTAATAG
1 TCGATACATTTAT-TAAAAGTATCGATCCCAAGAAACATCGAAACCGATAATTATAATGTAATAG
* * * * * * *
452985 GTAAATTAACAATGTAACCGGTATAAATATACCGGTTAATTAGAAAACATGTAAACATAATGTAT
65 GTAAATTTACAATGTAACCGGTATAAATATACCGTTTTATGAGAAAATATGTCATCATAATGTAT
*
453050 CGACACTTGTATAATTTGTGTTGATACTTATTGTCCAGAATGAATGCCCAAACGAGGTGCACGCA
130 CGACACTTGTA-AATTTGTGTCGATACTT-TTGTCCAGAATGAATG-CCAAACGAGGTGCACGCA
453115 TAAAGTG
192 TAAAGTG
* * * * * *
453122 TCGATACAATTATTAAAAATATCGATCCCAATAAA-ATCGAAACTGATAATTATAATTTAATATG
1 TCGATACATTTATTAAAAGTATCGATCCCAAGAAACATCGAAACCGATAATTATAATGTAATAGG
*
453186 TAAATTTACAATGTAACCGGTATAAATATACCAGTTTTATGAGAAAATATGTCATCATAAAGTAT
66 TAAATTTACAATGTAACCGGTATAAATATACC-GTTTTATGAGAAAATATGTCATCATAATGTAT
* *
453251 CGACACTTGTTAAATTTATGTCGATACATTTTGTCCATAATGAATGCCAAACG-GGTGCACGCAT
130 CGACACTTG-TAAATTTGTGTCGATAC-TTTTGTCCAGAATGAATGCCAAACGAGGTGCACGCAT
*
453315 AAAGTT
193 AAAGTG
* * *
453321 TCGATACATTTATTAAAAGTATCAATCCCAA-AAACATCGAAACCGATAATTACAATGTGATAGG
1 TCGATACATTTATTAAAAGTATCGATCCCAAGAAACATCGAAACCGATAATTATAATGTAATAGG
* * * * *
453385 TAAATTTACAATGT-ACTCGATAGATATATACCGATTTTATGAAAAAATATGTC-TAAATAATGT
66 TAAATTTACAATGTAAC-CGGTATAAATATACCG-TTTTATGAGAAAATATGTCAT-CATAATGT
* * * * * * *
453448 ATCGGCACTCTCTAAGTTTGTGTCGATACTTTTTTCCAGAATGAATGCCCAACGAGGTGGACTCA
128 ATCGACACT-TGTAAATTTGTGTCGATACTTTTGTCCAGAATGAATGCCAAACGAGGTGCACGCA
453513 TAAAGTG
192 TAAAGTG
* *
453520 TCGATACATTTA--AAATTGTATCGATCCAAAGAAACATCGAAACCGATAATTATAATGTAATAG
1 TCGATACATTTATTAAA-AGTATCGATCCCAAGAAACATCGAAACCGATAATTATAATGTAATAG
** *
453583 GTAAATTTACAATGTTGCCGGTATAAATATACCGATTTA
65 GTAAATTTACAATGTAACCGGTATAAATATACCGTTTTA
453622 CTTATAAAAT
Statistics
Matches: 433, Mismatches: 53, Indels: 30
0.84 0.10 0.06
Matches are distributed among these distances:
197 3 0.01
198 44 0.10
199 225 0.52
200 86 0.20
201 71 0.16
202 4 0.01
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (198 bp):
TCGATACATTTATTAAAAGTATCGATCCCAAGAAACATCGAAACCGATAATTATAATGTAATAGG
TAAATTTACAATGTAACCGGTATAAATATACCGTTTTATGAGAAAATATGTCATCATAATGTATC
GACACTTGTAAATTTGTGTCGATACTTTTGTCCAGAATGAATGCCAAACGAGGTGCACGCATAAA
GTG
Found at i:453667 original size:23 final size:23
Alignment explanation
Indices: 453638--453695 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
453628 AAATAGGTCA
*
453638 ATATAAGCGTTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
453661 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
453684 ATATAAGCGCTA
1 ATATAAGCGCTA
453696 GCTAATATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:453708 original size:23 final size:23
Alignment explanation
Indices: 453638--453702 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
453628 AAATAGGTCA
** *
453638 ATATAAGCGTTACCTATTACATT
1 ATATAAGCACTACCTAATACATT
*
453661 ATATAAGCACTACCTATTACATT
1 ATATAAGCACTACCTAATACATT
* *
453684 ATATAAGCGCTAGCTAATA
1 ATATAAGCACTACCTAATA
453703 TGTTATTGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.34
Consensus pattern (23 bp):
ATATAAGCACTACCTAATACATT
Found at i:453749 original size:87 final size:88
Alignment explanation
Indices: 453658--453823 Score: 280
Period size: 87 Copynumber: 1.9 Consensus size: 88
453648 TACCTATTAC
* *
453658 ATTATATAAGCACTACCTATTACATTATATAAGCGCTAGCTAATATGTTATTGTACTTGATAATA
1 ATTATATAAGCACTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTAATAATA
453723 -TTTCCGGTTAAATGTCTATTTT
66 TTTTCCGGTTAAATGTCTATTTT
**
453745 ATTATATAAGCGTTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTAATAATA
1 ATTATATAAGCACTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTAATAATA
*
453810 TTTTTCGGTTAAAT
66 TTTTCCGGTTAAAT
453824 AATATAACAT
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
87 61 0.84
88 12 0.16
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (88 bp):
ATTATATAAGCACTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTAATAATA
TTTTCCGGTTAAATGTCTATTTT
Found at i:453795 original size:23 final size:23
Alignment explanation
