Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008319.1 Hibiscus syriacus cultivar Beakdansim tig00111022_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: 4819703
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 21
Found at i:4134097 original size:20 final size:21
Alignment explanation
Indices: 4134054--4134103 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
4134044 TACCAAGGAT
*
4134054 GAGAAGACCTTTCATAACGAC
1 GAGAAGACCTTTCATAAAGAC
*
4134075 GAGAAGACC-TTCGTAAAGAC
1 GAGAAGACCTTTCATAAAGAC
4134095 GAGAAGACC
1 GAGAAGACC
4134104 ACATCACATG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 18 0.67
21 9 0.33
ACGTcount: A:0.40, C:0.22, G:0.24, T:0.14
Consensus pattern (21 bp):
GAGAAGACCTTTCATAAAGAC
Found at i:4138219 original size:125 final size:125
Alignment explanation
Indices: 4137997--4138249 Score: 346
Period size: 125 Copynumber: 2.0 Consensus size: 125
4137987 AATACCCACA
* * **
4137997 TTGGGGCACGATTGAACCCCCATCATTTTGAAATGACAAGATTCAGACAAAGAAGGCATCAAGAA
1 TTGGGGCACGACTGAACCCACATCATGATGAAATGACAAGATTCAGACAAAGAAGGCATCAAGAA
* * * * * * *
4138062 TGAGCCTTACAATTTGAGGTGATGGGGTATTTTGAAGGCCCGTACCAGTATGAGATAATG
66 TGAGCCTTACAATTTGAGATGATGAGGCATTTTGAAGGCCCGTACAAGAATAAAATAATG
* * **
4138122 TTGGGGCGCGACTGAACCCACATCATGATGAAATGACAAGATTCAGACCAAGAAGGCATTGAGAA
1 TTGGGGCACGACTGAACCCACATCATGATGAAATGACAAGATTCAGACAAAGAAGGCATCAAGAA
*
4138187 TGAGCCTTATAATTTGAGAT-ATTGAGGCATTTTGAAGGCCCGTACAAGAATAAAATAATG
66 TGAGCCTTACAATTTGAGATGA-TGAGGCATTTTGAAGGCCCGTACAAGAATAAAATAATG
4138247 TTG
1 TTG
4138250 CGACATTAGT
Statistics
Matches: 111, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
124 1 0.01
125 110 0.99
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (125 bp):
TTGGGGCACGACTGAACCCACATCATGATGAAATGACAAGATTCAGACAAAGAAGGCATCAAGAA
TGAGCCTTACAATTTGAGATGATGAGGCATTTTGAAGGCCCGTACAAGAATAAAATAATG
Found at i:4139588 original size:36 final size:36
Alignment explanation
Indices: 4139423--4139620 Score: 238
Period size: 36 Copynumber: 5.5 Consensus size: 36
4139413 GATTGGAGAA
*
4139423 AAACCATCCTAAGCCTTCACCGGAGAATAGTGAAGC
1 AAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGC
*
4139459 AAACCATCTGAAGCCTTCACCGGAGAATAGTGAAGC
1 AAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGC
* * *
4139495 AATCAATCTGAAGCCTTCACCGGAGAATAGTGAAGC
1 AAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGC
* * * *
4139531 AAACCATCATAAGTCTTCACCAGAGAGTAGTGAAGC
1 AAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGC
* * *
4139567 AAAGCATCTTAAGTCTTCACC--AAAAGTAGTGAAGC
1 AAACCATCTTAAGCCTTCACCGGAGAA-TAGTGAAGC
* *
4139602 AGATCCATTTTAAGCCTTC
1 A-AACCATCTTAAGCCTTC
4139621 TCAGAAGAGT
Statistics
Matches: 141, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
34 2 0.01
35 10 0.07
36 129 0.91
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (36 bp):
AAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGC
Found at i:4139617 original size:108 final size:107
Alignment explanation
Indices: 4139423--4139620 Score: 263
Period size: 108 Copynumber: 1.8 Consensus size: 107
4139413 GATTGGAGAA
* * *
4139423 AAACCATCCTAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTGAAGCCTTCACCGGAGAATA
1 AAACCATCATAAGCCTTCACCAGAGAATAGTGAAGCAAACCATCTGAAGCCTTCACC-GAAAATA
4139488 GTGAAGCAATCAATCTGAAGCCTTCACCGGAGAATAGTGAAGC
65 GTGAAGCAATCAATCTGAAGCCTTCACCGGAGAATAGTGAAGC
* * * * *
4139531 AAACCATCATAAGTCTTCACCAGAGAGTAGTGAAGCAAAGCATCTTAAGTCTTCACC-AAAAGTA
1 AAACCATCATAAGCCTTCACCAGAGAATAGTGAAGCAAACCATCTGAAGCCTTCACCGAAAA-TA
* * *
4139595 GTGAAGCAGATCCATTTTAAGCCTTC
65 GTGAAGCA-ATCAATCTGAAGCCTTC
4139621 TCAGAAGAGT
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
106 3 0.04
107 10 0.13
108 64 0.83
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (107 bp):
AAACCATCATAAGCCTTCACCAGAGAATAGTGAAGCAAACCATCTGAAGCCTTCACCGAAAATAG
TGAAGCAATCAATCTGAAGCCTTCACCGGAGAATAGTGAAGC
Found at i:4140067 original size:51 final size:51
Alignment explanation
Indices: 4140003--4140460 Score: 479
Period size: 51 Copynumber: 8.8 Consensus size: 51
4139993 AGATTATTTA
* *
4140003 AGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAGATTTTCG
1 AGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGATTTTCG
* * * * *
4140054 AGTTCTATACTCCCTGAAGAAAGAGGGAGAGAACCCGTTTTCAGAAGATCATTCA
1 AGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCG-TTT--GAAGAT-TTTCG
* * * * *
4140109 AGTTCTATACTTCCTTAAAGAAAGAAGGAGCGAACCCGTTTAAAGATGTTCG
1 AGTTCCATAC-TCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGATTTTCG
** * * *
4140161 AGTTCCATACTCTTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCTG
1 AGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGA-TTTTC-G
* * * * *
4140214 AGTTCCATACTCCCTAGAGAAAGCGGGAGCGAACCCGTGTGAAGATATGCG
1 AGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGATTTTCG
* * * * *
4140265 AGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCTG
1 AGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGA-TTTTC-G
* * * *
4140318 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATCCG
1 AGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGATTTTCG
* * *
4140369 AGTTCCATACTCCTTAATGAAAGAGGGAGCGAACCCG--TGAAGAGATGTTCG
1 AGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG-A-AGATTTTCG
* *
4140420 AGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCATTTG
1 AGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
4140461 TTGAAGATTG
Statistics
Matches: 336, Mismatches: 58, Indels: 24
0.80 0.14 0.06
Matches are distributed among these distances:
49 2 0.01
50 1 0.00
51 180 0.54
52 20 0.06
53 88 0.26
54 6 0.02
55 16 0.05
56 23 0.07
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (51 bp):
AGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGATTTTCG
Found at i:4140267 original size:104 final size:104
Alignment explanation
Indices: 4140003--4140455 Score: 583
Period size: 104 Copynumber: 4.3 Consensus size: 104
4139993 AGATTATTTA
* * * * *
4140003 AGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAGATTTTCGAGTTCTATACTCCC
1 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATTCGAGTTCCATACTCCT
* * * * *
4140068 TGAAGAAAGAGGGAGAGAACCCGTTTTCAGAAGATCAT-TC-A
66 TAAAGAAAGAAGGAGCGAACCCG-TTT--GAAGA-GATGTCTG
* * * * * * * *
4140109 AGTTCTATACTTCCTTAAAGAAAGAAGGAGCGAACCCGTTTAAAGATGTTCGAGTTCCATACTCT
1 AGTTCCATAC-TCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATTCGAGTTCCATACTCC
4140174 TTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCTG
65 TTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCTG
* * *
4140214 AGTTCCATACTCCCTAGAGAAAGCGGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATACTCCT
1 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATTCGAGTTCCATACTCCT
4140279 TAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCTG
66 TAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCTG
*
4140318 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATCCGAGTTCCATACTCCT
1 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATTCGAGTTCCATACTCCT
* *
4140383 TAATGAAAGAGGGAGCGAACCCG--TGAAGAGATGT-TCG
66 TAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT-G
* *
4140420 AGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCC
1 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCC
4140456 ATTTGTTGAA
Statistics
Matches: 312, Mismatches: 31, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
101 1 0.00
102 46 0.15
103 2 0.01
104 174 0.56
105 9 0.03
106 12 0.04
107 68 0.22
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (104 bp):
AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATTCGAGTTCCATACTCCT
TAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCTG
Found at i:4140397 original size:155 final size:153
Alignment explanation
Indices: 4140003--4140460 Score: 573
Period size: 155 Copynumber: 2.9 Consensus size: 153
4139993 AGATTATTTA
* * *
4140003 AGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAGATTTTCGAGTTCTATACTCCC
1 AGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAGATATCCGAGTTCCATACT-CC
* * * * *
4140068 TGAAGAAAGAGGGAGAGAACCCGTTTTCAGAAGATCATTCAAGTTCTATACTTCCTTAAAGAAAG
65 TTAAGAAAGAGGGAGCGAACCCG-TGT--GAAGAT-ATGCGAGTTCTATAC-TCCTTAAAGAAAG
4140133 AAGGAGCGAACCCGTTT-AAAGATGTTCG
125 AAGGAGCGAACCCGTTTGAAAGATGTTCG
** * * *
4140161 AGTTCCATACTCTTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCTGAGTTCCATACTC
1 AGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTG-A-AGATATCCGAGTTCCATACTC
* *
4140226 CCTAGAGAAAGCGGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATACTCCTTAAAGAAAGAAG
64 CTTA-AGAAAGAGGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATACTCCTTAAAGAAAGAAG
4140291 GAGCGAACCCGTTTGAAGAGATG-TCTG
128 GAGCGAACCCGTTTGAA-AGATGTTC-G
* *
4140318 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATCCGAGTTCCATACTCCT
1 AGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAGATATCCGAGTTCCATACTCCT
* * *
4140383 TAATGAAAGAGGGAGCGAACCC--GTGAAGAGATGTTCGAGTTCTATACTCCCTAAAGAAAGAGG
66 TAA-GAAAGAGGGAGCGAACCCGTGTGAAGATATG--CGAGTTCTATACTCCTTAAAGAAAGAAG
*
4140446 GAGCGAACCCATTTG
128 GAGCGAACCCGTTTG
4140461 TTGAAGATTG
Statistics
Matches: 264, Mismatches: 27, Indels: 21
0.85 0.09 0.07
Matches are distributed among these distances:
153 10 0.04
154 1 0.00
155 109 0.41
156 18 0.07
157 48 0.18
158 38 0.14
159 6 0.02
160 34 0.13
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (153 bp):
AGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAGATATCCGAGTTCCATACTCCT
TAAGAAAGAGGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATACTCCTTAAAGAAAGAAGGAG
CGAACCCGTTTGAAAGATGTTCG
Found at i:4140495 original size:55 final size:54
Alignment explanation
Indices: 4140003--4140772 Score: 381
Period size: 55 Copynumber: 14.5 Consensus size: 54
4139993 AGATTATTTA
* * * *
4140003 AGTTCCATACTCCCT-AGAGAAAGAAGGAGCGAACCC-GT-TTGAAGATT-TTCG
1 AGTTCTATACTCTCTGA-AGAAAGAGGGAGCGAACCCATTGTTGAAGATTGTTCG
* * * ** *
4140054 AGTTCTATACTCCCTGAAGAAAGAGGGAGAGAACCCGTT-TTCAGAAGATCATTCA
1 AGTTCTATACTCTCTGAAGAAAGAGGGAGCGAACCCATTGTT--GAAGATTGTTCG
* * * *
4140109 AGTTCTATACT-TCCTTAAAGAAAGAAGGAGCGAACCC-GT-TTAAAGA-TGTTCG
1 AGTTCTATACTCT-C-TGAAGAAAGAGGGAGCGAACCCATTGTTGAAGATTGTTCG
* * * * * *
