Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008893.1 Hibiscus syriacus cultivar Beakdansim tig00112159_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: 2797279
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 13
Found at i:2079937 original size:9 final size:9
Alignment explanation
Indices: 2079923--2079951 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2079913 TTCCGTTTGA
2079923 TTTTTTTC-
1 TTTTTTTCT
2079931 TTTTTTTCT
1 TTTTTTTCT
2079940 TTTTTTTCT
1 TTTTTTTCT
2079949 TTT
1 TTT
2079952 GATGAACTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:2081353 original size:32 final size:33
Alignment explanation
Indices: 2081272--2081356 Score: 109
Period size: 34 Copynumber: 2.6 Consensus size: 33
2081262 AATTGCACTA
* *
2081272 TGTACTTATACGCTTTCATTTCACTTTTGTACTG
1 TGTACTTATACGCTTGCATTTCACTTTTGCAC-G
* *
2081306 TGTACGTATACGCTTGCATTTCTCTTTTGCAC-
1 TGTACTTATACGCTTGCATTTCACTTTTGCACG
*
2081338 TGTACTTATATGCTTGCAT
1 TGTACTTATACGCTTGCAT
2081357 CTATTTTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 17 0.38
34 28 0.62
ACGTcount: A:0.18, C:0.21, G:0.14, T:0.47
Consensus pattern (33 bp):
TGTACTTATACGCTTGCATTTCACTTTTGCACG
Found at i:2082517 original size:15 final size:16
Alignment explanation
Indices: 2082490--2082519 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2082480 TTATTGTTTT
2082490 TAATATATAATTAAAA
1 TAATATATAATTAAAA
2082506 TAATAT-TAATTAAA
1 TAATATATAATTAAA
2082520 TGAAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATATATAATTAAAA
Found at i:2083518 original size:4 final size:4
Alignment explanation
Indices: 2083511--2083542 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
2083501 ATATACATAT
2083511 ATAA ATAA ATAA ATAA ATAA ATAA AT-A ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
2083543 AGGAATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:2085534 original size:84 final size:83
Alignment explanation
Indices: 2085159--2086040 Score: 785
Period size: 84 Copynumber: 10.7 Consensus size: 83
2085149 TTGAATATAA
* ** * *
2085159 TCGAACTCGAAGGTC--T-TTAGCAGATTGCCCTTCTCGACTTAAGTTATGATGCAAATGATGTA
1 TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
*
2085221 CCTTGGAGCTGAGCGTAG
66 CCTTCGAGCTGAGCGTAG
* ** * * * *
2085239 TCGAACTCGCAGGTCTTTGTTGATAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
* * *
2085304 CCCTCGAAGCTGAGTGTAA
66 CCTTCG-AGCTGAGCGTAG
* * * * *
2085323 TCGAACTCG-GGGTC--T-TTGGCAGATAACCCTTTTCGACTTAAGTTATACTGCAAATGATATT
1 TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
*
2085384 CCTT-GAAGCTGAGCATAG
66 CCTTCG-AGCTGAGCGTAG
* * * * *
2085402 TCGAACTCGAGGGTC--T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGTTGTAAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
* *
2085464 CCTTAGAGATGAGCGTAG
66 CCTTCGAGCTGAGCGTAG
* * * *
2085482 TCGAACTCGAAGGTATTTGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGTTGCAAATGATAT
1 TCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* *
2085547 GCCTTGGAGCTGAGCATAG
65 GCCTTCGAGCTGAGCGTAG
* * * * * * * *
2085566 TCGAACTCGAAGGTCTTTTCTTGACATATAACCC-TCTTAGCCTTGAGTTATGTTGTAAATGATG
1 TCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTC-TCGACTTAAGTTATGCTGCAAATGATG
* * *
2085630 TGCCCTCGAAGCTGAGTGTAA
64 TGCCTTCG-AGCTGAGCGTAG
* * * *
2085651 TCGAACTCGAAGGTC--T-TTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
* * * * *
2085713 TCATCGAATCTGAGTGTAA
66 CCTTCG-AGCTGAGCGTAG
* * * ** *
2085732 TCGAACTCAAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATATTACAAATGATGT
1 TCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
*
2085797 GCCTTTGAGCTGAGCGTAG
65 GCCTTCGAGCTGAGCGTAG
* ** * *** * * *
2085816 TCGAACTCGAAGGTCTTTCGGTAACAGATAACCATTCTATCCTTGAGTTATGTTGTAAATGATGT
1 TCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * * *
2085881 TCCCTCGAAGCTGAGTGTAA
65 GCCTTCG-AGCTGAGCGTAG
* * *
2085901 TCGAACTCGAGGGTC--T-TTGGCAGATAGCCC-TCATCGACTTAAGCTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTC-TCGACTTAAGTTATGCTGCAAATGATGT
*
2085962 GCCTTGGAGCTGAGCGTAG
65 GCCTTCGAGCTGAGCGTAG
* * *
2085981 TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGTCTTGAGTTATGCTGCAAATG
1 TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
2086041 TTGTCTTTAA
Statistics
Matches: 647, Mismatches: 131, Indels: 45
0.79 0.16 0.05
Matches are distributed among these distances:
79 20 0.03
80 150 0.23
81 104 0.16
82 6 0.01
83 80 0.12
84 194 0.30
85 93 0.14
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (83 bp):
TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
CCTTCGAGCTGAGCGTAG
Found at i:2085810 original size:165 final size:162
Alignment explanation
Indices: 2085156--2086040 Score: 857
Period size: 165 Copynumber: 5.4 Consensus size: 162
2085146 GAGTTGAATA
* ** * * *
2085156 TAATCGAACTCGAAGGTCTTTAGCAGATTGCCCTTCTCGACTTAAGTTATGATGCAAATGATGTA
1 TAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTT
* * ** * * * * *
2085221 CCTTGGAGCTGAGCGTAGTCGAACTCGCAGGTCTTTGTTGATAGATAACCCTTCTAGCCTTGAGT
66 CCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-TTGGCAGATAGCCCTTCTCGACTTAAGC
* * *
2085286 TATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
130 TATGTTGTAAATGATGTGCCTTCG-AGCTGAGCG
* * * * *
2085320 TAATCGAACTCG-GGGTCTTTGGCAGATAACCCTTTTCGACTTAAGTTATACTGCAAATGATATT
1 TAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTT
* *
2085384 CCTTGAAGCTGAGCATAGTCGAACTCGAGGGTC--TTTGGCAGATAGCCCTTCTCGACTTAAGCT
66 CCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTTGGCAGATAGCCCTTCTCGACTTAAGCT
* *
2085447 ATGTTGTAAATGATGTGCCTTAGAGATGAGCG
131 ATGTTGTAAATGATGTGCCTTCGAGCTGAGCG
* * * *
2085479 TAGTCGAACTCGAAGGTATTTGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGTTGCAAATGA
1 TAATCGAACTCGAAGG--TCT--TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGA
* * * * * * * * *
2085544 TATGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTTCTTGACATATAACCC-TCTTAGCC
62 TGTTCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTC-TTT-TTGGCAGATAGCCCTTC-TCGAC
* * * *
2085608 TTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTG
124 TTAAGCTATGTTGTAAATGATGTGCCTTCG-AGCTGAGCG
* * *
2085648 TAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTG
1 TAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT-
* * * * * *
2085713 TCATCGAATCTGAGTGTAATCGAACTCAAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAA
65 TCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTT--TTGGCAGATAGCCCTTCTCGACTTAA
* ** *
2085778 GCTATATTACAAATGATGTGCCTTTGAGCTGAGCG
128 GCTATGTTGTAAATGATGTGCCTTCGAGCTGAGCG
* * ** * * *
2085813 TAGTCGAACTCGAAGGTCTTTCGGTAACAGATAACCATTCTATCCTTGAGTTATGTTGTAAATGA
1 TAATCGAACTCGAAGGTCTTT-GG---CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGA
* * * *
2085878 TGTTCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC--TTTGGCAGATAGCCC-TCATCGACT
62 TGTT-CCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTTGGCAGATAGCCCTTC-TCGACT
* * *
2085940 TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCG
125 TAAGCTATGTTGTAAATGATGTGCCTTCGAGCTGAGCG
* * *
2085978 TAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGTCTTGAGTTATGCTGCAAATG
1 TAATCGAACTCGAAGGTC--T-TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATG
2086041 TTGTCTTTAA
Statistics
Matches: 602, Mismatches: 96, Indels: 46
0.81 0.13 0.06
Matches are distributed among these distances:
159 18 0.03
160 44 0.07
161 1 0.00
162 2 0.00
163 72 0.12
164 118 0.20
165 142 0.24
166 64 0.11
167 11 0.02
168 43 0.07
169 87 0.14
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (162 bp):
TAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTT
CCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTTGGCAGATAGCCCTTCTCGACTTAAGCT
ATGTTGTAAATGATGTGCCTTCGAGCTGAGCG
Found at i:2085828 original size:250 final size:247
Alignment explanation
Indices: 2085093--2086040 Score: 1045
Period size: 250 Copynumber: 3.8 Consensus size: 247
2085083 TCGACAATTA
* * * * *
2085093 TTGACAAATAACCCTTCTT-GCCTTGAGTTATGTTGTAAGCTTGATTTG-CCTCTG-AGTTGAAT
1 TTGACAGATAACCC-TCTTAGCCTTGAGTTATGTTGTAA--ATGATGTGCCCTC-GAAGCTGAGT
* * * *
2085155 ATAATCGAACTCGAAGGTCTTTAGCAGATTGCCCTTCTCGACTTAAGTTATGATGCAAATGATGT
62 ATAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* * * ** * *
2085220 ACCTTGGAGCTGAGCGTAGTCGAACTCGCAGGTCTTTGTTGATAGATAACCCTTCTAGCCTTGAG
127 GCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAG
* * * * * *
2085285 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG-GGGTC--T-
192 TTATGTTGCAAATGATGTGCCTTCG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTC
* * * * * ** * * * * * *
2085338 TTGGCAGATAACCCTTTTCGACTTAAGTTATACTGCAAATGATAT-TCCTTGAAGCTGAGCATAG
1 TTGACAGATAACCCTCTTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTATAA
* * *
2085402 TCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGTTGTAAATGATGTGCCT
66 TCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCT
* * *
2085467 T-AGAGATGAGCGTAGTCGAACTCGAAGGTATTTGGTTGGCAGATAACCCTTCTTGACTTAAGTT