Indices: 453745--453789 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
453735 TGTCTATTTT
* *
453745 ATTATATAAGCGTTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
453768 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
453790 TGTTATTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:457610 original size:2 final size:2
Alignment explanation
Indices: 457603--457629 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
457593 ACCTCAAGAG
457603 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
457630 AAGTCCTTTC
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:461220 original size:3 final size:3
Alignment explanation
Indices: 461212--461243 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
461202 TGAATGTTCA
461212 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
461244 AAGCAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:462531 original size:23 final size:23
Alignment explanation
Indices: 462505--462556 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
462495 TCACGATCAC
462505 TAAATGAATATGTTAGAAAACGA
1 TAAATGAATATGTTAGAAAACGA
* * *
462528 TAAATAAATATGTTAGCAAACGC
1 TAAATGAATATGTTAGAAAACGA
462551 TAAATG
1 TAAATG
462557 TATGTTTCGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (23 bp):
TAAATGAATATGTTAGAAAACGA
Found at i:465261 original size:17 final size:18
Alignment explanation
Indices: 465215--465260 Score: 69
Period size: 17 Copynumber: 2.6 Consensus size: 18
465205 TATACTGATA
465215 ATTTTT-TAAAATAAATT
1 ATTTTTATAAAATAAATT
465232 ATTTTTATAAAAT-AATT
1 ATTTTTATAAAATAAATT
465249 ATTTTTGATAAA
1 ATTTTT-ATAAA
465261 TTTTAAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.59
18 11 0.41
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
ATTTTTATAAAATAAATT
Found at i:467301 original size:44 final size:44
Alignment explanation
Indices: 467238--467412 Score: 296
Period size: 44 Copynumber: 4.0 Consensus size: 44
467228 TATTGACAAA
* *
467238 TCGTGAAGCTGCTCGCCTTGTGCTTTTAGGACTTACATACCAAT
1 TCGTGAAGCTGCTCGCCTTGTGCTTTTAGGACTAACATACGAAT
* *
467282 TCGTGAAGCTGCTCGCCTTGTGCATTAAGGACTAACATACGAAT
1 TCGTGAAGCTGCTCGCCTTGTGCTTTTAGGACTAACATACGAAT
*
467326 TCGTGAAGCTGCTTGCCTTGTGCTTTTAGGACTAACATACGAAT
1 TCGTGAAGCTGCTCGCCTTGTGCTTTTAGGACTAACATACGAAT
*
467370 TCGTGAAGCTGCTCGCCTTGTGCTTTTAGGACTAACGTACGAA
1 TCGTGAAGCTGCTCGCCTTGTGCTTTTAGGACTAACATACGAA
467413 CCTGTATGCG
Statistics
Matches: 122, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 122 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (44 bp):
TCGTGAAGCTGCTCGCCTTGTGCTTTTAGGACTAACATACGAAT
Found at i:469286 original size:2 final size:2
Alignment explanation
Indices: 469279--469321 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
469269 ATTAATTAAA
*
469279 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT 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
469321 A
1 A
469322 ATAAATGTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:469333 original size:14 final size:16
Alignment explanation
Indices: 469277--469356 Score: 65
Period size: 16 Copynumber: 5.1 Consensus size: 16
469267 TCATTAATTA
*
469277 AAATATATATATATAT
1 AAATGTATATATATAT
* *
469293 ATATATATATATATAT
1 AAATGTATATATATAT
*
469309 ATATGTATATATA-AT
1 AAATGTATATATATAT
*
469324 AAATGT-TATAATTTAT
1 AAATGTATAT-ATATAT
* * *
469340 TATTGAATATATATAT
1 AAATGTATATATATAT
469356 A
1 A
469357 TTAATTTATT
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
14 3 0.06
15 9 0.17
16 37 0.71
17 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (16 bp):
AAATGTATATATATAT
Found at i:471205 original size:18 final size:20
Alignment explanation
Indices: 471182--471231 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 20
471172 GCCATTTTTG
*
471182 GTATCGATACTCG-TGG-GA
1 GTATCGATACTCGAGGGAGA
471200 GTATCGATAC-CGAGGGTAGA
1 GTATCGATACTCGAGGG-AGA
471220 GTATCGATACTC
1 GTATCGATACTC
471232 CCTATAAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 2 0.07
18 12 0.44
20 12 0.44
21 1 0.04