4140161 AGTTCCATACTCTTTAAAGAAAGAAGGAGCGAACCC-GT-TTGAAGAGATG-TCTG
1 AGTTCTATACTCTCTGAAGAAAGAGGGAGCGAACCCATTGTTGAAGA-TTGTTC-G
* * * *
4140214 AGTTCCATACTCCCT-AGAGAAAGCGGGAGCGAACCC-GTG-TGAAGATATG--CG
1 AGTTCTATACTCTCTGA-AGAAAGAGGGAGCGAACCCATTGTTGAAGAT-TGTTCG
* * * *
4140265 AGTTCTATACTC-CTTAAAGAAAGAAGGAGCGAACCC-GT-TTGAAGAGATG-TCTG
1 AGTTCTATACTCTC-TGAAGAAAGAGGGAGCGAACCCATTGTTGAAGA-TTGTTC-G
* * * * *
4140318 AGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCC-GTG-TGAAGA-TATCCG
1 AGTTCTATACTCTCTGA-AGAAAGAGGGAGCGAACCCATTGTTGAAGATTGTTCG
* * *
4140369 AGTTCCATACTC-CTTAATGAAAGAGGGAGCGAACCC---G-TGAAGAGATGTTCG
1 AGTTCTATACTCTCTGAA-GAAAGAGGGAGCGAACCCATTGTTGAAGA-TTGTTCG
* *
4140420 AGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCATTTGTTGAAGATTGTTCG
1 AGTTCTATACTCTCTGAAGAAAGAGGGAGCGAACCCA-TTGTTGAAGATTGTTCG
* * *
4140475 AG-TCTTATACTCTCTGAAGAAATAGGG-G-GTAGACGCGATTGATGAAGATTG-T-G
1 AGTTC-TATACTCTCTGAAGAAAGAGGGAGCG-A-AC-CCATTGTTGAAGATTGTTCG
* * * * *
4140528 -GGTCTTATACTCTCTGAAGAAATAGGGGGC-AGACACAATCGTTGAAGATTGTTCG
1 AGTTC-TATACTCTCTGAAGAAAGAGGGAGCGA-AC-CCATTGTTGAAGATTGTTCG
* * * *
4140583 AG-TCTTATACTCTCTGAAGAAATAGGGGGC-AGACGCGATTGATGAAGATTG-T-G
1 AGTTC-TATACTCTCTGAAGAAAGAGGGAGCGA-AC-CCATTGTTGAAGATTGTTCG
* * * * *
4140636 -GGTCTTATACTCTCTGAAGAAATAGGGGGC-AGACGCAATCGTTGAAGATTGTTCG
1 AGTTC-TATACTCTCTGAAGAAAGAGGGAGCGA-AC-CCATTGTTGAAGATTGTTCG
* * * *
4140691 AG-TCTTATACTCTCTGAAGAAATAGGGGGC-AGACGCAATCGTTGAAGATTGTTCG
1 AGTTC-TATACTCTCTGAAGAAAGAGGGAGCGA-AC-CCATTGTTGAAGATTGTTCG
*
4140746 AG-TCTTATACTCTCTGAAGAAATAGGG
1 AGTTC-TATACTCTCTGAAGAAAGAGGG
4140773 GGCAGACAAG
Statistics
Matches: 619, Mismatches: 52, Indels: 92
0.81 0.07 0.12
Matches are distributed among these distances:
49 7 0.01
50 4 0.01
51 167 0.27
52 31 0.05
53 178 0.29
54 16 0.03
55 187 0.30
56 29 0.05
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (54 bp):
AGTTCTATACTCTCTGAAGAAAGAGGGAGCGAACCCATTGTTGAAGATTGTTCG
Found at i:4140580 original size:108 final size:108
Alignment explanation
Indices: 4140460--4140826 Score: 578
Period size: 108 Copynumber: 3.4 Consensus size: 108
4140450 GAACCCATTT
*
4140460 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGTAGACGCGATTGATGAAGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATT
4140525 GTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATC
66 GTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATC
4140568 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATT
*
4140633 GTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
66 GTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATC
* * *
4140676 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATT
* * *
4140741 GTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACA-AGTGT
66 G-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAAT-C
* * *
4140786 GTTGAAGA-TGATTCAAGTCTTATACCCTCTGAA-CAATAGGG
1 GTTGAAGATTG-TTCGAGTCTTATACTCTCTGAAGAAATAGGG
4140827 AGCGAACCCG
Statistics
Matches: 243, Mismatches: 12, Indels: 7
0.93 0.05 0.03
Matches are distributed among these distances:
108 169 0.70
109 12 0.05
110 62 0.26
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (108 bp):
GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATT
GTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATC
Found at i:4140631 original size:163 final size:165
Alignment explanation
Indices: 4140462--4140826 Score: 546
Period size: 163 Copynumber: 2.2 Consensus size: 165
4140452 ACCCATTTGT
* * *
4140462 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGTAGACGCGATTGATGAAGATTG-
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGATGAAGATTGT
*
4140526 T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATCGTTGAAGATTGTTCGAGTCTTA
66 TCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATCGTTGAAGATTGTTCGAGTCTTA
**
4140590 TACTCTCTGAAGAAATAGGGGGCAGACGCGAT-TGA
131 TACTCTCTGAAGAAATAGGGGGCAGACAAG-TGTGA
* *
4140625 TGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGATGAAGATTGT
*
4140688 TCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTA
66 TCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATCGTTGAAGATTGTTCGAGTCTTA
*
4140753 TACTCTCTGAAGAAATAGGGGGCAGACAAGTGTGT
131 TACTCTCTGAAGAAATAGGGGGCAGACAAGTGTGA
* * *
4140788 TGAAGA-TGATTCAAGTCTTATACCCTCTGAA-CAATAGGG
1 TGAAGATTG-TTCGAGTCTTATACTCTCTGAAGAAATAGGG
4140827 AGCGAACCCG
Statistics
Matches: 182, Mismatches: 14, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
161 47 0.26
162 5 0.03
163 106 0.58
164 8 0.04
165 16 0.09
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (165 bp):
TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGATGAAGATTGT
TCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATCGTTGAAGATTGTTCGAGTCTTA
TACTCTCTGAAGAAATAGGGGGCAGACAAGTGTGA
Found at i:4140773 original size:55 final size:55
Alignment explanation
Indices: 4140460--4140826 Score: 525
Period size: 55 Copynumber: 6.8 Consensus size: 55
4140450 GAACCCATTT
* * *
4140460 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGTAGACGCGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
* * *
4140515 GATGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATC
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
* *
4140568 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
* *
4140623 GATGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
4140676 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
*
4140731 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGA--CAAGTGT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAA-T-C
* * *
4140786 GTTGAAGA-TGATTCAAGTCTTATACCCTCTGAA-CAATAGGG
1 GTTGAAGATTG-TTCGAGTCTTATACTCTCTGAAGAAATAGGG
4140827 AGCGAACCCG
Statistics
Matches: 284, Mismatches: 21, Indels: 15
0.89 0.07 0.05
Matches are distributed among these distances:
53 97 0.34
54 14 0.05
55 173 0.61
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (55 bp):
GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
Found at i:4148674 original size:6 final size:6
Alignment explanation
Indices: 4148663--4148697 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
4148653 AGCTCAAGGT
4148663 ATACAC ATACAC ATACAC ATACAC ATACAC ATACA
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACA
4148698 TATGCATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.17
Consensus pattern (6 bp):
ATACAC
Found at i:4148709 original size:4 final size:4
Alignment explanation
Indices: 4148691--4148789 Score: 180
Period size: 4 Copynumber: 24.2 Consensus size: 4
4148681 ATACACATAC
4148691 ACAT ACAT ATGCAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT A--CAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
4148741 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
4148789 A
1 A
4148790 TATATATATA
Statistics
Matches: 93, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
4 89 0.96
6 4 0.04
ACGTcount: A:0.49, C:0.24, G:0.01, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:4151404 original size:19 final size:19
Alignment explanation
Indices: 4151380--4151429 Score: 84
Period size: 18 Copynumber: 2.7 Consensus size: 19
4151370 TTCAATATAA
*
4151380 ATATAAAATTTTCTTATGT
1 ATATAAAATTTTATTATGT
4151399 ATATAAAA-TTTATTATGT
1 ATATAAAATTTTATTATGT
4151417 ATATAAAATTTTA
1 ATATAAAATTTTA
4151430 GAGTTGGGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 17 0.59
19 12 0.41
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (19 bp):
ATATAAAATTTTATTATGT
Found at i:4151706 original size:23 final size:23
Alignment explanation
Indices: 4151676--4151721 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
4151666 TTACCTAAGC
4151676 TGGTAAACTGGTGTAACAGAATG
1 TGGTAAACTGGTGTAACAGAATG
4151699 TGGTAAACTGGTGTAACAGAATG
1 TGGTAAACTGGTGTAACAGAATG
4151722 CTAACAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.09, G:0.30, T:0.26
Consensus pattern (23 bp):
TGGTAAACTGGTGTAACAGAATG
Found at i:4154684 original size:11 final size:11
Alignment explanation
Indices: 4154668--4154698 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
4154658 ATTGCTTCAA
4154668 CATTCTAGACT
1 CATTCTAGACT
*
4154679 CATTCTAGATT
1 CATTCTAGACT
4154690 CATTCTAGA
1 CATTCTAGA
4154699 ACGTTTACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.39
Consensus pattern (11 bp):
CATTCTAGACT
Found at i:4159285 original size:18 final size:18
Alignment explanation
Indices: 4159262--4159301 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
4159252 ACTAAATTAT
*
4159262 TAAAATAAAATATAAATA
1 TAAAATAAAATAAAAATA
* *
4159280 TAAAATTAGATAAAAATA
1 TAAAATAAAATAAAAATA
4159298 TAAA
1 TAAA
4159302 TTTGTTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
TAAAATAAAATAAAAATA
Found at i:4162354 original size:20 final size:20
Alignment explanation
Indices: 4162326--4162363 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4162316 GTATAAGAGC
*
4162326 TCATATAGGATCATATAGAT
1 TCATATAGGAGCATATAGAT
*
4162346 TCATTTAGGAGCATATAG
1 TCATATAGGAGCATATAG
4162364 TTGCATGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (20 bp):
TCATATAGGAGCATATAGAT
Found at i:4165349 original size:31 final size:32
Alignment explanation
Indices: 4165314--4165373 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 32
4165304 GACCGATTTA
* * *
4165314 ATATTTATCCGACTTAAAATA-GATTGATATG
1 ATATTGATCCGACTCAAAAAATGATTGATATG
*
4165345 ATATTGATCTGACTCAAAAAATGATTGAT
1 ATATTGATCCGACTCAAAAAATGATTGAT
4165374 CCGATAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 17 0.71
32 7 0.29
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (32 bp):
ATATTGATCCGACTCAAAAAATGATTGATATG
Found at i:4168780 original size:37 final size:37
Alignment explanation
Indices: 4168702--4168780 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 37
4168692 CGATCTTTAT
* * * * **
4168702 AAATAACAACGATTCCTTTAAACATTTCGATAAATTA
1 AAATAAAAACAATTACTTTAAACACTTAAATAAATTA
* *
4168739 AAATAAAAACAATTACTTTAAACACTTAAATAAGTTG
1 AAATAAAAACAATTACTTTAAACACTTAAATAAATTA
4168776 AAATA
1 AAATA
4168781 CATCAAATAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.52, C:0.13, G:0.05, T:0.30
Consensus pattern (37 bp):
AAATAAAAACAATTACTTTAAACACTTAAATAAATTA
Found at i:4169536 original size:18 final size:18