131 TGA-AGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTAGACTTAAGTT
* * *
2085531 ATGTTGCAAATGATATGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTTC
194 ATGTTGCAAATGATGTGCCTTCGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTC
* *
2085586 TTGACATATAACCCTCTTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGACAGATAACCCTCTTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTATAA
* * * * *
2085651 TCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGTCA
66 TCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CC
* * * * * * * *
2085716 TCGAATCTGAGTGTAATCGAACTCAAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCT
130 TTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTAGACTTAAGTT
* * *
2085781 ATATTACAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTC
194 ATGTTGCAAATGATGTGCCTTCGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTC
* * * * * *
2085835 GGTAACAGATAACCAT-TCTATCCTTGAGTTATGTTGTAAATGATGTTCCCTCGAAGCTGAGTGT
1 -TTGACAGATAACCCTCT-TAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTAT
*
2085899 AATCGAACTCGAGGGTCTTTGGCAGATAGCCC-TCATCGACTTAAGCTATGCTGCAAATGATGTG
64 AATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTC-TCGACTTAAGCTATGCTGCAAATGATGTG
* * *
2085963 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGTCTTGAGT
128 CCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGT
*
2086028 TATGCTGCAAATG
193 TATGTTGCAAATG
2086041 TTGTCTTTAA
Statistics
Matches: 583, Mismatches: 104, Indels: 29
0.81 0.15 0.04
Matches are distributed among these distances:
242 1 0.00
243 120 0.21
244 50 0.09
245 26 0.04
247 1 0.00
248 69 0.12
249 105 0.18
250 210 0.36
251 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.32
Consensus pattern (247 bp):
TTGACAGATAACCCTCTTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTATAA
TCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCT
TGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTAT
GTTGCAAATGATGTGCCTTCGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTC
Found at i:2090777 original size:20 final size:20
Alignment explanation
Indices: 2090754--2090810 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
2090744 AAAAAGGAAA
2090754 AATATGAGATAAAAAATAAC
1 AATATGAGATAAAAAATAAC
2090774 AATAT-A-ATAATAAAA-AAC
1 AATATGAGATAA-AAAATAAC
*
2090792 AA-AGAGAGATAAAAAATAA
1 AATA-TGAGATAAAAAATAA
2090811 TAATGAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
17 1 0.03
18 9 0.29
19 10 0.32
20 11 0.35
ACGTcount: A:0.70, C:0.04, G:0.09, T:0.18
Consensus pattern (20 bp):
AATATGAGATAAAAAATAAC
Found at i:2090830 original size:39 final size:38
Alignment explanation
Indices: 2090759--2090833 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
2090749 GGAAAAATAT
* *
2090759 GAGATAAAAAATAACAATATAATAATAAAAAACAAAGA
1 GAGATAAAAAATAACAATAAAATAAGAAAAAACAAAGA
* * *
2090797 GAGATAAAAAATAATAATGAAAATACGATAAAACAAA
1 GAGATAAAAAATAACAAT-AAAATAAGAAAAAACAAA
2090834 CCAATATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
38 17 0.55
39 14 0.45
ACGTcount: A:0.69, C:0.05, G:0.09, T:0.16
Consensus pattern (38 bp):
GAGATAAAAAATAACAATAAAATAAGAAAAAACAAAGA
Found at i:2090904 original size:7 final size:7
Alignment explanation
Indices: 2090864--2090907 Score: 61
Period size: 7 Copynumber: 6.1 Consensus size: 7
2090854 AAATAAAAAT
*
2090864 AAATAAA
1 AAATGAA
2090871 AAATGAA
1 AAATGAA
*
2090878 ATATTGAA
1 A-AATGAA
2090886 AAATGAA
1 AAATGAA
2090893 AAATGAA
1 AAATGAA
2090900 AAATGAA
1 AAATGAA
2090907 A
1 A
2090908 CAATTGTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
7 27 0.82
8 6 0.18
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.18
Consensus pattern (7 bp):
AAATGAA
Found at i:2090976 original size:4 final size:4
Alignment explanation
Indices: 2090969--2090993 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2090959 ATATACATAT
2090969 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
2090994 AGATTTAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:2097714 original size:20 final size:21
Alignment explanation
Indices: 2097689--2097740 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2097679 TTTTCCCAAT
*
2097689 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
2097709 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
2097730 TCGCAATGCGA
1 TCGCAATGCGA
2097741 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:2097775 original size:21 final size:20
Alignment explanation
Indices: 2097726--2097776 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2097716 GCGAATTGGG
* *
2097726 AAAATCGCAATGCGATACTG
1 AAAATCGCAATGCGATAATA
**
2097746 ACTATCGCAATGCGATAATAA
1 AAAATCGCAATGCGATAAT-A
2097767 AAAATCGCAA
1 AAAATCGCAA
2097777 CGAGATACTT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.20
Consensus pattern (20 bp):
AAAATCGCAATGCGATAATA
Found at i:2097796 original size:20 final size:21
Alignment explanation
Indices: 2097771--2097822 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
2097761 TAATAAAAAA
*
2097771 TCGCAACGA-GATACTTACTT
1 TCGCAACGACGATACTGACTT
*
2097791 TCGCAAC-ACGATACTGATTT
1 TCGCAACGACGATACTGACTT
2097811 TCGCAACG-CGAT
1 TCGCAACGACGAT
2097823 TTACTTAGCG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (21 bp):
TCGCAACGACGATACTGACTT
Found at i:2097803 original size:41 final size:41
Alignment explanation
Indices: 2097726--2097803 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
2097716 GCGAATTGGG
* * **
2097726 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
* *
2097767 AAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATA
2097804 CTGATTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
Found at i:2098385 original size:19 final size:19
Alignment explanation
Indices: 2098342--2098406 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
2098332 CGAGAATGAG
* *
2098342 AATCGCAACGCGGAAATGAC
1 AATCGCAACGC-GAAATAAA
*
2098362 TATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
**
2098381 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAATAAA
2098400 AATCGCA
1 AATCGCA
2098407 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 29 0.74
20 10 0.26
ACGTcount: A:0.45, C:0.26, G:0.18, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:2098424 original size:19 final size:19
Alignment explanation
Indices: 2098402--2098585 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
2098392 GAAACCAAAA
*
2098402 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2098421 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
2098440 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
2098459 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
2098479 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
2098495 T-G-GTCGCGATAGTCA-T
1 TCGCGTTGCGATTTTCATT
2098511 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
2098525 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
2098544 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
2098564 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
2098584 TC
1 TC
2098586 AACCAAAAGA
Statistics
Matches: 138, Mismatches: 15, Indels: 24
0.78 0.08 0.14
Matches are distributed among these distances:
14 20 0.14
15 1 0.01
16 6 0.04
17 1 0.01
18 6 0.04
19 54 0.39
20 49 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2098479 original size:39 final size:38
Alignment explanation
Indices: 2098402--2098491 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
2098392 GAAACCAAAA
* *
2098402 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
2098440 TCGCGTTGCGATTTTAATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGC-GTTGCGATTTTCATT
2098479 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2098492 GTCTGGTCGC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 21 0.43
39 28 0.57
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
Found at i:2098519 original size:32 final size:33
Alignment explanation
Indices: 2098474--2098560 Score: 131
Period size: 32 Copynumber: 2.6 Consensus size: 33
2098464 GTTGCGATTT
* *
2098474 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
2098507 TCA-TTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
2098539 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
2098561 ATTATCTCGT
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
32 29 0.59
33 5 0.10
34 15 0.31
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.38
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:2098562 original size:20 final size:20
Alignment explanation
Indices: 2098528--2098585 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
2098518 GCGATTCTCT
**
2098528 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
2098548 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
2098568 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
2098586 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:2100639 original size:42 final size:42
Alignment explanation