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (20 bp):
GTATCGATACTCGAGGGAGA
Found at i:474695 original size:15 final size:15
Alignment explanation
Indices: 474667--474705 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
474657 ATAAAACATT
474667 TATTTAAT-ATAGGA
1 TATTTAATAATAGGA
474681 T-TTATAATAATAGGA
1 TATT-TAATAATAGGA
474696 TATTTAATAA
1 TATTTAATAA
474706 AAATATCAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 2 0.09
14 5 0.23
15 13 0.59
16 2 0.09
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (15 bp):
TATTTAATAATAGGA
Found at i:474896 original size:18 final size:17
Alignment explanation
Indices: 474878--474921 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 17
474868 TATTTATATA
*
474878 AATAATAATAATGAAAT
1 AATAATAATAAAGAAAT
*
474895 AATAAT--TAAAGCAAT
1 AATAATAATAAAGAAAT
474910 AATAATAATAAA
1 AATAATAATAAA
474922 ATAATATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 13 0.57
17 10 0.43
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (17 bp):
AATAATAATAAAGAAAT
Found at i:474936 original size:26 final size:27
Alignment explanation
Indices: 474874--474938 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 27
474864 TATTTATTTA
*
474874 TATAAATAATAATAATGAAATAATAAT
1 TATAAATAATAATAATAAAATAATAAT
*
474901 TAAAGCAATAATAATAATAAAATAAT-AT
1 TATA--AATAATAATAATAAAATAATAAT
*
474929 TGTAAATAAT
1 TATAAATAAT
474939 GATTAAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
26 6 0.19
27 3 0.09
28 4 0.12
29 19 0.59
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.32
Consensus pattern (27 bp):
TATAAATAATAATAATAAAATAATAAT
Found at i:476321 original size:3 final size:3
Alignment explanation
Indices: 476303--476364 Score: 81
Period size: 3 Copynumber: 20.0 Consensus size: 3
476293 TTTGGGCCTG
476303 TAA TATA TAA TAAA TAA TAA TAA TAA TAA TAA TAAA TAA TAA TAA TAA
1 TAA TA-A TAA T-AA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
*
476351 -AA AAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
476365 ATATAAAAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 8
0.86 0.02 0.13
Matches are distributed among these distances:
2 2 0.04
3 43 0.80
4 9 0.17
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:476807 original size:113 final size:114
Alignment explanation
Indices: 476591--477606 Score: 1199
Period size: 113 Copynumber: 9.0 Consensus size: 114
476581 GATAAAATCT
* * * *
476591 AGCAAAAGGTT-AAGCAAGTTATTCTCATTATGAACTCCTTCTTCC-TCTTCAGACGGGTTCTTC
1 AGCAAAAGGTTGAA-CAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * ** * *
476654 TCATTATGAACAC-CTTCTGGAAATGTTGATCCATC-AAGTGATGTATTTG
65 TCATTATGAACTCTATTCTGGAAATACTGATCCATCGAA-TGATGAATTTA
* *
476703 AGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * * *
476768 CATTATGAACTCTAAT-TGGCACTACTGATCCACCGAGTGATGAATTTA
66 CATTATGAACTCTATTCTGGAAATACTGATCCATCGAATGATGAATTTA
* *
476816 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * * * *
476881 CATTATGAACTCTA-ACTGGCACTGCTGATCAATCGAATGATGAATTCA
66 CATTATGAACTCTATTCTGGAAATACTGATCCATCGAATGATGAATTTA
*
476929 AGCGAAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AGC-AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * * * * *
476993 TCATTATGAACTCT-CTCTGGAAA-AGTTGATCCATCTAGTGATTAATTCA
65 TCATTATGAACTCTATTCTGGAAATA-CTGATCCATCGAATGATGAATTTA
* *
477042 AACGAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTC
1 AGC-AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * * * *
477106 TCATTATGAACTCGA-CCTGGTAATGCTGATCCATCGAATGATGAATTCA
65 TCATTATGAACTCTATTCTGGAAATACTGATCCATCGAATGATGAATTTA
* *
477155 AGCGAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATAAGTTCTTC
1 AGC-AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * * *
477219 TCATTATGAACTTTCTT-TGGAAATGA-TGATCCATCGAATGATGGATTTG
65 TCATTATGAACTCTATTCTGGAAAT-ACTGATCCATCGAATGATGAATTTA
* *
477268 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * * * *
477333 CATTCTGAACT-TTTTCTGGAAAAACTGATCCATCAAATGATGGATTTG