Alignment explanation
Indices: 4169510--4169572 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 18
4169500 TATATTAATT
*
4169510 TAAACTATAATAAAAATA
1 TAAAATATAATAAAAATA
*
4169528 T-AAA-AT-ATACAAATA
1 TAAAATATAATAAAAATA
4169543 -AAAATATAATAAAAATA
1 TAAAATATAATAAAAATA
**
4169560 TATTATATAATAA
1 TAAAATATAATAA
4169573 TTCACTATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
15 11 0.31
16 4 0.11
17 10 0.28
18 11 0.31
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAATATAATAAAAATA
Found at i:4169555 original size:11 final size:11
Alignment explanation
Indices: 4169515--4169561 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
4169505 TAATTTAAAC
4169515 TATAATAAAAA
1 TATAATAAAAA
*
4169526 TAT-A-AAATA
1 TATAATAAAAA
*
4169535 TACAAATAAAAA
1 TA-TAATAAAAA
4169547 TATAATAAAAA
1 TATAATAAAAA
4169558 TATA
1 TATA
4169562 TTATATAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
9 6 0.21
10 1 0.03
11 16 0.55
12 6 0.21
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (11 bp):
TATAATAAAAA
Found at i:4170027 original size:18 final size:18
Alignment explanation
Indices: 4170004--4170039 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
4169994 CTCTAAATTC
*
4170004 GAATAACAAATTAATTTA
1 GAATAAAAAATTAATTTA
4170022 GAATAAAAAATTAATTTA
1 GAATAAAAAATTAATTTA
4170040 AAATCTAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (18 bp):
GAATAAAAAATTAATTTA
Found at i:4172176 original size:32 final size:32
Alignment explanation
Indices: 4172138--4172202 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
4172128 GTTGGCCGGG
*
4172138 AATGTCATTCCCGGTAATCTTACATTACCAAT
1 AATGTCATTCCCGGTAATCTTAAATTACCAAT
4172170 AATGTCATTCCCGGTAATCTTAAATTACCAAT
1 AATGTCATTCCCGGTAATCTTAAATTACCAAT
4172202 A
1 A
4172203 GTGGATTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (32 bp):
AATGTCATTCCCGGTAATCTTAAATTACCAAT
Found at i:4172557 original size:36 final size:37
Alignment explanation
Indices: 4172482--4172557 Score: 84
Period size: 38 Copynumber: 2.1 Consensus size: 37
4172472 TTATATATTC
* * * *
4172482 AATTTTTTTAAAAAATATATATAGATTTTATGAATTT
1 AATTTTTTAAAAAAATATATAAAGATTGTATGAAGTT
*
4172519 AATTTTTTAAAGAAAATATATAAATATTGT-TG-AGTT
1 AATTTTTTAAA-AAAATATATAAAGATTGTATGAAGTT
4172555 AAT
1 AAT
4172558 CGATTGACGG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
36 6 0.18
37 12 0.36
38 15 0.45
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (37 bp):
AATTTTTTAAAAAAATATATAAAGATTGTATGAAGTT
Found at i:4173249 original size:19 final size:21
Alignment explanation
Indices: 4173224--4173263 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4173214 CCGTTGAAAA
4173224 GGGGG-GAATCGGTACCCTCT
1 GGGGGAGAATCGGTACCCTCT
*
4173244 GGGGGAGAATCGGTTCCCTC
1 GGGGGAGAATCGGTACCCTC
4173264 CGAGCATACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.15, C:0.25, G:0.40, T:0.20
Consensus pattern (21 bp):
GGGGGAGAATCGGTACCCTCT
Found at i:4175383 original size:23 final size:20
Alignment explanation
Indices: 4175333--4175412 Score: 65
Period size: 20 Copynumber: 3.9 Consensus size: 20
4175323 AGAACCCCAT
*
4175333 GGGGGCATCGATTTCCC-TACA
1 GGGGGAATCGA-TTCCCTTA-A
4175354 -GGGGAATCGATTCCCATTTAAA
1 GGGGGAATCGATTCCC--TT-AA
* *
4175376 GGGGGAATCGGTTCCCTTAT
1 GGGGGAATCGATTCCCTTAA
*
4175396 GGGGGTATCGATTCCCT
1 GGGGGAATCGATTCCCT
4175413 CTGCCAAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
19 5 0.10
20 25 0.51
21 2 0.04
22 2 0.04
23 15 0.31
ACGTcount: A:0.20, C:0.23, G:0.30, T:0.28
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTTAA
Found at i:4182959 original size:22 final size:23
Alignment explanation
Indices: 4182891--4182960 Score: 88
Period size: 23 Copynumber: 3.1 Consensus size: 23
4182881 AACCCTAAAC
*
4182891 AAGCCCAAAAATTATATCTGCTA
1 AAGCCCAAAAATCATATCTGCTA
*
4182914 AAGCCCAAAAATCATATATGCTA
1 AAGCCCAAAAATCATATCTGCTA
* * *
4182937 AAGCCC-ATAATCGTATCTTCTA
1 AAGCCCAAAAATCATATCTGCTA
4182959 AA
1 AA
4182961 CTCGTGATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
22 14 0.34
23 27 0.66
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.26
Consensus pattern (23 bp):
AAGCCCAAAAATCATATCTGCTA
Found at i:4186530 original size:21 final size:21
Alignment explanation
Indices: 4186506--4186547 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4186496 AGAAGAGCGT
4186506 GGAAATGAAGAACAAATTGGG
1 GGAAATGAAGAACAAATTGGG
* *
4186527 GGAAATGACGAAGAAATTGGG
1 GGAAATGAAGAACAAATTGGG
4186548 AGAAGTGGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.05, G:0.36, T:0.14
Consensus pattern (21 bp):
GGAAATGAAGAACAAATTGGG
Found at i:4192481 original size:30 final size:31
Alignment explanation
Indices: 4192447--4192534 Score: 119
Period size: 30 Copynumber: 2.9 Consensus size: 31
4192437 TTTATTTAAT
**
4192447 TATTAAATTTTAGATTGAATATTAATTTGA-
1 TATTAAATTTTAGATAAAATATTAATTTGAC
4192477 TATTAAATTTTAGATAAAATATT-ATTTGACC
1 TATTAAATTTTAGATAAAATATTAATTTGA-C
*
4192508 TA-TAAACTTTAGATAAAATATTAATTT
1 TATTAAATTTTAGATAAAATATTAATTT
4192535 TTTAAGTTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
29 6 0.12
30 40 0.77
31 6 0.12
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (31 bp):
TATTAAATTTTAGATAAAATATTAATTTGAC
Found at i:4193301 original size:14 final size:13
Alignment explanation
Indices: 4193274--4193331 Score: 62
Period size: 14 Copynumber: 4.2 Consensus size: 13
4193264 GTAATTGGTT
4193274 TTCTGAAAATTGAA
1 TTCTGAAAA-TGAA
4193288 TTCTGGAAAATGAA
1 TTCT-GAAAATGAA
* *
4193302 TTACTGAAATTTAA
1 TT-CTGAAAATGAA
4193316 TTCTGGAAAATGAA
1 TTCT-GAAAATGAA
4193330 TT
1 TT
4193332 ACATTTCTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
13 2 0.05
14 28 0.76
15 7 0.19
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (13 bp):
TTCTGAAAATGAA
Found at i:4193317 original size:28 final size:28
Alignment explanation
Indices: 4193280--4193333 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
4193270 GGTTTTCTGA
4193280 AAATTGAATTCTGGAAAATGAATTACTG
1 AAATTGAATTCTGGAAAATGAATTACTG
*
4193308 AAATTTAATTCTGGAAAATGAATTAC
1 AAATTGAATTCTGGAAAATGAATTAC
4193334 ATTTCTGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.33
Consensus pattern (28 bp):
AAATTGAATTCTGGAAAATGAATTACTG
Found at i:4193727 original size:23 final size:23
Alignment explanation
Indices: 4193672--4193728 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
4193662 AGTAATAGTG
4193672 TTATATATATTTTAAAAATATTAA
1 TTATA-ATATTTTAAAAATATTAA
* * *
4193696 TTAGT-ATATTTTAAATATCTTTA
1 TTA-TAATATTTTAAAAATATTAA
4193719 TTATAATATT
1 TTATAATATT
4193729 ATTAGATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 1 0.04
23 23 0.82
24 3 0.11
25 1 0.04
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
TTATAATATTTTAAAAATATTAA
Found at i:4193924 original size:22 final size:23
Alignment explanation
Indices: 4193896--4193954 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
4193886 TTGATTATTT
4193896 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
4193918 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
*
4193941 TAAATATAATATTA
1 T-ATTATAATATTA
4193955 TATTATTAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 17 0.55
23 4 0.13
24 10 0.32
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:4193938 original size:17 final size:17
Alignment explanation
Indices: 4193916--4193971 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
4193906 TTAAAAATAT
4193916 AATATTATATTATTAGA
1 AATATTATATTATTAGA
* * *
4193933 AATATTA-ATAAATA-T
1 AATATTATATTATTAGA
4193948 AATATTATATTATTAGA
1 AATATTATATTATTAGA
4193965 AATATTA
1 AATATTA
4193972 ATAAATATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
15 7 0.23
16 10 0.32
17 14 0.45
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.45
Consensus pattern (17 bp):
AATATTATATTATTAGA
Found at i:4193946 original size:32 final size:32
Alignment explanation
Indices: 4193889--4193980 Score: 152
Period size: 32 Copynumber: 2.9 Consensus size: 32
4193879 AGTATAATTG
* *
4193889 ATTATTTTATTA-TAATATTAA-AAATATAAT
1 ATTATATTATTAGAAATATTAATAAATATAAT
4193919 ATTATATTATTAGAAATATTAATAAATATAAT
1 ATTATATTATTAGAAATATTAATAAATATAAT
4193951 ATTATATTATTAGAAATATTAATAAATATA
1 ATTATATTATTAGAAATATTAATAAATATA
4193981 TTTTAAATAT
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
30 11 0.19
31 8 0.14
32 39 0.67
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (32 bp):
ATTATATTATTAGAAATATTAATAAATATAAT
Found at i:4193968 original size:54 final size:53
Alignment explanation
Indices: 4193896--4194006 Score: 129
Period size: 54 Copynumber: 2.1 Consensus size: 53
4193886 TTGATTATTT
*
4193896 TATTATAATATTAAAAATA-TAAT-ATTATATTATTAGAA-ATATTAATAAATATAA
1 TATTATAATATTAAAAATATTAATAAATATATT-TTA-AATATATTAAT-AAT-TAA
* * *
4193950 TATTATATTATTAGAAATATTAATAAATATATTTTAAATATTTTAATAATTAA
1 TATTATAATATTAAAAATATTAATAAATATATTTTAAATATATTAATAATTAA
4194003 TATT
1 TATT
4194007 TTGATTAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
53 7 0.14
54 22 0.44
55 14 0.28
56 7 0.14
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (53 bp):
TATTATAATATTAAAAATATTAATAAATATATTTTAAATATATTAATAATTAA
Found at i:4196285 original size:15 final size:15
Alignment explanation
Indices: 4196265--4196297 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
4196255 TAGTGTGACT
4196265 AAAATATAAATA-TTA
1 AAAATA-AAATACTTA
4196280 AAAATAAAATACTTA
1 AAAATAAAATACTTA
4196295 AAA
1 AAA
4196298 CAAAATAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATAAAATACTTA
Found at i:4197636 original size:3 final size:3
Alignment explanation
Indices: 4197621--4197672 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
4197611 TAAATACACT
* *
4197621 TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-T TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4197668 TAA TA
1 TAA TA
4197673 TTTTTTAACT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 1 0.02
3 43 0.98
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:4198057 original size:105 final size:106
Alignment explanation
Indices: 4197800--4198094 Score: 344
Period size: 105 Copynumber: 2.7 Consensus size: 106
4197790 TCGTTAGATT
** *
4197800 GAACAAGTTCTTCTCATTATGAAC-TTCTTTTTTCTCGTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTTC-TCCTT-T-AT-GATGAGTTCTTCTCATTATGAACTC