Indices: 2100579--2100701 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
2100569 GCCCGACTCG
* * *
2100579 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
2100621 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
2100663 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
2100702 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:2100659 original size:21 final size:21
Alignment explanation
Indices: 2100635--2100701 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2100625 TCATTCCTCG
2100635 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
2100656 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
2100677 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
2100698 AGAG
1 AGAG
2100702 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:2102074 original size:14 final size:14
Alignment explanation
Indices: 2102055--2102090 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2102045 ATTGTTTAAT
2102055 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
2102069 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
2102083 TGATTTGT
1 TGATTTGT
2102091 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:2102257 original size:19 final size:19
Alignment explanation
Indices: 2102235--2102352 Score: 67
Period size: 19 Copynumber: 6.7 Consensus size: 19
2102225 CGAAATTAAA
2102235 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
2102254 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
2102269 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
2102287 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
2102302 -TCTCGTTACGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
2102320 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
2102339 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
2102353 GGACATTAAG
Statistics
Matches: 71, Mismatches: 17, Indels: 21
0.65 0.16 0.19
Matches are distributed among these distances:
14 16 0.23
16 6 0.08
17 6 0.08
19 33 0.46
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:2102281 original size:33 final size:33
Alignment explanation
Indices: 2102239--2102332 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
2102229 ATTAAATTCG
2102239 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
2102272 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
2102305 CGTTACGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2102333 AGTAATTTCC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:2105224 original size:31 final size:31
Alignment explanation
Indices: 2105186--2105341 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
2105176 CCCGAAGGAC
* * *
2105186 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
2105217 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
2105248 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2105279 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2105310 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2105341 C
1 C
2105342 CCTCGACCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:2106140 original size:21 final size:21
Alignment explanation
Indices: 2106116--2106160 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2106106 TCTTGTTCGT
* *
2106116 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2106137 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2106158 TTG
1 TTG
2106161 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:2107019 original size:12 final size:12
Alignment explanation
Indices: 2107002--2107026 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2106992 TCTTCGGGGA
2107002 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2107014 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2107026 C
1 C
2107027 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2108513 original size:14 final size:14
Alignment explanation
Indices: 2108494--2108530 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2108484 CATCAATTAA
2108494 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2108508 ACAAATCATCTTTT
1 ACAAATCAACATTT
2108522 ACAAATCAA
1 ACAAATCAA
2108531 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2108831 original size:19 final size:19
Alignment explanation
Indices: 2108807--2108847 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2108797 CAATGGACAC
2108807 TTTCATAACGCATTGCGAT
1 TTTCATAACGCATTGCGAT
** *
2108826 TTTCATTTCGCGTTGCGAT
1 TTTCATAACGCATTGCGAT
2108845 TTT
1 TTT
2108848 GTCGTTGCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (19 bp):
TTTCATAACGCATTGCGAT
Found at i:2108855 original size:14 final size:14
Alignment explanation
Indices: 2108836--2108893 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2108826 TTTCATTTCG
2108836 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2108850 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
2108866 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
2108882 CGTTGCGATTTT
1 CGTTGCGATTTT
2108894 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2108900 original size:33 final size:33
Alignment explanation
Indices: 2108819--2108909 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
2108809 TCATAACGCA
2108819 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
2108852 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
2108884 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
2108910 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:2108928 original size:20 final size:19
Alignment explanation
Indices: 2108894--2108948 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
2108884 TTGCGATTTT
*
2108894 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
2108913 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
2108933 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
2108949 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:2109447 original size:18 final size:18
Alignment explanation
Indices: 2109421--2109465 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2109411 GTCGATCAGA
*
2109421 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
2109439 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
2109457 TGATGGCTC
1 TGATGGCTC
2109466 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:2110809 original size:20 final size:20
Alignment explanation
Indices: 2110784--2110821 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2110774 AATAGTTTCT
2110784 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
2110804 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
2110822 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:2111110 original size:22 final size:22
Alignment explanation
Indices: 2111085--2111128 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2111075 GATTTAGATA
2111085 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
2111107 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
2111129 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:2111341 original size:20 final size:20
Alignment explanation
Indices: 2111316--2111368 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2111306 GATTATGTAT
*
2111316 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
2111336 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
2111356 TATCTCGTTGCGA
1 TATCGCGTTGCGA
2111369 TTTTTTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:2111403 original size:20 final size:20
Alignment explanation
Indices: 2111296--2111411 Score: 81
Period size: 20 Copynumber: 5.7 Consensus size: 20
2111286 CGCTTTGAAA
*
2111296 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
2111317 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
2111337 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
2111357 ATCTCGTTGCGATTTTTTTATT
1 ATCGCATTGCGA--TAGTCAGT
2111379 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
2111399 ATCGCATTGCGAT
1 ATCGCATTGCGAT
2111412 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 11 0.14
22 13 0.17
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:2111444 original size:20 final size:20
Alignment explanation
Indices: 2111400--2111492 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
2111390 ATAGTCAGTA
* **
2111400 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
2111421 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
2111441 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
2111462 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
2111482 TCGCATTGCGA
1 TCGCATTGCGA
2111493 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:2111445 original size:41 final size:41
Alignment explanation
Indices: 2111400--2111495 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
2111390 ATAGTCAGTA
*
2111400 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
2111441 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
2111482 TCGCATTGCGAATT
1 TCGCATTGCGAATT
2111496 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:2111899 original size:58 final size:58