66 CATTATGAACTCTATTCTGGAAATACTGATCCATCGAATGATGAATTTA
* * *
477381 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGATTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * *
477446 CATTATGAACTTTTTTCTGGAAA-AGCTGATCCATCAAATGAT-AGATTTG
66 CATTATGAACTCTATTCTGGAAATA-CTGATCCATCGAATGATGA-ATTTA
* * *
477495 AGCAAAAGGTTGAATAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * *
477560 CATTATGAACT-TTTTCTGGAAA-AGTTGATCCATC-AAGTGATGGATTT
66 CATTATGAACTCTATTCTGGAAATA-CTGATCCATCGAA-TGATGAATTT
477607 GAATCTTTGC
Statistics
Matches: 807, Mismatches: 77, Indels: 39
0.87 0.08 0.04
Matches are distributed among these distances:
112 48 0.06
113 646 0.80
114 113 0.14
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (114 bp):
AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
CATTATGAACTCTATTCTGGAAATACTGATCCATCGAATGATGAATTTA
Found at i:478333 original size:23 final size:23
Alignment explanation
Indices: 478307--478351 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
478297 CACCACAGCT
*
478307 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
478330 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
478352 ATATAAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:478566 original size:149 final size:145
Alignment explanation
Indices: 478319--478629 Score: 534
Period size: 149 Copynumber: 2.1 Consensus size: 145
478309 TATAATTGCA
478319 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAAAATGTCCATAAGGACCATATTATTC
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAAAATGTCCATAAGGACCATATTATTC
478383 CTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCA
65 CTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCA
* *
478448 CAGAATATATATATATC
130 AAGAATATACATA-ATC
*
478465 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAA-AATGTCCATAAGGA-C-CATATTAT
478530 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
63 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
478595 CAAAGAATATACATAGTC
128 CAAAGAATATACATAATC
478613 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
478630 CCCTCGACTC
Statistics
Matches: 157, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
145 1 0.01
146 37 0.24
147 13 0.08
148 20 0.13
149 86 0.55
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (145 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAAAATGTCCATAAGGACCATATTATTCC
TTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAA
AGAATATACATAATC
Found at i:478749 original size:14 final size:14
Alignment explanation
Indices: 478730--478757 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
478720 AACTTGTAAT
478730 TCACGTATCACATA
1 TCACGTATCACATA
478744 TCACGTATCACATA
1 TCACGTATCACATA
478758 GCTTCTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (14 bp):
TCACGTATCACATA
Found at i:479181 original size:2 final size:2
Alignment explanation
Indices: 479174--479229 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
479164 TCTCTTAGAC
479174 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
479216 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
479230 TCACATGTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:480195 original size:21 final size:21
Alignment explanation
Indices: 480171--480215 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
480161 TGTTGTTCGT
* *
480171 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
480192 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
480213 TTG
1 TTG
480216 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:483512 original size:22 final size:23
Alignment explanation
Indices: 483487--483530 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
483477 CACCACAGCT
*
483487 CGTATAATTGCA-CGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
483509 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
483531 ATATAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:483804 original size:147 final size:148
Alignment explanation
Indices: 483506--483810 Score: 540