* * * *
4197864 TTTTGGAAATGTTGATCCAAAATCCTTTTGCGGTGGACTTAGAAA
62 TTCTGGAAATGTTGATCCAAAATCCATCTGCGGTGGAATTAGAAA
* * * *
4197909 GAACATGTTTTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
1 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTATGATGAGTTCTTCTCATTATGAACTCTTCT
* * ** * *
4197974 GGAAATGTTGGTTC-ACCTCCATCTGTGGT-GAATTTGAAA
66 GGAAATGTTGATCCAAAATCCATCTGCGGTGGAATTAGAAA
4198013 GGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTATGATGAGTTCTTCTCATTATGAACTCTTC
1 -GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTATGATGAGTTCTTCTCATTATGAACTCTTC
*
4198078 ATTGGAAATGTCGATCC
65 --TGGAAATGTTGATCC
4198095 CTCAAGCGAG
Statistics
Matches: 158, Mismatches: 24, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
104 8 0.05
105 70 0.44
106 39 0.25
107 12 0.08
108 1 0.01
109 25 0.16
110 3 0.02
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (106 bp):
GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTATGATGAGTTCTTCTCATTATGAACTCTTCT
GGAAATGTTGATCCAAAATCCATCTGCGGTGGAATTAGAAA
Found at i:4198076 original size:16 final size:16
Alignment explanation
Indices: 4198022--4198077 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 16
4198012 AGGAACAAGT
4198022 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
* *
4198038 T-TTCTCCTTTATGATGAGT
1 TCTTCT-CATTATGA--A-C
4198057 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
4198073 TCTTC
1 TCTTC
4198078 ATTGGAAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
15 4 0.13
16 13 0.42
17 1 0.03
18 1 0.03
19 8 0.26
20 4 0.13
ACGTcount: A:0.20, C:0.23, G:0.09, T:0.48
Consensus pattern (16 bp):
TCTTCTCATTATGAAC
Found at i:4198403 original size:225 final size:223
Alignment explanation
Indices: 4198014--4198451 Score: 639
Period size: 225 Copynumber: 2.0 Consensus size: 223
4198004 AATTTGAAAG
*
4198014 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTATGATGAGTTCTTCTCATTATGAACTCTTCA
1 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGATGAGTTCTTCTCATTATGAACTCTTCA
* * * * * * * * *
4198079 TTGGAAATGTCGATCCCTCAAGCGAGGCGTCACTGATTCGAAATGTCGTGAATCAAGTGATAGGT
66 CTGAAAATATCAATCCCTCAAGCGAGGCATCACTGATTCAAAATGTCATAAATCAAGTGATAAGT
* *
4198144 CAAAAAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTTTCATTATGAAC
131 CAAAAAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGAATGAGTTCTTCTCATTATGAAC
4198209 TCTCCATTGAAAATGTTGATGCGAATTT
196 TCTCCATTGAAAATGTTGATGCGAATTT
4198237 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTT-GGATGAGTTCTTCTCATTATGAACT
1 GAACAAGTTCTTCTCATTATGAAC-T-TTC-TCCT--TTAGGATGAGTTCTTCTCATTATGAACT
* *
4198301 C-TC-CTGAAAATATCAATCCCTCAAGCGAGGTATCACTGATTCAAAATGTCATAAATCGAGTGA
61 CTTCACTGAAAATATCAATCCCTCAAGCGAGGCATCACTGATTCAAAATGTCATAAATCAAGTGA
* * * *
4198364 TAATTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGAATGAGTTCTTCTCATTA
126 TAAGTCAAAAAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGAATGAGTTCTTCTCATTA
*
4198429 TGAACTCTCCATTGGAAATGTTG
191 TGAACTCTCCATTGAAAATGTTG
4198452 GTTCACCTCC
Statistics
Matches: 191, Mismatches: 19, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
223 24 0.13
224 1 0.01
225 133 0.70
226 6 0.03
227 25 0.13
228 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.36
Consensus pattern (223 bp):
GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGATGAGTTCTTCTCATTATGAACTCTTCA
CTGAAAATATCAATCCCTCAAGCGAGGCATCACTGATTCAAAATGTCATAAATCAAGTGATAAGT
CAAAAAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGAATGAGTTCTTCTCATTATGAAC
TCTCCATTGAAAATGTTGATGCGAATTT
Found at i:4199330 original size:8 final size:8
Alignment explanation
Indices: 4199319--4199409 Score: 60
Period size: 8 Copynumber: 12.5 Consensus size: 8
4199309 CCTTTTTCTC
4199319 TTTTCATT
1 TTTTCATT
4199327 TTTTCA--
1 TTTTCATT
*
4199333 -TTTCTTT
1 TTTTCATT
4199340 TTTTCA-T
1 TTTTCATT
4199347 TTTTCA--
1 TTTTCATT
4199353 TTTT--TT
1 TTTTCATT
4199359 TTTTCATT
1 TTTTCATT
4199367 TTTT--TCT
1 TTTTCAT-T
4199374 TTTTCATT
1 TTTTCATT
4199382 TTTTCATCT
1 TTTTCAT-T
4199391 TTTT-ATT
1 TTTTCATT
* *
4199398 TGTTCCTT
1 TTTTCATT
4199406 TTTT
1 TTTT
4199410 TCTTCAAGCA
Statistics
Matches: 66, Mismatches: 5, Indels: 24
0.69 0.05 0.25
Matches are distributed among these distances:
5 4 0.06
6 9 0.14
7 16 0.24
8 31 0.47
9 6 0.09
ACGTcount: A:0.09, C:0.13, G:0.01, T:0.77
Consensus pattern (8 bp):
TTTTCATT
Found at i:4199349 original size:19 final size:20
Alignment explanation
Indices: 4199319--4199369 Score: 86
Period size: 19 Copynumber: 2.5 Consensus size: 20
4199309 CCTTTTTCTC
4199319 TTTTCATTTTTTCATTTCTTT
1 TTTTCA-TTTTTCATTTCTTT
4199340 TTTTCATTTTTCATTT-TTT
1 TTTTCATTTTTCATTTCTTT
4199359 TTTTCATTTTT
1 TTTTCATTTTT
4199370 TTCTTTTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 14 0.47
20 10 0.33
21 6 0.20
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTCATTTTTCATTTCTTT
Found at i:4199351 original size:28 final size:28
Alignment explanation
Indices: 4199311--4199388 Score: 115
Period size: 28 Copynumber: 2.8 Consensus size: 28
4199301 CAAACCCTCC
4199311 TTTTTCTCTTTTCATTTTTTCATTTC-TT
1 TTTTTCT-TTTTCATTTTTTCATTTCATT
*
4199339 TTTTTCATTTTTCATTTTTT-TTTTCATT
1 TTTTTC-TTTTTCATTTTTTCATTTCATT
4199367 TTTTTCTTTTTCATTTTTTCAT
1 TTTTTCTTTTTCATTTTTTCAT
4199389 CTTTTTATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
27 17 0.38
28 27 0.60
29 1 0.02
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (28 bp):
TTTTTCTTTTTCATTTTTTCATTTCATT
Found at i:4211616 original size:15 final size:15
Alignment explanation
Indices: 4211596--4211628 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
4211586 TAGTGTGACT
4211596 AAAATATAAATA-TTA
1 AAAATA-AAATACTTA
4211611 AAAATAAAATACTTA
1 AAAATAAAATACTTA
4211626 AAA
1 AAA
4211629 CAAAATAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATAAAATACTTA
Found at i:4212964 original size:3 final size:3
Alignment explanation
Indices: 4212949--4213009 Score: 97
Period size: 3 Copynumber: 20.7 Consensus size: 3
4212939 TAAATACACT
*
4212949 TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
4212997 TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TA
4213010 TTTTTTTATC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
2 1 0.02
3 52 0.98
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:4216266 original size:28 final size:28
Alignment explanation
Indices: 4216222--4216278 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
4216212 CCGTCGTTGC
* *
4216222 TTTCAAACACTGTCTCGACGATATAATG
1 TTTCAAACACTGGCTCGACGACATAATG
* *
4216250 TTTCAAGCACTGGCTCGATGACATAATG
1 TTTCAAACACTGGCTCGACGACATAATG
4216278 T
1 T
4216279 AAATAGAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32
Consensus pattern (28 bp):
TTTCAAACACTGGCTCGACGACATAATG
Found at i:4231324 original size:59 final size:59
Alignment explanation
Indices: 4231225--4231351 Score: 173
Period size: 59 Copynumber: 2.2 Consensus size: 59
4231215 GTAGTGCTAT
* * * **
4231225 CCGAGTATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAGTC
1 CCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAGTC
* ** *
4231284 CCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTATTC
1 CCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAGTC
4231343 CCGAATATG
1 CCGAATATG
4231352 CAACATGCTG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (59 bp):
CCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAGTC
Found at i:4232857 original size:38 final size:38
Alignment explanation
Indices: 4232806--4232881 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
4232796 CAAAATCCTA
*
4232806 AGAAAATTGCTTAAAAATTTGAGTTGAAGATTTCTCAC
1 AGAAAATTGCTTAAAAAATTGAGTTGAAGATTTCTCAC
4232844 AGAAAATTGCTTAAAAAATTGAGTTGAAGATTTCTCAC
1 AGAAAATTGCTTAAAAAATTGAGTTGAAGATTTCTCAC
4232882 CCTTTGAAGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.33
Consensus pattern (38 bp):
AGAAAATTGCTTAAAAAATTGAGTTGAAGATTTCTCAC
Found at i:4233368 original size:2 final size:2
Alignment explanation
Indices: 4233363--4233396 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4233353 AAACACCTTT
4233363 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
4233397 ACACACACAC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:4234359 original size:24 final size:24
Alignment explanation
Indices: 4234323--4234386 Score: 119
Period size: 24 Copynumber: 2.7 Consensus size: 24
4234313 CTATTGACTA
4234323 GCACCGAAAGGTGCATAAATTAAT
1 GCACCGAAAGGTGCATAAATTAAT
*
4234347 GCATCGAAAGGTGCATAAATTAAT
1 GCACCGAAAGGTGCATAAATTAAT
4234371 GCACCGAAAGGTGCAT
1 GCACCGAAAGGTGCAT
4234387 GACCCCTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.20
Consensus pattern (24 bp):
GCACCGAAAGGTGCATAAATTAAT
Found at i:4246082 original size:29 final size:29
Alignment explanation
Indices: 4246040--4246121 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
4246030 AAACTAAATT
4246040 GATGTCATTGCTTACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
4246069 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
4246098 GATATCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
4246122 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:4247273 original size:12 final size:14
Alignment explanation
Indices: 4247242--4247268 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4247232 GGATCATTGC
4247242 AAGCATAAGAAGAG
1 AAGCATAAGAAGAG
4247256 AAGCATAAGAAGA
1 AAGCATAAGAAGA
4247269 AGCATGAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.07, G:0.26, T:0.07
Consensus pattern (14 bp):
AAGCATAAGAAGAG
Found at i:4247389 original size:24 final size:24
Alignment explanation
Indices: 4247362--4247434 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
4247352 CAAGGCAGAG
*
4247362 GTAGAGGCCATGGACGAGGTGGAA
1 GTAGAGGTCATGGACGAGGTGGAA
*
4247386 GTAGAGGTCATAGACGAGGTGGAA
1 GTAGAGGTCATGGACGAGGTGGAA
*
4247410 GTTGAGGTCATGGACGAGGCTGGAA
1 GTAGAGGTCATGGACGAGG-TGGAA
4247435 TTACAACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
24 39 0.89
25 5 0.11
ACGTcount: A:0.29, C:0.11, G:0.44, T:0.16
Consensus pattern (24 bp):
GTAGAGGTCATGGACGAGGTGGAA
Found at i:4250862 original size:29 final size:29
Alignment explanation
Indices: 4250818--4250899 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