Alignment explanation
Indices: 2111837--2111972 Score: 166
Period size: 58 Copynumber: 2.3 Consensus size: 58
2111827 ATCTCATACG
*
2111837 TTTTTAAATTATGAATTTCATTTTAAATT-ATTTTCTAAACTTTTGAACATTTCAATTT
1 TTTTTAAATTATGAATTTCATTTTAAATTAATTCTC-AAACTTTTGAACATTTCAATTT
* * * * *
2111895 TTTTTAATTTATGATTTTTATTTTAAATTAATTCTCAAACTTTTGGATATTTCAATTT
1 TTTTTAAATTATGAATTTCATTTTAAATTAATTCTCAAACTTTTGAACATTTCAATTT
* *
2111953 TATTCTCAAATTATAAATTT
1 T-TT-TTAAATTATGAATTT
2111973 TTCAGACTTT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
58 47 0.72
59 7 0.11
60 11 0.17
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (58 bp):
TTTTTAAATTATGAATTTCATTTTAAATTAATTCTCAAACTTTTGAACATTTCAATTT
Found at i:2126618 original size:22 final size:22
Alignment explanation
Indices: 2126593--2126636 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2126583 TATGTTAATA
2126593 ATCCATAGAATACACATTGTTC
1 ATCCATAGAATACACATTGTTC
2126615 ATCCATAGAATACACATTGTTC
1 ATCCATAGAATACACATTGTTC
2126637 GTGATTGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.32
Consensus pattern (22 bp):
ATCCATAGAATACACATTGTTC
Found at i:2132900 original size:21 final size:21
Alignment explanation
Indices: 2132854--2132907 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
2132844 AATTTAGACT
*
2132854 ATCGCATTGCGATTTTTCAAA
1 ATCGCATTGCGATTTTACAAA
* * *
2132875 TTCGCGTTGCGATTTTAGAAA
1 ATCGCATTGCGATTTTACAAA
*
2132896 ATCGCAATGCGA
1 ATCGCATTGCGA
2132908 ATATGTAAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (21 bp):
ATCGCATTGCGATTTTACAAA
Found at i:2132948 original size:20 final size:20
Alignment explanation
Indices: 2132925--2132989 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
2132915 AATCGTAACA
2132925 CGATTCTGACTATCGCAACG
1 CGATTCTGACTATCGCAACG
* **
2132945 CGATAATAT-AAAATCGCAACG
1 CGAT--TCTGACTATCGCAACG
*
2132966 CGATTCTGACTATCGCAATG
1 CGATTCTGACTATCGCAACG
2132986 CGAT
1 CGAT
2132990 AATACAAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
19 2 0.06
20 17 0.49
21 14 0.40
22 2 0.06
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
CGATTCTGACTATCGCAACG
Found at i:2132959 original size:41 final size:41
Alignment explanation
Indices: 2132914--2133000 Score: 138
Period size: 41 Copynumber: 2.1 Consensus size: 41
2132904 GCGAATATGT
* *
2132914 AAATCGTAACACGATTCTGACTATCGCAACGCGATAATATA
1 AAATCGCAACACGATTCTGACTATCGCAACGCGATAATACA
* *
2132955 AAATCGCAACGCGATTCTGACTATCGCAATGCGATAATACA
1 AAATCGCAACACGATTCTGACTATCGCAACGCGATAATACA
2132996 AAATC
1 AAATC
2133001 ACAATGCGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.23
Consensus pattern (41 bp):
AAATCGCAACACGATTCTGACTATCGCAACGCGATAATACA
Found at i:2133010 original size:41 final size:41
Alignment explanation
Indices: 2132925--2133011 Score: 138
Period size: 41 Copynumber: 2.1 Consensus size: 41
2132915 AATCGTAACA
* *
2132925 CGATTCTGACTATCGCAACGCGATAATATAAAATCGCAACG
1 CGATTCTGACTATCGCAACGCGATAATACAAAATCACAACG
* *
2132966 CGATTCTGACTATCGCAATGCGATAATACAAAATCACAATG
1 CGATTCTGACTATCGCAACGCGATAATACAAAATCACAACG
2133007 CGATT
1 CGATT
2133012 TTTCAAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (41 bp):
CGATTCTGACTATCGCAACGCGATAATACAAAATCACAACG
Found at i:2133508 original size:19 final size:19
Alignment explanation
Indices: 2133484--2133592 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 19
2133474 TTATTTTGGA
2133484 TTTTTCACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
2133503 TTTTTCACTATCGCAACAAAAC
1 TTTTTCACTATCGCAAC---AC
**
2133525 GTTTTTCAAACGCTCGCAACAC
1 -TTTTTC--ACTATCGCAACAC
* * *
2133547 ATTTTAACTATTGCAACAC
1 TTTTTCACTATCGCAACAC
* * *
2133566 ATTTTAACTATCACAACAC
1 TTTTTCACTATCGCAACAC
2133585 ATTTTTCA
1 -TTTTTCA
2133593 AAATCGCGTT
Statistics
Matches: 72, Mismatches: 11, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
19 44 0.61
20 5 0.07
21 4 0.06
22 4 0.06
23 6 0.08
25 9 0.12
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.35
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:2143445 original size:5 final size:5
Alignment explanation
Indices: 2143435--2143459 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2143425 AATAAAAATT
2143435 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
2143460 AGCATCTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:2154084 original size:2 final size:2
Alignment explanation
Indices: 2154077--2154115 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2154067 TCTGGCTTAA
2154077 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2154116 AACTCATCTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2154576 original size:28 final size:28
Alignment explanation
Indices: 2154541--2154597 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 28
2154531 TAAAACCCTA
2154541 AATTATAAACAT-TAAACCCTAAA-CCAT
1 AATTATAAA-ATCTAAACCCTAAATCCAT
2154568 AATTCATAAAATCTAAACCCTAAATCCAT
1 AATT-ATAAAATCTAAACCCTAAATCCAT
2154597 A
1 A
2154598 TTTTAGGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 6 0.22
28 16 0.59
29 5 0.19
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (28 bp):
AATTATAAAATCTAAACCCTAAATCCAT
Found at i:2158908 original size:30 final size:30
Alignment explanation
Indices: 2158874--2158968 Score: 190
Period size: 30 Copynumber: 3.2 Consensus size: 30
2158864 GAATAAATTG
2158874 CTAAAACAACCAAATCTGATAATTTAGGTA
1 CTAAAACAACCAAATCTGATAATTTAGGTA
2158904 CTAAAACAACCAAATCTGATAATTTAGGTA
1 CTAAAACAACCAAATCTGATAATTTAGGTA
2158934 CTAAAACAACCAAATCTGATAATTTAGGTA
1 CTAAAACAACCAAATCTGATAATTTAGGTA
2158964 CTAAA
1 CTAAA
2158969 CACATGATTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.47, C:0.17, G:0.09, T:0.26
Consensus pattern (30 bp):
CTAAAACAACCAAATCTGATAATTTAGGTA
Found at i:2161231 original size:23 final size:22
Alignment explanation
Indices: 2161205--2161268 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
2161195 CAGCTCATAT
2161205 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* * *
2161228 AATTGTACACGAGTGCCGCGTAG
1 AATTGCAC-CTAGTGCCACGTAG
2161251 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
2161269 TGTAATAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
22 1 0.03
23 31 0.94
24 1 0.03
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:2161455 original size:103 final size:103
Alignment explanation
Indices: 2161284--2161501 Score: 418
Period size: 103 Copynumber: 2.1 Consensus size: 103
2161274 TAATGTCCAT
2161284 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
2161349 GACCTCACACATGTTCCAAAGAATAAATATATGTCCCG
66 GACCTCACACATATTCCAAAGAATAAATATATGTCCCG
2161387 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
2161452 GACCTCACACATATTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATATTCCAAAGAATAAATATATGTCCCG
2161490 AAGGACCACATA
1 AAGGACCACATA
2161502 GACCCTCTAC
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 113 1.00
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.24
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACCTCACACATATTCCAAAGAATAAATATATGTCCCG
Found at i:2162012 original size:20 final size:20
Alignment explanation
Indices: 2161984--2162022 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2161974 CTTTTATTAT
*
2161984 GGGGAATCGTTTCCCCCCTG
1 GGGGAATCGATTCCCCCCTG
*
2162004 GGGGTATCGATTCCCCCCT
1 GGGGAATCGATTCCCCCCT
2162023 AGCATTCTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.10, C:0.36, G:0.28, T:0.26
Consensus pattern (20 bp):
GGGGAATCGATTCCCCCCTG
Found at i:2168194 original size:23 final size:23
Alignment explanation
Indices: 2168134--2168195 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
2168124 GCTCATATAG
2168134 TTGCACC-TAAGTGCCACGTAGAA
1 TTGCACCGT-AGTGCCACGTAGAA
* * *
2168157 TTGCACCGGAATGCCGCGTAGAA
1 TTGCACCGTAGTGCCACGTAGAA
2168180 TTGCACCGTAGTGCCA
1 TTGCACCGTAGTGCCA
2168196 TGTAATAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.26, C:0.27, G:0.26, T:0.21
Consensus pattern (23 bp):
TTGCACCGTAGTGCCACGTAGAA
Found at i:2168382 original size:103 final size:103
Alignment explanation
Indices: 2168214--2168428 Score: 378
Period size: 103 Copynumber: 2.1 Consensus size: 103
2168204 TGTCCATAAG
*
2168214 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATCAAGTATGTGTCTCACCAGAC
*
2168279 CTCACACATGTTCCAAAGAATACATATATGTCTCGAA-
66 CTCACACATGTTCCAAAGAATACATATATGTCCCGAAT
*
2168316 GAACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATCAAGTATGTGTCTCACTAGA
1 G-ACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATCAAGTATGTGTCTCACCAGA
*
2168381 CCTCACACATGTTCCAAATAATACATATATGTCCCGAAT
65 CCTCACACATGTTCCAAAGAATACATATATGTCCCGAAT
2168420 GACCACATA
1 GACCACATA
2168429 GACCCTCTAT
Statistics
Matches: 107, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
102 1 0.01
103 105 0.98
104 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.27
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATCAAGTATGTGTCTCACCAGAC
CTCACACATGTTCCAAAGAATACATATATGTCCCGAAT
Found at i:2168941 original size:20 final size:20
Alignment explanation