Period size: 147 Copynumber: 2.1 Consensus size: 148
483496 GCACGAAGTG
483506 CCGCGTAGAATTGCACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTATTCCTTAAG
1 CCGCGTAGAATTGCACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTATTCCTTAAG
*
483571 AATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCACAGAAT
66 AATCA-ATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAAT
*
483636 ATATATATATCCCGAAAGA
130 ATACATATATCCCGAAAGA
**
483655 CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATTATTCCTTAAG
1 CCGCGTAGAATTGCACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTATTCCTTAAG
483720 AATC-ATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATA
66 AATCAATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATA
* *
483784 TACATATGTCCCGAAGGA
131 TACATATATCCCGAAAGA
483802 CCGCGTAGA
1 CCGCGTAGA
483811 CCTCGACTCT
Statistics
Matches: 150, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
147 83 0.55
149 67 0.45
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (148 bp):
CCGCGTAGAATTGCACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTATTCCTTAAG
AATCAATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATA
TACATATATCCCGAAAGA
Found at i:485304 original size:21 final size:21
Alignment explanation
Indices: 485280--485324 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
485270 TGTTGTTCGT
* *
485280 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
485301 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
485322 TTG
1 TTG
485325 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:486421 original size:22 final size:22
Alignment explanation
Indices: 486396--486450 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
486386 GATAAAGCTT
*
486396 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
486418 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
486440 TCATCTTTGAA
1 TCATCTTTGAA
486451 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:489199 original size:114 final size:114
Alignment explanation
Indices: 488999--489218 Score: 377
Period size: 114 Copynumber: 1.9 Consensus size: 114
488989 GATCATGCAG
* * *
488999 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
489064 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTACAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
* * *
489113 TTCATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
489178 ACACTTACAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
66 ACACTTACAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
489219 CGAGAACGTG
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 99 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTACAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:490889 original size:32 final size:32
Alignment explanation
Indices: 490848--490909 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
490838 GAAGAAATGA
*
490848 TTGTTATGCTCATCTTGTAGAGATACTTCTCG
1 TTGTTATGCTCATCTGGTAGAGATACTTCTCG
490880 TTGTTATGCTCATCTGGTAGAGATACTTCT
1 TTGTTATGCTCATCTGGTAGAGATACTTCT
490910 TGTGTCTGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.44
Consensus pattern (32 bp):
TTGTTATGCTCATCTGGTAGAGATACTTCTCG
Found at i:491551 original size:4 final size:4
Alignment explanation
Indices: 491544--491604 Score: 54
Period size: 4 Copynumber: 14.8 Consensus size: 4
491534 CCTTCTTTTT
* *
491544 TTTC TTTC TTTT TTTC TTTC TTTT TTTC TTTC TTTAC TGGATT- TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT-C T---TTC TTTC
491591 TTT- TTTC TTTC TTT
1 TTTC TTTC TTTC TTT
491605 GCTGGATGAG
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
3 5 0.11
4 37 0.79
5 2 0.04
6 1 0.02
8 2 0.04
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:491555 original size:12 final size:12
Alignment explanation
Indices: 491529--491578 Score: 82
Period size: 12 Copynumber: 4.1 Consensus size: 12
491519 CCCCTTTTTC
*
491529 TTTTTCCTTCTTT
1 TTTTTCTTTC-TT
491542 TTTTTCTTTCTT
1 TTTTTCTTTCTT
491554 TTTTTCTTTCTT