4250808 AAACTAAATT
4250818 GATGTCATTGCTTACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
* *
4250847 GTTGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
4250876 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
4250900 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:4253788 original size:18 final size:19
Alignment explanation
Indices: 4253741--4253805 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 19
4253731 CAAATTAAAC
* *
4253741 TATAATAAAAATATAAAACA
1 TATAATAAAAA-ATATAATA
*
4253761 TACAAATAAAAAATATAAT-
1 TA-TAATAAAAAATATAATA
*
4253780 TATAAT-AAAAATATATTA
1 TATAATAAAAAATATAATA
4253798 TATAATAA
1 TATAATAA
4253806 TTCACTATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
17 10 0.27
18 9 0.24
19 3 0.08
20 7 0.19
21 8 0.22
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (19 bp):
TATAATAAAAAATATAATA
Found at i:4253791 original size:17 final size:18
Alignment explanation
Indices: 4253741--4253805 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 18
4253731 CAAATTAAAC
*
4253741 TATAATAAAAATATAAAACA
1 TATAATAAAAATAT--AATA
*
4253761 TACAAATAAAAAATATAAT-
1 TA-TAAT-AAAAATATAATA
*
4253780 TATAATAAAAATATATTA
1 TATAATAAAAATATAATA
4253798 TATAATAA
1 TATAATAA
4253806 TTCACTATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
17 10 0.26
18 11 0.29
19 2 0.05
20 4 0.11
21 3 0.08
22 8 0.21
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
TATAATAAAAATATAATA
Found at i:4253925 original size:18 final size:18
Alignment explanation
Indices: 4253902--4253941 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
4253892 ACTAAATTAT
*
4253902 TAAAATAAAATATAAATA
1 TAAAATAAAATAAAAATA
* *
4253920 TAAAATTAGATAAAAATA
1 TAAAATAAAATAAAAATA
4253938 TAAA
1 TAAA
4253942 TTTGCTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
TAAAATAAAATAAAAATA
Found at i:4253975 original size:9 final size:9
Alignment explanation
Indices: 4253956--4253984 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
4253946 CTTTTAAACG
4253956 AAAAATT-A
1 AAAAATTAA
4253964 AAAAATTAA
1 AAAAATTAA
4253973 AAAAATTAA
1 AAAAATTAA
4253982 AAA
1 AAA
4253985 TTCAAACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 7 0.35
9 13 0.65
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAAATTAA
Found at i:4255388 original size:183 final size:180
Alignment explanation
Indices: 4255071--4255397 Score: 478
Period size: 181 Copynumber: 1.8 Consensus size: 180
4255061 AAAAAAAGTT
*
4255071 ATCACATGGCATGGATGCTTTCAATTTTTAACTGATAGTGCAAGACAGAATACTAATCATAAAAT
1 ATCACATGGCATGAATGCTTTCAATTTTTAACTGATAGTGCAAGACAGAATACTAATCATAAAAT
* * * * * * * *
4255136 AATTCAGTCCACCAGATTTGAATATTTTGAGTCATTAAATTTTTATTAGGTTAAGTTAGACGTAT
66 AATTAAGTCCACCAAATTTAAACATCTTGAGCCATTAAATTTTTAATAGGTTAAGTTAGACGAAT
4255201 CACATGTAGATTGGGTTAATAGATCAAAGATACATAGAATGATATAAGCA
131 CACATGTAGATTGGGTTAATAGATCAAAGATACATAGAATGATATAAGCA
* * * *
4255251 ATCACATGGCATGAATGCATTTCAATTTTTTTAACTG-TAGTGGAAGACCGAATATTTATCATAA
1 ATCACATGGCATGAATGC-TTTCAA--TTTTTAACTGATAGTGCAAGACAGAATACTAATCATAA
4255315 AAT-ATTAAGTCCACCAAATTTAAACATCTTGAGCCATTAAACTTTTTAATAGGTTAAAGTTAGA
63 AATAATTAAGTCCACCAAATTTAAACATCTTGAGCCATTAAA-TTTTTAATAGGTT-AAGTTAGA
4255379 CGAATCACATGTAGATTGG
126 CGAATCACATGTAGATTGG
4255398 TTTTAATTGG
Statistics
Matches: 129, Mismatches: 13, Indels: 7
0.87 0.09 0.05
Matches are distributed among these distances:
180 17 0.13
181 38 0.29
182 38 0.29
183 36 0.28
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (180 bp):
ATCACATGGCATGAATGCTTTCAATTTTTAACTGATAGTGCAAGACAGAATACTAATCATAAAAT
AATTAAGTCCACCAAATTTAAACATCTTGAGCCATTAAATTTTTAATAGGTTAAGTTAGACGAAT
CACATGTAGATTGGGTTAATAGATCAAAGATACATAGAATGATATAAGCA
Found at i:4256263 original size:3 final size:3
Alignment explanation
Indices: 4256241--4256281 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
4256231 TAAACATTAA
* * *
4256241 AAT AAT AAG GAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4256282 AAACACAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:4258295 original size:31 final size:31
Alignment explanation
Indices: 4258260--4258322 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
4258250 AATTCGGTGA
*
4258260 ATTCAATATGTCCTTCTCACTAGGAACTCCC
1 ATTCAATATGTCCTTCTCACTAGAAACTCCC
*
4258291 ATTCAATATGTCCTTCTCATTAGAAACTCCC
1 ATTCAATATGTCCTTCTCACTAGAAACTCCC
4258322 A
1 A
4258323 AACTCTTGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (31 bp):
ATTCAATATGTCCTTCTCACTAGAAACTCCC
Found at i:4261744 original size:21 final size:21
Alignment explanation
Indices: 4261719--4261776 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
4261709 AGACAATATT
4261719 GTTAAAGCTTAATAAATTGTC
1 GTTAAAGCTTAATAAATTGTC
*
4261740 GTTAAAGCTTAATAAATTTTC
1 GTTAAAGCTTAATAAATTGTC
*
4261761 ATTAAAGCTTAATAAA
1 GTTAAAGCTTAATAAA
4261777 CAATTCAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.38
Consensus pattern (21 bp):
GTTAAAGCTTAATAAATTGTC
Found at i:4264639 original size:23 final size:25
Alignment explanation
Indices: 4264604--4264658 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
4264594 AAATATCCCT
* *
4264604 AAAAAATTCAAAC-AATGTTAGATA
1 AAAAAAATCAAACTAATGTTAAATA
4264628 AAAAAAAT-AAACTAATGTTAAATA
1 AAAAAAATCAAACTAATGTTAAATA
*
4264652 AATAAAA
1 AAAAAAA
4264659 GGGAAAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.24
Consensus pattern (25 bp):
AAAAAAATCAAACTAATGTTAAATA
Found at i:4264688 original size:24 final size:26
Alignment explanation
Indices: 4264647--4264718 Score: 69
Period size: 25 Copynumber: 2.8 Consensus size: 26
4264637 AACTAATGTT
*
4264647 AAATAAATAAAAGGGAAAA-AGAAAA
1 AAATAAATAAAAGAGAAAATAGAAAA
* *
4264672 AAATAAA-GAAAGAGAAAATATAAAA
1 AAATAAATAAAAGAGAAAATAGAAAA
*
4264697 ATATAAATCATAAAGA-AAAATA
1 AAATAAAT-A-AAAGAGAAAATA
4264719 ATAATAGTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
24 9 0.24
25 18 0.47
27 6 0.16
28 5 0.13
ACGTcount: A:0.74, C:0.01, G:0.11, T:0.14
Consensus pattern (26 bp):
AAATAAATAAAAGAGAAAATAGAAAA
Found at i:4265179 original size:20 final size:20
Alignment explanation
Indices: 4265154--4265261 Score: 171
Period size: 20 Copynumber: 5.4 Consensus size: 20
4265144 CATTGCGACA
*
4265154 ATCGCAATGCGAATCTGACT
1 ATCGCAACGCGAATCTGACT
*
4265174 ATCGCAACGCGTATCTGACT
1 ATCGCAACGCGAATCTGACT
*
4265194 ATCGCAACGCGTATCTGACT
1 ATCGCAACGCGAATCTGACT
4265214 ATCGCAACGCGAATCTGACT
1 ATCGCAACGCGAATCTGACT
* *
4265234 ATCGCGACGCGATTCTGACT
1 ATCGCAACGCGAATCTGACT
4265254 ATCGCAAC
1 ATCGCAAC
4265262 ACTGAAGTTC
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 82 1.00
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGAATCTGACT
Found at i:4265298 original size:20 final size:20
Alignment explanation
Indices: 4265273--4265343 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
4265263 CTGAAGTTCA
4265273 AATTCACAACTCGATTTCTG
1 AATTCACAACTCGATTTCTG
* *
4265293 AATTCACAACACTGAATTTC-A
1 AATTCACAACTC-G-ATTTCTG
*
4265314 AATTCGCAACTCGATTTCTG
1 AATTCACAACTCGATTTCTG
4265334 AATTCACAAC
1 AATTCACAAC
4265344 AGGTTTTACT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 5 0.12
20 21 0.50
21 11 0.26
22 5 0.12
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.31
Consensus pattern (20 bp):
AATTCACAACTCGATTTCTG
Found at i:4265303 original size:41 final size:41
Alignment explanation
Indices: 4265258--4265344 Score: 156
Period size: 41 Copynumber: 2.1 Consensus size: 41
4265248 CTGACTATCG
4265258 CAACACTGAAGTTCAAATTCACAACTCGATTTCTGAATTCA
1 CAACACTGAAGTTCAAATTCACAACTCGATTTCTGAATTCA
* *
4265299 CAACACTGAATTTCAAATTCGCAACTCGATTTCTGAATTCA
1 CAACACTGAAGTTCAAATTCACAACTCGATTTCTGAATTCA
4265340 CAACA
1 CAACA
4265345 GGTTTTACTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.37, C:0.25, G:0.09, T:0.29
Consensus pattern (41 bp):
CAACACTGAAGTTCAAATTCACAACTCGATTTCTGAATTCA
Found at i:4265323 original size:21 final size:21
Alignment explanation
Indices: 4265258--4265344 Score: 74
Period size: 20 Copynumber: 4.2 Consensus size: 21
4265248 CTGACTATCG
*
4265258 CAACACTGAAGTTCAAATTCA
1 CAACACTGAATTTCAAATTCA
* *
4265279 CAACTC-G-ATTTCTGAATTCA
1 CAACACTGAATTTC-AAATTCA
*
4265299 CAACACTGAATTTCAAATTCG
1 CAACACTGAATTTCAAATTCA
* *
4265320 CAACTC-G-ATTTCTGAATTCA
1 CAACACTGAATTTC-AAATTCA
4265340 CAACA
1 CAACA
4265345 GGTTTTACTT
Statistics
Matches: 52, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
19 9 0.17
20 22 0.42
21 16 0.31
22 5 0.10
ACGTcount: A:0.37, C:0.25, G:0.09, T:0.29
Consensus pattern (21 bp):
CAACACTGAATTTCAAATTCA
Found at i:4265501 original size:22 final size:22
Alignment explanation
Indices: 4265459--4265502 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
4265449 CTCTCTCCGG
*
4265459 CGACATCCGTTCCTATATCTAA
1 CGACATCCGTTCCCATATCTAA
*
4265481 CGACATCC-TTCCCCATCTCTAA
1 CGACATCCGTT-CCCATATCTAA
4265503 ATTTTTTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.25, C:0.39, G:0.07, T:0.30
Consensus pattern (22 bp):
CGACATCCGTTCCCATATCTAA
Found at i:4266549 original size:14 final size:14
Alignment explanation
Indices: 4266523--4266559 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
4266513 AGAAAAAGAA
4266523 GAAGAATAAGTCCCC
1 GAAGAA-AAGTCCCC
4266538 GAAGAAAAGTCCCC
1 GAAGAAAAGTCCCC
4266552 GAAGAAAA
1 GAAGAAAA
4266560 TACCATGGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.49, C:0.22, G:0.22, T:0.08
Consensus pattern (14 bp):
GAAGAAAAGTCCCC
Found at i:4268314 original size:19 final size:19
Alignment explanation
Indices: 4268290--4268327 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
4268280 AACATTGCTA
4268290 TGATCTGTTCAGTTGTTAT
1 TGATCTGTTCAGTTGTTAT
4268309 TGATCTGTTCAGTTGTTAT
1 TGATCTGTTCAGTTGTTAT
4268328 CACTCTAATT
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:0.16, C:0.11, G:0.21, T:0.53
Consensus pattern (19 bp):
TGATCTGTTCAGTTGTTAT
Found at i:4268364 original size:20 final size:20
Alignment explanation
Indices: 4268339--4268618 Score: 202
Period size: 20 Copynumber: 14.9 Consensus size: 20
4268329 ACTCTAATTC
*
4268339 ATTTGACTATTGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
4268359 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
4268379 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
*