Indices: 2168913--2168951 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2168903 TTTTTATTAT
*
2168913 GGGGAATCGGTTCCCCCCTG
1 GGGGAATCGATTCCCCCCTG
*
2168933 GGGGTATCGATTCCCCCCT
1 GGGGAATCGATTCCCCCCT
2168952 AGCATTCTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.10, C:0.36, G:0.31, T:0.23
Consensus pattern (20 bp):
GGGGAATCGATTCCCCCCTG
Found at i:2169872 original size:2 final size:2
Alignment explanation
Indices: 2169865--2169918 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
2169855 AAGAACTAAA
2169865 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
2169907 AT AT AT AT AT AT
1 AT AT AT AT AT AT
2169919 TCATTATCTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2170689 original size:3 final size:3
Alignment explanation
Indices: 2170681--2170715 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2170671 AATTTATAAT
2170681 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2170716 TCTACATGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2173461 original size:10 final size:10
Alignment explanation
Indices: 2173446--2173475 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2173436 TCTCATATAA
2173446 TTTTTATTTT
1 TTTTTATTTT
2173456 TTTTTA-TTT
1 TTTTTATTTT
2173465 TTTTTATTTT
1 TTTTTATTTT
2173475 T
1 T
2173476 ACTTAATCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTATTTT
Found at i:2173465 original size:9 final size:9
Alignment explanation
Indices: 2173446--2173475 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
2173436 TCTCATATAA
2173446 TTTTTATTTT
1 TTTTTA-TTT
2173456 TTTTTATTT
1 TTTTTATTT
2173465 TTTTTATTT
1 TTTTTATTT
2173474 TT
1 TT
2173476 ACTTAATCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 14 0.70
10 6 0.30
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTATTT
Found at i:2181995 original size:16 final size:17
Alignment explanation
Indices: 2181964--2181996 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2181954 CTATGAGAAT
2181964 TTACATGAACTATGTGA
1 TTACATGAACTATGTGA
*
2181981 TTACATGTA-TATGTGA
1 TTACATGAACTATGTGA
2181997 ATGAAGTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.39
Consensus pattern (17 bp):
TTACATGAACTATGTGA
Found at i:2182289 original size:23 final size:23
Alignment explanation
Indices: 2182256--2182323 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
2182246 CATATTATAT
2182256 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
2182279 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
2182302 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
2182324 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:2194114 original size:3 final size:3
Alignment explanation
Indices: 2194106--2194145 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
2194096 ATGTCTACAC
*
2194106 TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2194146 CTCTTTGTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2194620 original size:20 final size:20
Alignment explanation
Indices: 2194595--2194632 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2194585 TTTGGTTCAC
* *
2194595 GGAATATAAGATTACCAGTA
1 GGAATAAAAAATTACCAGTA
2194615 GGAATAAAAAATTACCAG
1 GGAATAAAAAATTACCAG
2194633 GGAATAGGAT
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:0.50, C:0.11, G:0.18, T:0.21
Consensus pattern (20 bp):
GGAATAAAAAATTACCAGTA
Found at i:2194636 original size:18 final size:19
Alignment explanation
Indices: 2194595--2194638 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
2194585 TTTGGTTCAC
* *
2194595 GGAATATAAGATTACCAGTA
1 GGAATAAAAAATTACCAG-A
2194615 GGAATAAAAAATTACCAG-
1 GGAATAAAAAATTACCAGA
2194633 GGAATA
1 GGAATA
2194639 GGATTGCTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
20 16 0.73
ACGTcount: A:0.50, C:0.09, G:0.20, T:0.20
Consensus pattern (19 bp):
GGAATAAAAAATTACCAGA
Found at i:2195452 original size:39 final size:39
Alignment explanation
Indices: 2195409--2195496 Score: 151
Period size: 39 Copynumber: 2.3 Consensus size: 39
2195399 ACTTAAATGG
2195409 TAATATTATTAATAATTTATTTTTGAAAAAATAAAATCT
1 TAATATTATTAATAATTTATTTTTGAAAAAATAAAATCT
* *
2195448 TAATATAATTAATAATTTATTTTTTAAAAAATAAAATCT
1 TAATATTATTAATAATTTATTTTTGAAAAAATAAAATCT
2195487 TAATA-TATTA
1 TAATATTATTA
2195497 TGTTTTCGAG
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 4 0.09
39 42 0.91
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (39 bp):
TAATATTATTAATAATTTATTTTTGAAAAAATAAAATCT
Found at i:2197309 original size:17 final size:18
Alignment explanation
Indices: 2197271--2197306 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2197261 TTAGTAAGCG
* *
2197271 AGAAATGGAGAGATTAAA
1 AGAAATGGAGAAACTAAA
2197289 AGAAATGGAGAAACTAAA
1 AGAAATGGAGAAACTAAA
2197307 GAAGCAGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.03, G:0.25, T:0.14
Consensus pattern (18 bp):
AGAAATGGAGAAACTAAA
Found at i:2208329 original size:20 final size:21
Alignment explanation
Indices: 2208299--2208349 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
2208289 TATTTCAATT
*
2208299 AAAATAGTATTTAAAA-AAATA
1 AAAATA-TATTCAAAATAAATA
*
2208320 AAAATATATTCAAAATAAGTA
1 AAAATATATTCAAAATAAATA
*
2208341 AATATATAT
1 AAAATATAT
2208350 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (21 bp):
AAAATATATTCAAAATAAATA
Found at i:2211557 original size:31 final size:31
Alignment explanation
Indices: 2211499--2211558 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
2211489 TAGTTGTATG
* **
2211499 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAACTTCAGTATTACAAAACTAA
2211530 AATTATTTAAACTTCAGTATTACAAAACT
1 AATTATTTAAACTTCAGTATTACAAAACT
2211559 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (31 bp):
AATTATTTAAACTTCAGTATTACAAAACTAA
Found at i:2223865 original size:387 final size:384
Alignment explanation
Indices: 2223128--2223898 Score: 1276
Period size: 387 Copynumber: 2.0 Consensus size: 384
2223118 ACTAAATGTA
*
2223128 TAATTTACCTTTTTTATATAAACGATGATAGAGTTTAACAATTTAATTACTATTTTAATATTATT
1 TAATTTACCCTTTTTATATAAACGATGATAGAGTTTAACAATTTAATTACTATTTTAATATTATT
*
2223193 GTGAAAATTATTTTGTAATAGTTCGATAAATTTTATAGTTTTCTATTGCATCATGGTGATCATTA
66 GTGAAAATTATTTTGTAATAGTTCGATAAATTTTATAGTTTTCTATTGCATCATGATGATCATTA
2223258 TATAAAAATTTGACAAAAAAATATCAGAGGCCTTGTACTTTAAAAAAAAATCAATACGACCATTA
131 TATAAAAATTTGACAAAAAAATATCAGAGGCCTTGTACTTTAAAAAAAAATCAATACGACCATTA
* * * *
2223323 TATTATTATTTTTTCAATGTGGCCCTTGAACTTAGAAAATAAACTCAATGTGGCCCTTTGACCAA
196 TATTATTATTTTTTCAATGTGGCCCTTCAACTTAGAAAACAAACTCAATGTGACCATTTGACCAA
* *
2223388 CATTTTTTTGTCGTTGACTGTTACGATGCCGACGTGACAGTTCACGTTGCTGATGTGGTGGTCTA
261 CATTTTTTTATCGTTGACTGTTACGATGCCAACGTGACAGTTCACGTTGCTGATGTGGTGGTCTA
*
2223453 CGATGTTGACATGGTAGTCCACGGTGGTTGATAATGTGACGAATAACACGACAGATGGG
326 CGATGTTGACATGGTAGTCCACGGTGGTTGATAATGTGACGAATAACACGAAAGATGGG
2223512 TAATTTACCCTTTTTATATAAAGTACGATGATAGAGTTTAACAATTTAATTACTATTTTAATATT
1 TAATTTACCCTTTTTATAT-AA--ACGATGATAGAGTTTAACAATTTAATTACTATTTTAATATT
*
2223577 ATTGTGAAAATTATTTTGTAATAGTTCGATAAATTTTATAGTTTTCTATTGTATCATGATGATCA
63 ATTGTGAAAATTATTTTGTAATAGTTCGATAAATTTTATAGTTTTCTATTGCATCATGATGATCA
* * * **
2223642 TTTTATAAAATTTTGACAAAAAAATATCAGAGGCCTTGTACTTTTAAAAAAAATCAATGTGA-CA
128 TTATATAAAAATTTGACAAAAAAATATCAGAGGCCTTGTACTTTAAAAAAAAATCAATACGACCA
* * *
2223706 TGTGTATTATTATTTTTTCAATGTGGTCCTTCAACTTA-AAAACCAAACTTAATGTGACCATTTG
193 T-TATATTATTATTTTTTCAATGTGGCCCTTCAACTTAGAAAA-CAAACTCAATGTGACCATTTG
* * **
2223770 ACCAACATTTTTTTATCTTTGACTGTTACGGTGCCAACGTGGTAGTTCACGTTGCTGATGTGGTG
256 ACCAACATTTTTTTATCGTTGACTGTTACGATGCCAACGTGACAGTTCACGTTGCTGATGTGGTG
*
2223835 GTCTACGATGTTGACATGGTAGTTCACGGTGGTTGATAATGTGACGAATAACACGAAAGATGGG
321 GTCTACGATGTTGACATGGTAGTCCACGGTGGTTGATAATGTGACGAATAACACGAAAGATGGG
2223899 CTAAATTGAT
Statistics
Matches: 359, Mismatches: 23, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
384 18 0.05
385 2 0.01
386 7 0.02
387 332 0.92
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (384 bp):
TAATTTACCCTTTTTATATAAACGATGATAGAGTTTAACAATTTAATTACTATTTTAATATTATT
GTGAAAATTATTTTGTAATAGTTCGATAAATTTTATAGTTTTCTATTGCATCATGATGATCATTA
TATAAAAATTTGACAAAAAAATATCAGAGGCCTTGTACTTTAAAAAAAAATCAATACGACCATTA
TATTATTATTTTTTCAATGTGGCCCTTCAACTTAGAAAACAAACTCAATGTGACCATTTGACCAA
CATTTTTTTATCGTTGACTGTTACGATGCCAACGTGACAGTTCACGTTGCTGATGTGGTGGTCTA
CGATGTTGACATGGTAGTCCACGGTGGTTGATAATGTGACGAATAACACGAAAGATGGG
Found at i:2224541 original size:19 final size:19
Alignment explanation
Indices: 2224517--2224555 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2224507 TAAGTGATAC
*
2224517 GAACGACGACATATTCACT
1 GAACGAAGACATATTCACT
2224536 GAACGAAGACATATTCACT
1 GAACGAAGACATATTCACT
2224555 G
1 G
2224556 CCCCGATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (19 bp):
GAACGAAGACATATTCACT
Found at i:2225157 original size:71 final size:71
Alignment explanation
Indices: 2225072--2225266 Score: 318
Period size: 71 Copynumber: 2.7 Consensus size: 71
2225062 TTTTGGCCCC
* * * * *
2225072 TAATTTTATTTTGAAACATTTTGACCTCTAATGTTCTATTTTAAGGTAAAAAAGCCCCTACTATT