1 TTTTTCTTTCTT
491566 TTTTTCTTTCTT
1 TTTTTCTTTCTT
491578 T
1 T
491579 ACTGGATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
12 27 0.75
13 9 0.25
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTCTTTCTT
Found at i:491563 original size:16 final size:16
Alignment explanation
Indices: 491523--491578 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
491513 ATTTCTCCCC
*
491523 TTTTTCTTT-TTCCTT
1 TTTTTCTTTCTTTCTT
491538 CTTTTT-TTTCTTTCTT
1 -TTTTTCTTTCTTTCTT
491554 TTTTTCTTTCTTT-TT
1 TTTTTCTTTCTTTCTT
491569 TTCTTTCTTT
1 TT-TTTCTTT
491579 ACTGGATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
15 12 0.33
16 24 0.67
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTCTTTCTTTCTT
Found at i:491594 original size:26 final size:27
Alignment explanation
Indices: 491560--491611 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
491550 TCTTTTTTTC
491560 TTTCTTTTTTTCTTTCTTTACTGGATT
1 TTTCTTTTTTTCTTTCTTTACTGGATT
*
491587 TTTC-TTTTTTCTTTCTTTGCTGGAT
1 TTTCTTTTTTTCTTTCTTTACTGGAT
491612 GAGTATATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.06, C:0.15, G:0.10, T:0.69
Consensus pattern (27 bp):
TTTCTTTTTTTCTTTCTTTACTGGATT
Found at i:495162 original size:14 final size:14
Alignment explanation
Indices: 495128--495181 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
495118 CATAAAAATA
* *
495128 CAAATGCAAAGATG
1 CAAATGTAAATATG
495142 CCAAATGTAAATATG
1 -CAAATGTAAATATG
*
495157 CAAATGTAAAAATG
1 CAAATGTAAATATG
*
495171 TAAATGTAAAT
1 CAAATGTAAAT
495182 GTAAATTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:499064 original size:3 final size:3
Alignment explanation
Indices: 499046--499104 Score: 73
Period size: 3 Copynumber: 19.0 Consensus size: 3
499036 TTTGGGCCTG
* * *
499046 TAA TATA TAA TAAA TAA TAA TAT TAA TAA TAA TAA TAA AAA TAA AAA
1 TAA TA-A TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
499093 TAA TAA TAA TAA
1 TAA TAA TAA TAA
499105 ATATAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
3 42 0.88
4 6 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:504556 original size:22 final size:22
Alignment explanation
Indices: 504528--504580 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
504518 GTGAACAGTG
504528 GGGGAATCGATTCCCTGTAGCA
1 GGGGAATCGATTCCCTGTAGCA
504550 GGGGAATCGATTCCCTGTAGCA
1 GGGGAATCGATTCCCTGTAGCA
504572 GGGGAATCG
1 GGGGAATCG
504581 GTACCCCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.23, C:0.21, G:0.36, T:0.21
Consensus pattern (22 bp):
GGGGAATCGATTCCCTGTAGCA
Found at i:514366 original size:26 final size:26
Alignment explanation
Indices: 514337--514412 Score: 64
Period size: 26 Copynumber: 2.9 Consensus size: 26
514327 TTTATTCCAA
514337 TCATTACAGAGCTCAAG-GATATTCAC
1 TCATTACAGAGCT-AAGTGATATTCAC
* * **
514363 TCATTCCTGAGCTTGGTGATATTCAC
1 TCATTACAGAGCTAAGTGATATTCAC
* * **
514389 TCATTCCTGAGCTTGGTGATATTC
1 TCATTACAGAGCTAAGTGATATTC
514413 TTGGTCATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
25 1 0.02
26 44 0.98
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (26 bp):
TCATTACAGAGCTAAGTGATATTCAC
Found at i:518068 original size:27 final size:27
Alignment explanation
Indices: 518034--518087 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
518024 ACTATTATTT
*
518034 TATTACAAAATGGTCACTCGATCGTTA
1 TATTACAAAATGGTCACTCAATCGTTA
518061 TATTACAAAATGGTCACTCAATCGTTA
1 TATTACAAAATGGTCACTCAATCGTTA
518088 ACCCCATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (27 bp):
TATTACAAAATGGTCACTCAATCGTTA
Found at i:519232 original size:25 final size:26
Alignment explanation
Indices: 519198--519256 Score: 104
Period size: 25 Copynumber: 2.3 Consensus size: 26
519188 GAAAAGATTT
519198 TTTTTAAAGAATTTATATATTTTTTC
1 TTTTTAAAGAATTTATATATTTTTTC
519224 TTTTT-AAGAATTTATATATTTTTTC
1 TTTTTAAAGAATTTATATATTTTTTC
519249 -TTTTAAAG
1 TTTTTAAAG
519257 GGGGTGCCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 4 0.12
25 23 0.72
26 5 0.16
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (26 bp):