4268399 ATTTGACTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
*
4268419 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* * *
4268439 A----A--ATTGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
4268453 ATTTGACTATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
*
4268473 A----A--ATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
* * *
4268487 ATATGACTATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
* * *
4268507 ATTTGACTATTGTAACGTGA
1 ATTTGACTATCGCAACGCGA
*
4268527 ATTTGATTATCGCAACAG-GA
1 ATTTGACTATCGCAAC-GCGA
* *
4268547 ATTTGACTATCGTAACGAG-
1 ATTTGACTATCGCAACGCGA
*
4268566 A---GA--ATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
* *
4268581 AATGGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
4268601 ATTTCACTATCGCAACGC
1 ATTTGACTATCGCAACGC
4268619 AAAAATCGCA
Statistics
Matches: 204, Mismatches: 36, Indels: 40
0.73 0.13 0.14
Matches are distributed among these distances:
14 28 0.14
15 1 0.00
16 4 0.02
18 4 0.02
19 2 0.01
20 164 0.80
21 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:4268462 original size:34 final size:34
Alignment explanation
Indices: 4268407--4268501 Score: 111
Period size: 34 Copynumber: 2.8 Consensus size: 34
4268397 GAATTTGACT
**
4268407 ATCGCAACGGGAATTTGACTATCGCAACGAGAAA
1 ATCGCAACACGAATTTGACTATCGCAACGAGAAA
* * * *
4268441 ATTGCAA-AGCGTATTTGACTATCGCAATGCGAAA
1 ATCGCAACA-CGAATTTGACTATCGCAACGAGAAA
*
4268475 ATCGCAACACGAATATGACTATCGCAA
1 ATCGCAACACGAATTTGACTATCGCAA
4268502 AGCGTATTTG
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
34 49 0.98
35 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (34 bp):
ATCGCAACACGAATTTGACTATCGCAACGAGAAA
Found at i:4268589 original size:128 final size:128
Alignment explanation
Indices: 4268350--4268601 Score: 333
Period size: 128 Copynumber: 2.0 Consensus size: 128
4268340 TTTGACTATT
* * * * *
4268350 GCAACGCGAATTTGACTATCGCAACGTGAATTTGATTATCGCAACGGGAATTTGACTATCGCAAC
1 GCAACACGAATATGACTATCGCAAAGCGAATTTGACTATCGCAACGGGAATTTGACTATCGCAAC
* * * * * *
4268415 GGGAATTTGACTATCGCAACGAGAAAATTGCAAAGCGTATTTGACTATCGCAATGCGAAAATC
66 AGGAATTTGACTATCGCAACGAGAAAATCGCAAAGCGAAATGGACTATCGCAACGCGAAAATC
* * * * *
4268478 GCAACACGAATATGACTATCGCAAAGCGTATTTGACTATTGTAACGTGAATTTGATTATCGCAAC
1 GCAACACGAATATGACTATCGCAAAGCGAATTTGACTATCGCAACGGGAATTTGACTATCGCAAC
* * *
4268543 AGGAATTTGACTATCGTAACGAGAGAATCGCAATGCGAAATGGACTATCGCAACGCGAA
66 AGGAATTTGACTATCGCAACGAGAAAATCGCAAAGCGAAATGGACTATCGCAACGCGAA
4268602 TTTCACTATC
Statistics
Matches: 105, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
128 105 1.00
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.25
Consensus pattern (128 bp):
GCAACACGAATATGACTATCGCAAAGCGAATTTGACTATCGCAACGGGAATTTGACTATCGCAAC
AGGAATTTGACTATCGCAACGAGAAAATCGCAAAGCGAAATGGACTATCGCAACGCGAAAATC
Found at i:4268610 original size:148 final size:147
Alignment explanation
Indices: 4268341--4268646 Score: 366
Period size: 148 Copynumber: 2.1 Consensus size: 147
4268331 TCTAATTCAT
* * *
4268341 TTGACTATTGCAACGCGAATTTGACTATCGCAACGTGAATTTGATTATCGCAACGGGAATTTGAC
1 TTGACTATCGCAAAGCGAATTTGACTATCGCAACGTGAATTTGATTATCGCAACAGGAATTTGAC
* * * * * * *
4268406 TATCGCAACGGGAATTTGACTATCGCAACGAGAAAATTGCAAAGCGTATTTGACTATCGCAATGC
66 TATCGCAACGGGAATTCGACAATCGAAACGAGAAAATCGCAAAGCGAATTTCACTATCGCAACGC
*
4268471 GAAAATCGCAACACGAA
131 AAAAATCGCAACACGAA
* * *
4268488 TATGACTATCGCAAAGCGTATTTGACTATTGTAACGTGAATTTGATTATCGCAACAGGAATTTGA
1 T-TGACTATCGCAAAGCGAATTTGACTATCGCAACGTGAATTTGATTATCGCAACAGGAATTTGA
* * ** *
4268553 CTATCGTAACGAGAGAA-TCG-CAATGCGAAATG-GACTATCGCAACGCGAATTTCACTATCGCA
65 CTATCGCAACG-G-GAATTCGACAAT-CGAAACGAGAAAATCGCAAAGCGAATTTCACTATCGCA
*
4268615 ACGCAAAAATCGCAACGCGAA
127 ACGCAAAAATCGCAACACGAA
*
4268636 TTGACTTTCGC
1 TTGACTATCGC
4268647 GTTGCGATTT
Statistics
Matches: 134, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
147 10 0.07
148 113 0.84
149 8 0.06
150 3 0.02
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (147 bp):
TTGACTATCGCAAAGCGAATTTGACTATCGCAACGTGAATTTGATTATCGCAACAGGAATTTGAC
TATCGCAACGGGAATTCGACAATCGAAACGAGAAAATCGCAAAGCGAATTTCACTATCGCAACGC
AAAAATCGCAACACGAA
Found at i:4268691 original size:20 final size:20
Alignment explanation
Indices: 4268639--4268693 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
4268629 ACGCGAATTG
* *
4268639 ACTTTCGCGTTGCGATTTTA
1 ACTTTAGCGTTGCGATTCTA
* * *
4268659 ACTTTCGCATTGCGATTCTG
1 ACTTTAGCGTTGCGATTCTA
*
4268679 AGTTTAGCGTTGCGA
1 ACTTTAGCGTTGCGA
4268694 AAGTGTACCT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (20 bp):
ACTTTAGCGTTGCGATTCTA
Found at i:4270271 original size:21 final size:20
Alignment explanation
Indices: 4270247--4270319 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 20
4270237 GAGAATCGGG
*
4270247 CTCTTGAACGGTGGGAGAGAC
1 CTCTTGAACGGTGGGAG-GGC
* * **
4270268 CTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGC
4270289 CTCTTGAACGGTGGGACGGGC
1 CTCTTGAACGGTGGGA-GGGC
4270310 CTCTTGAACG
1 CTCTTGAACG
4270320 ATGATAGGGG
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 40 0.98
22 1 0.02
ACGTcount: A:0.21, C:0.25, G:0.33, T:0.22
Consensus pattern (20 bp):
CTCTTGAACGGTGGGAGGGC
Found at i:4270313 original size:42 final size:42
Alignment explanation
Indices: 4270247--4270369 Score: 133
Period size: 42 Copynumber: 2.9 Consensus size: 42
4270237 GAGAATCGGG
*
4270247 CTCTTGAACGGTGGGAGAGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGAGACCTCTTCAACGATGACAGGGGC
* * *
4270289 CTCTTGAACGGTGGGACG-GGCCTCTTGAACGATGATAGGGGC
1 CTCTTGAACGGTGGGA-GAGACCTCTTCAACGATGACAGGGGC
* * * * *
4270331 CCCTTGAACGATAGAAGA-AGCCTCTTGAACGATGACAGG
1 CTCTTGAACGGTGGGAGAGA-CCTCTTCAACGATGACAGG
4270370 TGAATCAGAC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 1 0.01
42 66 0.97
43 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.32, T:0.20
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGAGACCTCTTCAACGATGACAGGGGC
Found at i:4270330 original size:21 final size:20
Alignment explanation
Indices: 4270267--4270365 Score: 90
Period size: 21 Copynumber: 4.8 Consensus size: 20
4270257 GTGGGAGAGA
* *
4270267 CCTCTTCAACGATGACAGTGG
1 CCTCTTGAACGATGA-AGGGG
* * *
4270288 CCTCTTGAACGGTGGGACGGG
1 CCTCTTGAACGAT-GAAGGGG
4270309 CCTCTTGAACGATGATAGGGG
1 CCTCTTGAACGATGA-AGGGG
* **
4270330 CCCCTTGAACGATAGAAGAAG
1 CCTCTTGAACGAT-GAAGGGG
4270351 CCTCTTGAACGATGA
1 CCTCTTGAACGATGA
4270366 CAGGTGAATC
Statistics
Matches: 63, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
20 3 0.05
21 57 0.90
22 3 0.05
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.21
Consensus pattern (20 bp):
CCTCTTGAACGATGAAGGGG
Found at i:4270707 original size:20 final size:20
Alignment explanation
Indices: 4270684--4270731 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
4270674 GAAACATAAA
4270684 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
4270704 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
4270724 ATCGCAAC
1 ATCGCAAC
4270732 ACGTATTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.27, G:0.21, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:4270781 original size:19 final size:19
Alignment explanation
Indices: 4270757--4270810 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
4270747 GCAACGAGAG
4270757 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
4270776 AATCGCAACGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
4270796 AAACGCAATGC-AAAT
1 AATCGCAATGCGAAAT
4270811 TTAGTTTCGC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.13
19 11 0.35
20 16 0.52
ACGTcount: A:0.50, C:0.19, G:0.19, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:4270892 original size:20 final size:20
Alignment explanation
Indices: 4270867--4270935 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
4270857 GCGATTCTCT
**
4270867 CGTTGCGATAGTCAAATACG
1 CGTTGCGATAGTCATTTACG
*
4270887 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTACG
* *
4270907 CGTTGTGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTACG
4270927 CGTTGCGAT
1 CGTTGCGAT
4270936 TTTATGTTTC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTACG
Found at i:4274726 original size:20 final size:20
Alignment explanation
Indices: 4274703--4274775 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
4274693 GAAACTTAAA
*
4274703 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
4274723 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
* **
4274743 ATTGCAACGCG-AAATGAAA
1 ATCGCAACGCGAAAATGACT
4274762 ATCGCAACGC-AAAA
1 ATCGCAACGCGAAAA
4274776 CTAAAATAGC
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
19 16 0.37
20 27 0.63
ACGTcount: A:0.42, C:0.23, G:0.18, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:4275206 original size:22 final size:22
Alignment explanation
Indices: 4275179--4275220 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
4275169 AGATAGACAC
4275179 ATTTCGTCGGAGATGGGGACGG
1 ATTTCGTCGGAGATGGGGACGG
4275201 ATTTCGTCGGAGATGGGGAC
1 ATTTCGTCGGAGATGGGGAC
4275221 AGATGTCGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.14, G:0.43, T:0.24
Consensus pattern (22 bp):
ATTTCGTCGGAGATGGGGACGG
Found at i:4275483 original size:20 final size:20
Alignment explanation
Indices: 4275417--4275487 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
4275407 TTTTGTATTA
* *
4275417 TCGCGTTGCGATAATCAGAT
1 TCGCATTGCGATAGTCAGAT
* *
4275437 TCGCGTTGCGATAGTCAGAA
1 TCGCATTGCGATAGTCAGAT
4275457 TCGCATTGCGATAGTCAGAT
1 TCGCATTGCGATAGTCAGAT
*
4275477 TCACATTGCGA
1 TCGCATTGCGA
4275488 ATTTGGAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.28
Consensus pattern (20 bp):
TCGCATTGCGATAGTCAGAT
Found at i:4275510 original size:41 final size:41
Alignment explanation
Indices: 4275455--4275537 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
4275445 CGATAGTCAG
* * *
4275455 AATCGCATTGCGATAGTCAGATTCACATTGCGAATTTGGAA
1 AATCGCAATGCGATAGTCAGAATCACATTGCGAATCTGGAA
* *
4275496 AATCGCAATGCGATAGTTAGAATCGCATTGCGAATCTGGAA
1 AATCGCAATGCGATAGTCAGAATCACATTGCGAATCTGGAA
4275537 A
1 A
4275538 CTGATTTGCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.27
Consensus pattern (41 bp):
AATCGCAATGCGATAGTCAGAATCACATTGCGAATCTGGAA
Found at i:4281494 original size:13 final size:14