1 TAATTTTCTTTTGAAACATTTTAAACTCTAATGTTCTATTTTAGGGTAAAAAAGACCCTACTATT
2225137 TGACCA
66 TGACCA
* *
2225143 TAATTTTCTTTTGAAATATTTTAAACTCTAATGTTCTATTTTAGGGTAAAAAAGACTCTACTATT
1 TAATTTTCTTTTGAAACATTTTAAACTCTAATGTTCTATTTTAGGGTAAAAAAGACCCTACTATT
2225208 TGACCA
66 TGACCA
*
2225214 TAATTTTCTTTTGAAACATTTTTAACTCTAATGTTCTATTTTAGGGTAAAAAA
1 TAATTTTCTTTTGAAACATTTTAAACTCTAATGTTCTATTTTAGGGTAAAAAA
2225267 ATTCTACTAT
Statistics
Matches: 115, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 115 1.00
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (71 bp):
TAATTTTCTTTTGAAACATTTTAAACTCTAATGTTCTATTTTAGGGTAAAAAAGACCCTACTATT
TGACCA
Found at i:2225672 original size:21 final size:21
Alignment explanation
Indices: 2225555--2225692 Score: 59
Period size: 21 Copynumber: 6.7 Consensus size: 21
2225545 ACGCGAAATA
**
2225555 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
2225575 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
*
2225595 AAAATCGCAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* * ** *
2225616 AAAATCGCGATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* * **
2225637 ATATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
* * * *
2225658 ATAATCGCAACGCGAATAT-G
1 AAAATCGCAACGCGATTTTCC
2225678 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
2225693 ACACATAAAT
Statistics
Matches: 85, Mismatches: 29, Indels: 8
0.70 0.24 0.07
Matches are distributed among these distances:
19 1 0.01
20 38 0.45
21 44 0.52
22 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:2225754 original size:20 final size:20
Alignment explanation
Indices: 2225660--2226028 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
2225650 GATTTTCCAT
* ** *
2225660 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
2225680 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
2225700 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2225720 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
2225740 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
2225760 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2225780 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2225800 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
2225820 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2225840 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2225860 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2225880 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2225900 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
2225920 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2225940 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
2225960 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
2225980 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
2226000 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
2226020 AATCACAAC
1 AATCGCAAC
2226029 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:2226362 original size:19 final size:19
Alignment explanation
Indices: 2226272--2226354 Score: 104
Period size: 20 Copynumber: 4.6 Consensus size: 19
2226262 AAATTATAAA
2226272 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2226291 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
2226311 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
*
2226327 CG--TTACGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2226344 CGCATTGCGAT
1 CGCATTGCGAT
2226355 AGTCATTTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
14 5 0.09
16 7 0.13
17 7 0.13
19 16 0.30
20 19 0.35
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:2226480 original size:14 final size:14
Alignment explanation
Indices: 2226461--2226497 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2226451 CATCAATTAC
2226461 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2226475 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2226489 ACAAATCAA
1 ACAAATCAA
2226498 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2228496 original size:14 final size:14
Alignment explanation
Indices: 2228477--2228533 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2228467 GCGAAATTAA
*
2228477 AATCGCAACGACAG
1 AATCGCAACGAAAG
2228491 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
2228508 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
2228524 AATCGCAACG
1 AATCGCAACG
2228534 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:2228504 original size:33 final size:33
Alignment explanation
Indices: 2228458--2228550 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
2228448 GCGAAACCAA
* *
2228458 AATCGCAACGCGAAATTAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
2228491 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
2228524 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
2228551 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:2228515 original size:19 final size:19
Alignment explanation
Indices: 2228421--2228555 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
2228411 TAGTTTACTT
* *
2228421 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
2228441 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
2228460 TCGCAACGCGAAATTAAAA
1 TCGCAACGCGAAATGAAAA
*
2228479 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
2228493 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
2228512 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
2228526 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2228545 TCGCAATGCGA
1 TCGCAACGCGA
2228556 TTTTGGTTTC
Statistics
Matches: 96, Mismatches: 9, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
14 16 0.17
16 10 0.10
17 11 0.11
19 47 0.49
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2228573 original size:19 final size:19
Alignment explanation
Indices: 2228551--2228679 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2228541 AAAATCGCAA
2228551 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2228570 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
2228584 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2228603 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
2228617 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
2228636 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
2228655 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
2228675 TGCGA
1 TGCGA
2228680 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:2228593 original size:33 final size:33
Alignment explanation
Indices: 2228551--2228642 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
2228541 AAAATCGCAA
2228551 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
2228584 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
2228617 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
2228643 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:2229106 original size:92 final size:93
Alignment explanation
Indices: 2228723--2229287 Score: 1098
Period size: 93 Copynumber: 6.1 Consensus size: 93
2228713 TTGAATGGAT
2228723 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2228788 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
2228816 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2228881 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
2228909 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2228974 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
2229002 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
2229066 AGTTTAGCAGAATTGGCAGTAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
2229094 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2229158 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
2229186 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
2229251 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
2229279 AAATTTACT
1 AAATTTACT
2229288 AAGCAATCTA
Statistics
Matches: 468, Mismatches: 3, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
92 182 0.39
93 286 0.61
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:2231014 original size:14 final size:14
Alignment explanation
Indices: 2230995--2231084 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
2230985 TTGAAATGAA
2230995 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2231009 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
2231026 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
2231042 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2231061 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2231075 AATCGCAACG
1 AATCGCAACG
2231085 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2231032 original size:33 final size:33
Alignment explanation
Indices: 2230987--2231101 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
2230977 TCTTTTGGTT
2230987 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
2231020 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2231053 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2231086 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