TTTTTAAAGAATTTATATATTTTTTC
Found at i:523429 original size:27 final size:27
Alignment explanation
Indices: 523399--523469 Score: 124
Period size: 27 Copynumber: 2.6 Consensus size: 27
523389 ATTGTAGGAA
*
523399 CTATAGAGAGATGATTTGTTACCATTC
1 CTATAGAGATATGATTTGTTACCATTC
*
523426 CTATATAGATATGATTTGTTACCATTC
1 CTATAGAGATATGATTTGTTACCATTC
523453 CTATAGAGATATGATTT
1 CTATAGAGATATGATTT
523470 TGTAAATAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (27 bp):
CTATAGAGATATGATTTGTTACCATTC
Found at i:527042 original size:27 final size:27
Alignment explanation
Indices: 527010--527070 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
527000 AATTAAAGAG
527010 ATGATTTGTTACCATTCCTATAGAGAT
1 ATGATTTGTTACCATTCCTATAGAGAT
527037 ATGATTTGTTACCATTCCTATAGAGAT
1 ATGATTTGTTACCATTCCTATAGAGAT
527064 ATGATTT
1 ATGATTT
527071 TGTAAATAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.43
Consensus pattern (27 bp):
ATGATTTGTTACCATTCCTATAGAGAT
Found at i:545630 original size:13 final size:13
Alignment explanation
Indices: 545612--545645 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
545602 CGACTCCCAA
545612 CATTTCAAAAAAT
1 CATTTCAAAAAAT
545625 CATTTC--AAAAT
1 CATTTCAAAAAAT
545636 CATTTCAAAA
1 CATTTCAAAA
545646 CCTCCCCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.58
13 8 0.42
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (13 bp):
CATTTCAAAAAAT
Found at i:548008 original size:50 final size:50
Alignment explanation
Indices: 547930--548029 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
547920 ATTAAAAGAT
*
547930 CAACGAGATGAGATCAACCAAAAGCTAGGTCAAAGTGAGAACAGATTGAG
1 CAACGAGATGAGATCAACCAAAAACTAGGTCAAAGTGAGAACAGATTGAG
*
547980 CAACGAGATGAGATCAACCAAAAACTAGGTCAAAGTGAGAATAGATTGAG
1 CAACGAGATGAGATCAACCAAAAACTAGGTCAAAGTGAGAACAGATTGAG
548030 TAACTTAAAG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.45, C:0.15, G:0.25, T:0.15
Consensus pattern (50 bp):
CAACGAGATGAGATCAACCAAAAACTAGGTCAAAGTGAGAACAGATTGAG
Found at i:550907 original size:30 final size:30
Alignment explanation
Indices: 550873--550945 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
550863 CCCGAAGGAC
550873 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
550903 CTATCCAGAGGTCATAATGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
550933 CTATCCATAGGTC
1 CTATCCAGAGGTC
550946 CCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:556496 original size:30 final size:30
Alignment explanation
Indices: 556462--556534 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
556452 CCCGAAGGAC
556462 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
556492 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
556522 CTGTCCATAGGTC
1 CTATCCAGAGGTC
556535 CCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:571176 original size:19 final size:17
Alignment explanation
Indices: 571149--571195 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
571139 AATATATTAT
*
571149 TAATATAAAATATAAAAA
1 TAATTTAAAATAT-AAAA
*
571167 TATATTTAAAATATATAA
1 TA-ATTTAAAATATAAAA
571185 TAATTTAAAAT
1 TAATTTAAAAT
571196 TTTTAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 9 0.35
18 7 0.27
19 10 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATTTAAAATATAAAA
Found at i:571187 original size:24 final size:26
Alignment explanation
Indices: 571129--571186 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
571119 TAAAATTCTA
* *
571129 AAAACATAAAAATATATTATTAATAT
1 AAAATATAAAAATATATTATAAATAT
571155 AAAATATAAAAATATATT-TAAAATAT
1 AAAATATAAAAATATATTAT-AAATAT
*
571181 ATAATA
1 AAAATA
571187 ATTTAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 1 0.04
26 27 0.96
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (26 bp):
AAAATATAAAAATATATTATAAATAT
Found at i:580228 original size:39 final size:40
Alignment explanation
Indices: 580143--580228 Score: 93
Period size: 39 Copynumber: 2.1 Consensus size: 40
580133 TAAAAAATCT