Alignment explanation
Indices: 4281471--4281500 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
4281461 TATGGGAAAG
4281471 AAATAATAATAATA
1 AAATAATAATAATA
4281485 AAATAA-AATAATA
1 AAATAATAATAATA
4281498 AAA
1 AAA
4281501 GAAATGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAATAATAATAATA
Found at i:4282771 original size:14 final size:14
Alignment explanation
Indices: 4282743--4282787 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
4282733 TGGACAATTA
*
4282743 AAATGAAAATAAAAT
1 AAATAAAAAT-AAAT
*
4282758 TAATAAAAATAAAT
1 AAATAAAAATAAAT
4282772 AAATAAAAATAAAT
1 AAATAAAAATAAAT
4282786 AA
1 AA
4282788 CAACGATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 19 0.70
15 8 0.30
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (14 bp):
AAATAAAAATAAAT
Found at i:4282863 original size:30 final size:31
Alignment explanation
Indices: 4282823--4282962 Score: 119
Period size: 30 Copynumber: 4.5 Consensus size: 31
4282813 TATTTTCTAC
*
4282823 AAACTATATATATATTTTCAAAA-GTATTTTA
1 AAACTATATATATATTTTCAAAACGT-TTTCA
* *
4282854 AAA-TATATATATTTTTTAAAAACGTTTTCA
1 AAACTATATATATATTTTCAAAACGTTTTCA
* * *
4282884 AAA-T-TATATA-GTTTTCAAAAATGTTTTTA
1 AAACTATATATATATTTTC-AAAACGTTTTCA
* *
4282913 AAACTATATATTATAAGTTTTCAAAATGATTTCA
1 AAACTATATA-TAT-A-TTTTCAAAACGTTTTCA
4282947 AAACTATATAATATAT
1 AAACTATAT-ATATAT
4282963 ATATGTTTTC
Statistics
Matches: 90, Mismatches: 10, Indels: 17
0.77 0.09 0.15
Matches are distributed among these distances:
28 4 0.04
29 19 0.21
30 26 0.29
31 9 0.10
32 3 0.03
33 1 0.01
34 22 0.24
35 6 0.07
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (31 bp):
AAACTATATATATATTTTCAAAACGTTTTCA
Found at i:4282926 original size:36 final size:35
Alignment explanation
Indices: 4282886--4283145 Score: 205
Period size: 36 Copynumber: 7.3 Consensus size: 35
4282876 CGTTTTCAAA
4282886 ATTATATAGTTTTCAAAAATGTTTTTAAAACTATAT
1 ATTATATA-TTTTCAAAAATGTTTTTAAAACTATAT
* *
4282922 ATTATA-AGTTTTC-AAAATGATTTCAAAACTATAT
1 ATTATATA-TTTTCAAAAATGTTTTTAAAACTATAT
4282956 AATATATATATGTTTTC-AAAATGTTTCTTTTTAAAA--AT-T
1 -AT-TATATA--TTTTCAAAAATG----TTTTTAAAACTATAT
* *
4282995 A-TATTTATTTT-AAAAATGTTTTTAAAACCATAT
1 ATTATATATTTTCAAAAATGTTTTTAAAACTATAT
* * *
4283028 AATATATATTTTCAAAAACGTTTTAAAAACTATAT
1 ATTATATATTTTCAAAAATGTTTTTAAAACTATAT
* *
4283063 ATTATATTTATTTTC-AAAGTGTTTTAAAAACTATAT
1 ATTATA--TATTTTCAAAAATGTTTTTAAAACTATAT
* * * *
4283099 AATATATAAATGTTTCAAATATATTTTCAAAACTATAT
1 -AT-TATATAT-TTTCAAAAATGTTTTTAAAACTATAT
4283137 ATTATATAT
1 ATTATATAT
4283146 ATATATATAT
Statistics
Matches: 186, Mismatches: 18, Indels: 40
0.76 0.07 0.16
Matches are distributed among these distances:
30 9 0.05
32 2 0.01
33 2 0.01
34 38 0.20
35 33 0.18
36 42 0.23
37 16 0.09
38 34 0.18
39 1 0.01
40 2 0.01
42 7 0.04
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (35 bp):
ATTATATATTTTCAAAAATGTTTTTAAAACTATAT
Found at i:4283010 original size:106 final size:105
Alignment explanation
Indices: 4282878--4283086 Score: 264
Period size: 106 Copynumber: 2.0 Consensus size: 105
4282868 TTTAAAAACG
* * * *
4282878 TTTTCAAAATTATATAGTTTTCAAAAATGTTTTTAAAACTATATATTATA-AGTTTTC-AAAATG
1 TTTTAAAAATTATATAGTTTTCAAAAATGTTTTTAAAACCATATAATATATA-TTTTCAAAAACG
* *
4282941 ATTTCAAAACTATATAATATATATATGTTTTCAAAATGTTTCT
65 ATTTAAAAACTATAT-AT-TATATATATTTTCAAAATGTTTCT
4282984 TTTTAAAAATTATATTTA-TTTT-AAAAATGTTTTTAAAACCATATAATATATATTTTCAAAAAC
1 TTTTAAAAATTATA--TAGTTTTCAAAAATGTTTTTAAAACCATATAATATATATTTTCAAAAAC
* * *
4283047 GTTTTAAAAACTATATATTATATTTATTTTCAAAGTGTTT
64 GATTTAAAAACTATATATTATATATATTTTCAAAATGTTT
4283087 TAAAAACTAT
Statistics
Matches: 90, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
105 19 0.21
106 46 0.51
107 23 0.26
108 2 0.02
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (105 bp):
TTTTAAAAATTATATAGTTTTCAAAAATGTTTTTAAAACCATATAATATATATTTTCAAAAACGA
TTTAAAAACTATATATTATATATATTTTCAAAATGTTTCT
Found at i:4283038 original size:34 final size:35
Alignment explanation
Indices: 4282888--4283144 Score: 170
Period size: 34 Copynumber: 7.2 Consensus size: 35
4282878 TTTTCAAAAT
*
4282888 TATATAGTTTTCAAAAATGTTTTTAAAACTATATAT
1 TATATAGTTTT-AAAAATGTTTTTAAAACTATATAA
* * *
4282924 TATA-AGTTTTCAAAATGATTTCAAAACTATATAATA
1 TATATAGTTTTAAAAATGTTTTTAAAACTATAT-A-A
*
4282960 TATATATGTTTTCAAAATGTTTCTTTTTAAAA--AT-T-A
1 TATATA-GTTTTAAAAATG----TTTTTAAAACTATATAA
* *
4282996 TATTTA-TTTTAAAAATGTTTTTAAAACCATATAA
1 TATATAGTTTTAAAAATGTTTTTAAAACTATATAA
* *
4283030 TATATA-TTTTCAAAAACGTTTTAAAAACTATATATTA
1 TATATAGTTTT-AAAAATGTTTTTAAAACTATATA--A
* * * *
4283067 TATTTA-TTTTCAAAGTGTTTTAAAAACTATATAA
1 TATATAGTTTTAAAAATGTTTTTAAAACTATATAA
* * * * *
4283101 TATATAAATGTTTCAAATATATTTTCAAAACTATATAT
1 TATAT--A-GTTTTAAAAATGTTTTTAAAACTATATAA
4283139 TATATA
1 TATATA
4283145 TATATATATA
Statistics
Matches: 178, Mismatches: 24, Indels: 38
0.74 0.10 0.16
Matches are distributed among these distances:
30 9 0.05
32 2 0.01
33 1 0.01
34 44 0.25
35 27 0.15
36 36 0.20
37 11 0.06
38 38 0.21
39 1 0.01
40 2 0.01
42 7 0.04
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (35 bp):
TATATAGTTTTAAAAATGTTTTTAAAACTATATAA
Found at i:4283086 original size:71 final size:73
Alignment explanation
Indices: 4282992--4283143 Score: 209
Period size: 71 Copynumber: 2.1 Consensus size: 73
4282982 CTTTTTAAAA
* *
4282992 ATTATATTTATTTTAAAAATGTTTTTAAAACCATATAATATAT-AT-TTTCAAAAACGTTTTAAA
1 ATTATATTTATTTTAAAAATGTTTTAAAAACCATATAATATATAATGTTTCAAAAACATTTTAAA
4283055 AACTATAT
66 AACTATAT
* * * * * *
4283063 ATTATATTTATTTTCAAAGTGTTTTAAAAACTATATAATATATAAATGTTTCAAATATATTTTCA
1 ATTATATTTATTTTAAAAATGTTTTAAAAACCATATAATATAT-AATGTTTCAAAAACATTTTAA
4283128 AAACTATAT
65 AAACTATAT
4283137 ATTATAT
1 ATTATAT
4283144 ATATATATAT
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
71 39 0.56
73 2 0.03
74 29 0.41
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (73 bp):
ATTATATTTATTTTAAAAATGTTTTAAAAACCATATAATATATAATGTTTCAAAAACATTTTAAA
AACTATAT
Found at i:4283137 original size:2 final size:2
Alignment explanation
Indices: 4283132--4283174 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
4283122 TTTTCAAAAC
*
4283132 TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4283173 TA
1 TA
4283175 AAAAATAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4283241 original size:2 final size:2
Alignment explanation
Indices: 4283234--4283271 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
4283224 GTCTATTGGT
*
4283234 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4283272 AAAAATAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4283254 original size:97 final size:97
Alignment explanation
Indices: 4283139--4283330 Score: 384
Period size: 97 Copynumber: 2.0 Consensus size: 97
4283129 AACTATATAT
4283139 TATATATATATATATATATATATATATGTATATATAAAAAATAAATAAAAAAAATGAGACGAAAA
1 TATATATATATATATATATATATATATGTATATATAAAAAATAAATAAAAAAAATGAGACGAAAA
4283204 TGGGTGTCTACATTAATGATGTCTATTGGTTA
66 TGGGTGTCTACATTAATGATGTCTATTGGTTA
4283236 TATATATATATATATATATATATATATGTATATATAAAAAATAAATAAAAAAAATGAGACGAAAA
1 TATATATATATATATATATATATATATGTATATATAAAAAATAAATAAAAAAAATGAGACGAAAA
4283301 TGGGTGTCTACATTAATGATGTCTATTGGT
66 TGGGTGTCTACATTAATGATGTCTATTGGT
4283331 ACCGTCGTTG
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 95 1.00
ACGTcount: A:0.47, C:0.04, G:0.12, T:0.36
Consensus pattern (97 bp):
TATATATATATATATATATATATATATGTATATATAAAAAATAAATAAAAAAAATGAGACGAAAA
TGGGTGTCTACATTAATGATGTCTATTGGTTA
Found at i:4286590 original size:20 final size:20
Alignment explanation
Indices: 4286565--4286657 Score: 132
Period size: 20 Copynumber: 4.7 Consensus size: 20
4286555 ATAATAAAAA
*
4286565 ATCGCAACGCGATTGTGACT
1 ATCGCAACGCGATTCTGACT
*
4286585 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATTCTGACT
* * *
4286605 TTCGCAACACGATGCTGACT
1 ATCGCAACGCGATTCTGACT
*
4286625 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
4286645 ATCGCAACGCGAT
1 ATCGCAACGCGAT
4286658 AATACAAAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:4286876 original size:22 final size:22
Alignment explanation
Indices: 4286851--4286901 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
4286841 CTACGGCGAC
4286851 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* * *
4286873 ATCCATCTCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
4286895 ATCCGTC
1 ATCCGTC
4286902 TATCTCCATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.43, G:0.14, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:4287262 original size:19 final size:19
Alignment explanation
Indices: 4287238--4287295 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
4287228 ATTTGAAACC
4287238 GAGAATCGCAACACGAAAT
1 GAGAATCGCAACACGAAAT
*
4287257 GAGAATCGCAACGACAAAAT
1 GAGAATCGCAAC-ACGAAAT
**
4287277 GACTATCGCAACACGAAAT
1 GAGAATCGCAACACGAAAT
4287296 TGACTATCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (19 bp):
GAGAATCGCAACACGAAAT
Found at i:4287320 original size:40 final size:40
Alignment explanation
Indices: 4287242--4287350 Score: 148
Period size: 40 Copynumber: 2.8 Consensus size: 40
4287232 GAAACCGAGA
**
4287242 ATCGCAACACGAAA-TGAGAATCGCAACGACAAAATGACT
1 ATCGCAACACGAAATTGACTATCGCAACGACAAAATGACT
*** *
4287281 ATCGCAACACGAAATTGACTATCGCAACGTGGAATTGACT
1 ATCGCAACACGAAATTGACTATCGCAACGACAAAATGACT
*
4287321 ATCGCAACGCGAAATTGACTATCGCAACGA
1 ATCGCAACACGAAATTGACTATCGCAACGA
4287351 GAGAATCGCA
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
39 14 0.23
40 47 0.77
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.17
Consensus pattern (40 bp):
ATCGCAACACGAAATTGACTATCGCAACGACAAAATGACT
Found at i:4287349 original size:20 final size:20
Alignment explanation
Indices: 4287242--4287349 Score: 130
Period size: 20 Copynumber: 5.5 Consensus size: 20
4287232 GAAACCGAGA
* **
4287242 ATCGCAACACGAAA-TGAGA
1 ATCGCAACGCGAAATTGACT
*
4287261 ATCGCAACGAC-AAAATGACT
1 ATCGCAACG-CGAAATTGACT
*
4287281 ATCGCAACACGAAATTGACT
1 ATCGCAACGCGAAATTGACT
* *
4287301 ATCGCAACGTGGAATTGACT
1 ATCGCAACGCGAAATTGACT
4287321 ATCGCAACGCGAAATTGACT
1 ATCGCAACGCGAAATTGACT
4287341 ATCGCAACG
1 ATCGCAACG
4287350 AGAGAATCGC
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.16
20 64 0.84