2231102 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2231033 original size:19 final size:18
Alignment explanation
Indices: 2230994--2231106 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
2230984 GTTGAAATGA
2230994 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
2231009 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
2231026 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
2231042 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
2231059 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
2231075 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
2231092 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
2231107 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:2231137 original size:14 final size:14
Alignment explanation
Indices: 2231118--2231172 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2231108 TTTGGTTTCG
2231118 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2231132 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2231151 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2231165 CGTTGCGA
1 CGTTGCGA
2231173 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2231150 original size:33 final size:33
Alignment explanation
Indices: 2231102--2231172 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2231092 AAAATCGCAA
**
2231102 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2231135 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2231168 TGCGA
1 TGCGA
2231173 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:2231180 original size:33 final size:33
Alignment explanation
Indices: 2231113--2231194 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
2231103 GCGATTTTGG
***
2231113 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
2231146 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
2231179 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
2231195 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:2231199 original size:20 final size:20
Alignment explanation
Indices: 2231125--2231213 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
2231115 TCGCGTTGCG
2231125 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
2231145 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
2231158 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
2231178 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
2231198 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
2231214 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:2231335 original size:33 final size:33
Alignment explanation
Indices: 2231293--2231363 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2231283 AATACTAACT
*
2231293 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
2231326 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
2231359 TGAAA
1 TGAAA
2231364 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:2231596 original size:22 final size:22
Alignment explanation
Indices: 2231544--2231598 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
2231534 TGGTTGTGAG
**
2231544 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
2231566 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
2231588 GGATTTCTTCG
1 GGATTTCTTCG
2231599 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:2231769 original size:20 final size:20
Alignment explanation
Indices: 2231744--2231936 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
2231734 CTTTAAATAT
2231744 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2231764 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
2231786 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2231805 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
2231825 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
2231845 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2231865 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2231885 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
2231905 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
2231925 CGCGTTGCGATT
1 CGCGTTGCGATT
2231937 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2231931 original size:60 final size:60
Alignment explanation
Indices: 2231744--2231936 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
2231734 CTTTAAATAT
**
2231744 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
2231805 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
2231865 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
2231925 CGCGTTGCGATT
1 CGCGTTGCGATT
2231937 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:2232017 original size:20 final size:20
Alignment explanation
Indices: 2231992--2232043 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
2231982 AAGAATCGCG
*
2231992 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
2232012 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
2232032 TTGCGATTCTGG
1 TTGCGATTCTGG
2232044 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:2237149 original size:14 final size:15
Alignment explanation
Indices: 2237124--2237156 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
2237114 TACTTTTAAA
2237124 ATTTTAATTTTTTT-
1 ATTTTAATTTTTTTC
2237138 ATTTTAATTTTTTTC
1 ATTTTAATTTTTTTC
2237153 ATTT
1 ATTT
2237157 ATTTAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTTAATTTTTTTC
Found at i:2237167 original size:20 final size:18
Alignment explanation
Indices: 2237091--2237190 Score: 53
Period size: 20 Copynumber: 5.3 Consensus size: 18
2237081 AGTTTTTTTC
2237091 TTTTTTTATTTCATTT--A
1 TTTTTTTATTT-ATTTAAA
* * *
2237108 TTTTATTACTT-TTAAAA
1 TTTTTTTATTTATTTAAA
* *
2237125 TTTTAATTTTTTTATTTTAA
1 TTTT--TTTATTTATTTAAA
2237145 TTTTTTTCATTTATTTAATA
1 TTTTTTT-ATTTATTTAA-A
* *
2237165 TTTATTTATTATATCTAACA
1 TTTTTTTATT-TATTTAA-A
2237185 TTTTTT
1 TTTTTT
2237191 GACTATTTAG
Statistics
Matches: 61, Mismatches: 14, Indels: 13
0.69 0.16 0.15
Matches are distributed among these distances:
15 2 0.03
17 14 0.23
18 3 0.05
19 15 0.25
20 27 0.44
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTTTTATTTATTTAAA
Found at i:2237264 original size:12 final size:13
Alignment explanation
Indices: 2237242--2237270 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2237232 TGAATCGATG
2237242 TTTTAAATTTTAA
1 TTTTAAATTTTAA
2237255 TTTT-AATTTTAA
1 TTTTAAATTTTAA
2237267 TTTT
1 TTTT
2237271 CGCAATTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:2240950 original size:20 final size:17
Alignment explanation
Indices: 2240907--2240964 Score: 80
Period size: 17 Copynumber: 3.2 Consensus size: 17
2240897 CACAAAATAG
2240907 AATCACATGAATAATTA
1 AATCACATGAATAATTA
2240924 AATCACATGAATAATTA
1 AATCACATGAATAATTA
*
2240941 ATTTATCACATGAATAATCA
1 A---ATCACATGAATAATTA
2240961 AATC
1 AATC
2240965 TTTAATTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
17 21 0.57
20 16 0.43
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.31
Consensus pattern (17 bp):
AATCACATGAATAATTA
Found at i:2247287 original size:3 final size:3
Alignment explanation
Indices: 2247279--2247335 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
2247269 GACATGATTC
2247279 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2247327 ATT ATT ATT
1 ATT ATT ATT
2247336 TGAGTGAATG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2250191 original size:13 final size:14
Alignment explanation
Indices: 2250173--2250202 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2250163 AGTTGGACAA
2250173 TCTTCATATGCA-G
1 TCTTCATATGCACG
2250186 TCTTCATATGCACG
1 TCTTCATATGCACG
2250200 TCT
1 TCT
2250203 GTAATGGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.20, C:0.27, G:0.13, T:0.40
Consensus pattern (14 bp):
TCTTCATATGCACG
Found at i:2258921 original size:3 final size:3
Alignment explanation
Indices: 2258913--2258940 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2258903 ACTCTATCCT
2258913 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
2258941 AAGTCACTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2263505 original size:25 final size:25
Alignment explanation
Indices: 2263471--2263526 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
2263461 ATGGATTAGA
2263471 GAAATCCGGGAAAGATTATGCACTC
1 GAAATCCGGGAAAGATTATGCACTC
2263496 GAAATCCGGGAAAGATTATGCACTC
1 GAAATCCGGGAAAGATTATGCACTC
2263521 GAAATC
1 GAAATC
2263527 ACATCCATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.20
Consensus pattern (25 bp):
GAAATCCGGGAAAGATTATGCACTC
Found at i:2268334 original size:19 final size:18
Alignment explanation
Indices: 2268307--2268409 Score: 52
Period size: 19 Copynumber: 5.5 Consensus size: 18
2268297 TATATTAGAA
2268307 AATAATTATTAAATTTAT
1 AATAATTATTAAATTTAT
* *
2268325 CAATATTTA-T-GA-TTAT
1 -AATAATTATTAAATTTAT
**
2268341 AATTTTTATTAAACTATTAT
1 AATAATTATTAAA-T-TTAT
*
2268361 AA-AATTATCAATATATTAT
1 AATAATTATTAA-AT-TTAT
2268380 AAAATAATTATTAAATTTAT
1 --AATAATTATTAAATTTAT