**
580143 ATTTTTATCCGAAAAAAAATCCAGATTTTTAAAAAAATTGG
1 ATTTTTATCCG-AAAAAAATCCAGATTTTTAAAAAAACCGG
** * *
580184 ATTTTTATCCG-AAAAAATCTGGTTTTTTTAAAAAACCGG
1 ATTTTTATCCGAAAAAAATCCAGATTTTTAAAAAAACCGG
*
580223 TTTTTT
1 ATTTTT
580229 TGCAAACCGA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
39 27 0.71
41 11 0.29
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (40 bp):
ATTTTTATCCGAAAAAAATCCAGATTTTTAAAAAAACCGG
Found at i:588438 original size:16 final size:16
Alignment explanation
Indices: 588417--588460 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
588407 CGACAAAATT
*
588417 TTTACTATTTACGAAA
1 TTTACTATTCACGAAA
588433 TTTACTATTCACGAAA
1 TTTACTATTCACGAAA
*
588449 TTCACTATTCAC
1 TTTACTATTCAC
588461 ATGAATAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.41
Consensus pattern (16 bp):
TTTACTATTCACGAAA
Found at i:593660 original size:6 final size:6
Alignment explanation
Indices: 593649--593694 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
593639 TTTCCCTTTG
* *
593649 TTTTTA TTTTTA TTTTTG TTTTT- TCTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
593695 TCTCATTTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
5 4 0.11
6 32 0.89
ACGTcount: A:0.11, C:0.02, G:0.02, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:593664 original size:23 final size:23
Alignment explanation
Indices: 593638--593687 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
593628 TCCATTATTT
593638 TTTTCCCTTTGTT-TTTATTTTTA
1 TTTT-CCTTTGTTCTTTATTTTTA
** *
593661 TTTTTGTTTTTTCTTTATTTTTA
1 TTTTCCTTTGTTCTTTATTTTTA
593684 TTTT
1 TTTT
593688 TATTTTTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.08, C:0.08, G:0.04, T:0.80
Consensus pattern (23 bp):
TTTTCCTTTGTTCTTTATTTTTA
Found at i:593688 original size:23 final size:23
Alignment explanation
Indices: 593651--593726 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
593641 TCCCTTTGTT
593651 TTTATTTTTATTTTTGTTTTTTC
1 TTTATTTTTATTTTTGTTTTTTC
*
593674 TTTATTTTTATTTTTATTTTTTC
1 TTTATTTTTATTTTTGTTTTTTC
*
593697 -TCATTTTGT-TTGTTTGTTTTATT-
1 TTTATTTT-TATT-TTTGTTTT-TTC
593720 TTTATTT
1 TTTATTT
593727 ATTTTACCAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
22 8 0.18
23 30 0.67
24 7 0.16
ACGTcount: A:0.11, C:0.04, G:0.05, T:0.80
Consensus pattern (23 bp):
TTTATTTTTATTTTTGTTTTTTC
Found at i:593776 original size:36 final size:35
Alignment explanation
Indices: 593680--593787 Score: 89
Period size: 36 Copynumber: 3.1 Consensus size: 35
593670 TTTCTTTATT
* * *
593680 TTTATTTTTATT--TTTT-CTCATTTTGTTTGTTTG
1 TTTATTTTTATTCATTTTAC-CATGTTATTTTTTTG
*
593713 TTTTATTTTTATTTATTTTACCATGTTATTTATTTTG
1 -TTTATTTTTATTCATTTTACCATGTTATTT-TTTTG
* *
593750 TTTATTTTTA-TCATTTTTCCTTTGTTATTTTTTGTG
1 TTTATTTTTATTCATTTTACC-ATGTTATTTTTT-TG
593786 TT
1 TT
593788 GTTCATTATT
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
34 12 0.19
35 11 0.18
36 34 0.55
37 5 0.08
ACGTcount: A:0.13, C:0.06, G:0.07, T:0.73
Consensus pattern (35 bp):
TTTATTTTTATTCATTTTACCATGTTATTTTTTTG
Found at i:604002 original size:62 final size:62
Alignment explanation
Indices: 603917--604093 Score: 212
Period size: 62 Copynumber: 2.8 Consensus size: 62
603907 TCATTTAGTA
* * * * * *
603917 TGAAAACCTGAGAGGGTGTCCTAAGTCGAAAAAAGAAAAGAAAAAAGAAAAAACGTTTAGGG
1 TGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAGAAAAGAAAAAAGAAAAAACGTTTAGGG
* *
603979 TGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAA-AAAAGAAAAAAAAGAAAAATGTTTAGGG
1 TGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAGAAAAGAAAAAAGA-AAAAACGTTTAGGG
** * *
604041 TGAAAAATCGAAAGGGCACCCTAAATTGAAAAAAGAGAAAAAGAAAAAGAAAA
1 TGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAGA-AAAGA-AAAAAGAAAA
604094 TAAGGAGGGT
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
61 12 0.12
62 72 0.73
63 1 0.01
64 7 0.07
65 6 0.06
ACGTcount: A:0.55, C:0.10, G:0.22, T:0.12
Consensus pattern (62 bp):
TGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAGAAAAGAAAAAAGAAAAAACGTTTAGGG
Done.