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAATTGACT
Found at i:4287463 original size:32 final size:34
Alignment explanation
Indices: 4287396--4287487 Score: 98
Period size: 32 Copynumber: 2.8 Consensus size: 34
4287386 ACCAAATTCG
* *
4287396 CGTTGCGATTTTCATTTCCGCATTGCCATTTTCT
1 CGTTGCGATTTTCAATTCCGCATTGCCATTCTCT
* *
4287430 CGTTGTGA-TTTCAATT-CGCATTGCGATTCTCT
1 CGTTGCGATTTTCAATTCCGCATTGCCATTCTCT
* ** *
4287462 CGTTGCAATAGTCAATTCCGCGTTGC
1 CGTTGCGATTTTCAATTCCGCATTGC
4287488 GATAGTCATT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
32 20 0.43
33 13 0.28
34 14 0.30
ACGTcount: A:0.15, C:0.25, G:0.18, T:0.41
Consensus pattern (34 bp):
CGTTGCGATTTTCAATTCCGCATTGCCATTCTCT
Found at i:4287521 original size:19 final size:21
Alignment explanation
Indices: 4287482--4287530 Score: 84
Period size: 20 Copynumber: 2.4 Consensus size: 21
4287472 GTCAATTCCG
4287482 CGTTGCGATAGTCATTTTTGT
1 CGTTGCGATAGTCATTTTTGT
4287503 -GTTGCGATAGTCA-TTTTGT
1 CGTTGCGATAGTCATTTTTGT
4287522 CGTTGCGAT
1 CGTTGCGAT
4287531 TTTAAGTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.14, C:0.14, G:0.27, T:0.45
Consensus pattern (21 bp):
CGTTGCGATAGTCATTTTTGT
Found at i:4289477 original size:20 final size:20
Alignment explanation
Indices: 4289452--4289500 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
4289442 CAACGAGAGA
*
4289452 ATCGCAATGCAAAAATAACT
1 ATCGCAACGCAAAAATAACT
*
4289472 ATCGCAACGCAAAAATGACT
1 ATCGCAACGCAAAAATAACT
*
4289492 ATCGAAACG
1 ATCGCAACG
4289501 AAAGAATCGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.47, C:0.22, G:0.14, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCAAAAATAACT
Found at i:4289638 original size:18 final size:19
Alignment explanation
Indices: 4289596--4289642 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
4289586 TCAATTCTCT
4289596 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
4289616 CGTTGCGATAGTCA-TTCG
1 CGTTGCGATAGTCATTTCG
*
4289634 TGTTGCGAT
1 CGTTGCGAT
4289643 TTTAAGTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 12 0.46
20 14 0.54
ACGTcount: A:0.15, C:0.19, G:0.28, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:4290163 original size:21 final size:20
Alignment explanation
Indices: 4290137--4290206 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
4290127 CTGTCATCCC
4290137 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* **
4290158 TCAAGACG-CCCCTATCATCCC
1 TCAAGA-GTCCCCT-CCATCGT
*
4290179 TCAAGAGTCCCCTCCCACCGT
1 TCAAGAGTCCCCT-CCATCGT
4290200 TCAAGAG
1 TCAAGAG
4290207 GCCACTGTCA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
20 1 0.03
21 35 0.92
22 2 0.05
ACGTcount: A:0.24, C:0.41, G:0.14, T:0.20
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:4290218 original size:42 final size:42
Alignment explanation
Indices: 4290127--4290218 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
4290117 CCCGACTCAC
* *
4290127 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGACGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGACGCCA
* * *
4290169 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGACGCCA
4290211 CTGTCATC
1 CTGTCATC
4290219 GTTGAAGAGG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.22, C:0.42, G:0.14, T:0.22
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGACGCCA
Found at i:4291813 original size:19 final size:19
Alignment explanation
Indices: 4291798--4291834 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4291788 ATACGAAATG
4291798 AAAATCGCAACGCGAAACT
1 AAAATCGCAACGCGAAACT
*
4291817 AAAATCGTAACGCGAAAC
1 AAAATCGCAACGCGAAAC
4291835 CAATTCGCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACT
Found at i:4291862 original size:19 final size:19
Alignment explanation
Indices: 4291838--4291942 Score: 87
Period size: 20 Copynumber: 5.7 Consensus size: 19
4291828 GCGAAACCAA
4291838 TTCGCGTTGCGATTTT-AGT
1 TTCGCGTTGCGATTTTCA-T
4291857 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
4291876 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* **
4291891 -TCCCGTTGCGATAGTCATT
1 TTCGCGTTGCGATTTTCA-T
**
4291910 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATTTTCA-T
4291930 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
4291943 AGTCATTTCC
Statistics
Matches: 74, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
14 9 0.12
16 2 0.03
17 3 0.04
19 28 0.38
20 32 0.43
ACGTcount: A:0.12, C:0.22, G:0.24, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:4291958 original size:19 final size:20
Alignment explanation
Indices: 4291894--4291950 Score: 114
Period size: 20 Copynumber: 2.9 Consensus size: 20
4291884 GCGATTCTCC
4291894 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
4291914 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
4291934 CGTTGCGATAGTCATTT
1 CGTTGCGATAGTCATTT
4291951 CCTTTTGCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.19, G:0.25, T:0.40
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:4292539 original size:6 final size:6
Alignment explanation
Indices: 4292518--4292574 Score: 60
Period size: 6 Copynumber: 9.5 Consensus size: 6
4292508 ATTTATATTG
* * * * * *
4292518 AAATTC AAACTC AAATTG AAATTT AAATTC AAACTC AAATTG AAATTT
1 AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC
4292566 AAATTC AAA
1 AAATTC AAA
4292575 CTCCAATTAC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.53, C:0.12, G:0.04, T:0.32
Consensus pattern (6 bp):
AAATTC
Found at i:4292593 original size:24 final size:24
Alignment explanation
Indices: 4292518--4292582 Score: 121
Period size: 24 Copynumber: 2.7 Consensus size: 24
4292508 ATTTATATTG
4292518 AAATTCAAACTCAAATTGAAATTT
1 AAATTCAAACTCAAATTGAAATTT
4292542 AAATTCAAACTCAAATTGAAATTT
1 AAATTCAAACTCAAATTGAAATTT
*
4292566 AAATTCAAACTCCAATT
1 AAATTCAAACTCAAATT
4292583 ACATATAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.49, C:0.15, G:0.03, T:0.32
Consensus pattern (24 bp):
AAATTCAAACTCAAATTGAAATTT
Found at i:4296079 original size:20 final size:20
Alignment explanation
Indices: 4296054--4296268 Score: 234
Period size: 20 Copynumber: 10.8 Consensus size: 20
4296044 TGTTGCAATT
* *
4296054 TCAGAATCGTGTTGCGATAG
1 TCAGAATCGCGTTGCGAAAG
4296074 TCAGAATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
* *
4296094 TCAGCATCACGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
* * *
4296114 TCAGCATCACGTTGCAAAAG
1 TCAGAATCGCGTTGCGAAAG
* * * *
4296134 TCAGTATCTCGTTGCGATAT
1 TCAGAATCGCGTTGCGAAAG
* * *
4296154 TCAGAATCGTGTTACGATAG
1 TCAGAATCGCGTTGCGAAAG
*
4296174 TCAGCATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
* *
4296194 TCAGTATCGCGTTGCGATAG
1 TCAGAATCGCGTTGCGAAAG
4296214 TCAGAATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
* *
4296234 TCAGCATCACGTTGC-AATAG
1 TCAGAATCGCGTTGCGAA-AG
*
4296254 TCACAATCGCGTTGC
1 TCAGAATCGCGTTGC
4296269 AATTTTGTAT
Statistics
Matches: 166, Mismatches: 28, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
19 2 0.01
20 164 0.99
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.26
Consensus pattern (20 bp):
TCAGAATCGCGTTGCGAAAG
Found at i:4296136 original size:60 final size:60
Alignment explanation
Indices: 4296072--4296268 Score: 268
Period size: 60 Copynumber: 3.3 Consensus size: 60
4296062 GTGTTGCGAT
* * *
4296072 AGTCAGAATCGCGTTGCGAAAGTCAGCATCACGTTGCGAAAGTCAGCATCACGTTGCAAA
1 AGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGAAAGTCAGCATCACGTTGCAAA
* * * * * * * *
4296132 AGTCAGTATCTCGTTGCGATATTCAGAATCGTGTTACGATAGTCAGCATCGCGTTGCGAA
1 AGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGAAAGTCAGCATCACGTTGCAAA
* *
4296192 AGTCAGTATCGCGTTGCGATAGTCAGAATCGCGTTGCGAAAGTCAGCATCACGTTGCAAT
1 AGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGAAAGTCAGCATCACGTTGCAAA
*
4296252 AGTCACAATCGCGTTGC
1 AGTCAGAATCGCGTTGC
4296269 AATTTTGTAT
Statistics
Matches: 116, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 116 1.00
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.25
Consensus pattern (60 bp):
AGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGAAAGTCAGCATCACGTTGCAAA
Found at i:4296285 original size:21 final size:22
Alignment explanation
Indices: 4296259--4296301 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
4296249 AATAGTCACA
4296259 ATCGCGTTGCAATTT-TGTATT
1 ATCGCGTTGCAATTTATGTATT
*
4296280 ATCGCGTTGCGATTTATGTATT
1 ATCGCGTTGCAATTTATGTATT
4296302 CGCATTGCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.19, C:0.14, G:0.21, T:0.47
Consensus pattern (22 bp):
ATCGCGTTGCAATTTATGTATT
Found at i:4296332 original size:21 final size:21
Alignment explanation
Indices: 4296308--4296347 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4296298 TATTCGCATT
*
4296308 GCGAATAGGGAAAATCGCAAC
1 GCGAATACGGAAAATCGCAAC
*
4296329 GCGAATCCGGAAAATCGCA
1 GCGAATACGGAAAATCGCA
4296348 TTACGATAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.23, G:0.28, T:0.10
Consensus pattern (21 bp):
GCGAATACGGAAAATCGCAAC
Found at i:4309451 original size:19 final size:20
Alignment explanation
Indices: 4309422--4309459 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
4309412 TTGCAAAATA
4309422 GCTTGGTGCATCGATGCATG
1 GCTTGGTGCATCGATGCATG
4309442 GCTT-GTGCATCGATGCAT
1 GCTTGGTGCATCGATGCAT
4309460 CAATGCATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.16, C:0.21, G:0.32, T:0.32
Consensus pattern (20 bp):
GCTTGGTGCATCGATGCATG
Found at i:4309505 original size:64 final size:61
Alignment explanation
Indices: 4309381--4309538 Score: 178
Period size: 64 Copynumber: 2.5 Consensus size: 61
4309371 CGGTGCACCA
4309381 AGTGTGCATCGATGCATGAAATGCATTCGA-TTTGCAAAATAGCTTGGTGCATCGATGCATGG
1 AGTGTGCATCGATGCAT-AAATGCATTCGATTTTGCAAAATA-CTTGGTGCATCGATGCATGG
** *
4309443 CTTGTGCATCGATGCATCAATGCATTCGATGTTTTG-AAAATA-TTCAGAGTGCATCGATGCATG
1 AGTGTGCATCGATGCATAAATGCATTCGA--TTTTGCAAAATACTT--G-GTGCATCGATGCATG
4309506 G
61 G
* **
4309507 AGAGTGCATCGATGCATGGATGCATTCGATTT
1 AGTGTGCATCGATGCATAAATGCATTCGATTT
4309539 CAATTAATTC
Statistics
Matches: 82, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
61 13 0.16
62 18 0.22
63 7 0.09
64 44 0.54
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (61 bp):
AGTGTGCATCGATGCATAAATGCATTCGATTTTGCAAAATACTTGGTGCATCGATGCATGG
Done.