*
2268400 CAATATTTAT
1 -AATAATTAT
2268410 GATTATAAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
15 7 0.11
16 5 0.08
17 2 0.03
18 1 0.02
19 27 0.42
20 11 0.17
21 4 0.06
22 8 0.12
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.49
Consensus pattern (18 bp):
AATAATTATTAAATTTAT
Found at i:2268360 original size:75 final size:75
Alignment explanation
Indices: 2268257--2268417 Score: 304
Period size: 75 Copynumber: 2.1 Consensus size: 75
2268247 TCGTTGTAAA
2268257 ATGATTATTAATTTTTATTAAACTATTATAAAATTATCAATATATTAGAAAATAATTATTAAATT
1 ATGATTA-TAATTTTTATTAAACTATTATAAAATTATCAATATATTAGAAAATAATTATTAAATT
2268322 TATCAATATTT
65 TATCAATATTT
*
2268333 ATGATTATAATTTTTATTAAACTATTATAAAATTATCAATATATTATAAAATAATTATTAAATTT
1 ATGATTATAATTTTTATTAAACTATTATAAAATTATCAATATATTAGAAAATAATTATTAAATTT
2268398 ATCAATATTT
66 ATCAATATTT
2268408 ATGATTATAA
1 ATGATTATAA
2268418 AAACATAATG
Statistics
Matches: 84, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
75 77 0.92
76 7 0.08
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (75 bp):
ATGATTATAATTTTTATTAAACTATTATAAAATTATCAATATATTAGAAAATAATTATTAAATTT
ATCAATATTT
Found at i:2271178 original size:30 final size:30
Alignment explanation
Indices: 2271142--2271198 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
2271132 TAATGCAAAA
2271142 ATTTATTACAAGCAAATCAAACCTTAATCG
1 ATTTATTACAAGCAAATCAAACCTTAATCG
* *
2271172 ATTTATTACAAGTAAATTAAACCTTAA
1 ATTTATTACAAGCAAATCAAACCTTAA
2271199 ACGGATAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.46, C:0.16, G:0.05, T:0.33
Consensus pattern (30 bp):
ATTTATTACAAGCAAATCAAACCTTAATCG
Found at i:2275065 original size:16 final size:16
Alignment explanation
Indices: 2275020--2275070 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
2275010 AGGATGTTGG
*
2275020 TTCAGATACTAAATGA
1 TTCAAATACTAAATGA
* *
2275036 TT-AAGTACTGAATGA
1 TTCAAATACTAAATGA
2275051 TTCAAATACTAAATGA
1 TTCAAATACTAAATGA
2275067 TTCA
1 TTCA
2275071 GAGACTTTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
15 12 0.41
16 17 0.59
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (16 bp):
TTCAAATACTAAATGA
Found at i:2275337 original size:28 final size:29
Alignment explanation
Indices: 2275306--2275368 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
2275296 TGGTATGTAT
** *
2275306 TTTATTTGTTTTTATTA-ATTTAGAGCAA
1 TTTATTTCCTTTTATTACATTTAGACCAA
*
2275334 TTTATTTCCTTTTATTAGCATTTTGACCAA
1 TTTATTTCCTTTTATTA-CATTTAGACCAA
2275364 TTTAT
1 TTTAT
2275369 AATAAAAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 15 0.52
30 14 0.48
ACGTcount: A:0.25, C:0.10, G:0.08, T:0.57
Consensus pattern (29 bp):
TTTATTTCCTTTTATTACATTTAGACCAA
Found at i:2284237 original size:17 final size:16
Alignment explanation
Indices: 2284217--2284252 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2284207 AAAAATTTGA
2284217 TTAGAAAAAAAATAAAT
1 TTAG-AAAAAAATAAAT
*
2284234 TTAGATAAAAATAAAT
1 TTAGAAAAAAATAAAT
2284250 TTA
1 TTA
2284253 ATGTTTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (16 bp):
TTAGAAAAAAATAAAT
Found at i:2289256 original size:19 final size:17
Alignment explanation
Indices: 2289223--2289258 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
2289213 AAAATTATTC
2289223 AAATTTAAATATTATAA
1 AAATTTAAATATTATAA
2289240 AAATATTAAAGTATTATAA
1 AAAT-TTAAA-TATTATAA
2289259 TATTTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 5 0.29
19 8 0.47
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
AAATTTAAATATTATAA
Found at i:2291534 original size:25 final size:24
Alignment explanation
Indices: 2291492--2291539 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
2291482 TTAAATGAAC
*
2291492 AAATAGAAATAATCAAGCCAAAAT
1 AAATAGAAATAATCAAGCAAAAAT
2291516 AAATAAGAAATAAAT-AAGCAAAAA
1 AAAT-AGAAAT-AATCAAGCAAAAA
2291540 GGGAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 14 0.67
26 3 0.14
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (24 bp):
AAATAGAAATAATCAAGCAAAAAT
Found at i:2299223 original size:2 final size:2
Alignment explanation
Indices: 2299216--2299242 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2299206 AATTGTTTAA
2299216 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
2299243 ATCTTTTTTG
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:2300464 original size:116 final size:116
Alignment explanation
Indices: 2300260--2300492 Score: 466
Period size: 116 Copynumber: 2.0 Consensus size: 116
2300250 TTTTTATCAA
2300260 TGATTATGAAATATAAGGACCAGATCATGAACAAATGAAGGGAAGGTGCTGATTTCGCAATTTGT
1 TGATTATGAAATATAAGGACCAGATCATGAACAAATGAAGGGAAGGTGCTGATTTCGCAATTTGT
2300325 AAAGGGGTCATTTCATAATTAGACCTTTTTGTTGAGCATGAGCAACAATGC
66 AAAGGGGTCATTTCATAATTAGACCTTTTTGTTGAGCATGAGCAACAATGC
2300376 TGATTATGAAATATAAGGACCAGATCATGAACAAATGAAGGGAAGGTGCTGATTTCGCAATTTGT
1 TGATTATGAAATATAAGGACCAGATCATGAACAAATGAAGGGAAGGTGCTGATTTCGCAATTTGT
2300441 AAAGGGGTCATTTCATAATTAGACCTTTTTGTTGAGCATGAGCAACAATGC
66 AAAGGGGTCATTTCATAATTAGACCTTTTTGTTGAGCATGAGCAACAATGC
2300492 T
1 T
2300493 TCAGCCTTCA
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 117 1.00
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (116 bp):
TGATTATGAAATATAAGGACCAGATCATGAACAAATGAAGGGAAGGTGCTGATTTCGCAATTTGT
AAAGGGGTCATTTCATAATTAGACCTTTTTGTTGAGCATGAGCAACAATGC
Found at i:2302398 original size:37 final size:38
Alignment explanation
Indices: 2302342--2302425 Score: 125
Period size: 38 Copynumber: 2.2 Consensus size: 38
2302332 TTTTTAAATC
* *
2302342 CACACACACCCATGTAGTTACA-TCTCAAATTCACACT
1 CACACTCACCCATGCAGTTACATTCTCAAATTCACACT
* *
2302379 CACACTCACCTATGCAGTTACATTCTCAAATTCACGCT
1 CACACTCACCCATGCAGTTACATTCTCAAATTCACACT
2302417 CACACTCAC
1 CACACTCAC
2302426 TATCTAATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
37 19 0.45
38 23 0.55
ACGTcount: A:0.32, C:0.37, G:0.06, T:0.25
Consensus pattern (38 bp):
CACACTCACCCATGCAGTTACATTCTCAAATTCACACT
Found at i:2304561 original size:31 final size:31
Alignment explanation
Indices: 2304502--2304562 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
2304492 ATAAAATTTT
**
2304502 AAACTTTATAAAAAAATCAATTTGACTCATA
1 AAACTTTATAAAAAAATCAATTAAACTCATA
* * *
2304533 AAACTTTCTAAAAGAGTCAATTAAACTCAT
1 AAACTTTATAAAAAAATCAATTAAACTCAT
2304563 TGACAATAGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (31 bp):
AAACTTTATAAAAAAATCAATTAAACTCATA
Found at i:2307276 original size:22 final size:22
Alignment explanation
Indices: 2307235--2307276 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2307225 TGGTAACCCT
*
2307235 ATAATTGACACACGTACTAAAA
1 ATAATTGACACACCTACTAAAA
2307257 ATAATTGTACACACCT-CTAA
1 ATAATTG-ACACACCTACTAA
2307277 TCAAGGCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.45, C:0.21, G:0.07, T:0.26
Consensus pattern (22 bp):
ATAATTGACACACCTACTAAAA
Found at i:2313630 original size:26 final size:24
Alignment explanation
Indices: 2313595--2313646 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 24
2313585 TCATTTGTAA
2313595 TTAATAATATAATATATATATGACTAT
1 TTAATAATAT-AT-TAT-TATGACTAT
*
2313622 TTAA-AATATATTATTATGATTAT
1 TTAATAATATATTATTATGACTAT
2313645 TT
1 TT
2313647 TTAATTATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 10 0.42
24 3 0.12
25 2 0.08
26 5 0.21
27 4 0.17
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (24 bp):
TTAATAATATATTATTATGACTAT
Found at i:2321014 original size:3 final size:3
Alignment explanation
Indices: 2321000--2321029 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2320990 TGACGTGGAT
*
2321000 GAA GAC GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
2321030 TTGGAGAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.03, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2326069 original size:23 final size:23
Alignment explanation
Indices: 2326039--2326083 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
2326029 TTCCTCAAGT
2326039 TGTAATCAAGAAAATTGAACAGC
1 TGTAATCAAGAAAATTGAACAGC
2326062 TGTAATCAAGAAAATTGAACAG
1 TGTAATCAAGAAAATTGAACAG
2326084 TTGTGTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.49, C:0.11, G:0.18, T:0.22
Consensus pattern (23 bp):
TGTAATCAAGAAAATTGAACAGC
Found at i:2327971 original size:31 final size:31
Alignment explanation
Indices: 2327905--2328056 Score: 150
Period size: 31 Copynumber: 4.8 Consensus size: 31
2327895 TATGGTCACC
2327905 AAAATCGAACGGGAGTTAAT-A-GTTGAGGGACT
1 AAAATCGAAC-GGA-TTAATAATGTT-AGGGACT
* * *
2327937 AAAATCAAATGGATTAATAATGTTAGGGATT
1 AAAATCGAACGGATTAATAATGTTAGGGACT
*
2327968 AAAATCGAACGAGAGTTAAT-A-GCTGAGGGACT
1 AAAATCGAACG-GA-TTAATAATG-TTAGGGACT
* *
2328000 AAAATCGAATGGATTAATAATGTTAGGGATT
1 AAAATCGAACGGATTAATAATGTTAGGGACT
* *
2328031 AAAATCGAACGGATCAATAACGTTAG
1 AAAATCGAACGGATTAATAATGTTAG
2328057 AGATCATTCT
Statistics
Matches: 100, Mismatches: 13, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
30 10 0.10
31 53 0.53
32 32 0.32
33 5 0.05
ACGTcount: A:0.42, C:0.09, G:0.24, T:0.25
Consensus pattern (31 bp):
AAAATCGAACGGATTAATAATGTTAGGGACT
Done.