Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009643.1 Hibiscus syriacus cultivar Beakdansim tig00117056_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: 8859806
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 41
Found at i:4408880 original size:36 final size:36
Alignment explanation
Indices: 4408827--4408900 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
4408817 ATTTGGGGTA
*
4408827 GCCATATCCTTGTCATTA-TCATTCTCATCGAGCGCG
1 GCCATATCCTTGTCATTAGT-ATTCTCATCAAGCGCG
4408863 GCCATATCCTT-TCCATTAGTATTCTCATCAAGCGCG
1 GCCATATCCTTGT-CATTAGTATTCTCATCAAGCGCG
4408899 GC
1 GC
4408901 AAATCTGGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
35 1 0.03
36 33 0.94
37 1 0.03
ACGTcount: A:0.20, C:0.31, G:0.16, T:0.32
Consensus pattern (36 bp):
GCCATATCCTTGTCATTAGTATTCTCATCAAGCGCG
Found at i:4410782 original size:14 final size:15
Alignment explanation
Indices: 4410763--4410791 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4410753 TGATATAAAA
4410763 AAATATTTTT-TATT
1 AAATATTTTTATATT
4410777 AAATATTTTTATATT
1 AAATATTTTTATATT
4410792 TTTATTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
AAATATTTTTATATT
Found at i:4411400 original size:32 final size:31
Alignment explanation
Indices: 4411348--4411408 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 31
4411338 ATAAAAATAC
4411348 AATAAAAAAAGAATTAAAAGTGAATAAAATTT
1 AATAAAAAAAGAATTAAAAGTGAA-AAAATTT
*
4411380 AATAAAAAAAGAA-TATAAAGTTAAAAAAT
1 AATAAAAAAAGAATTA-AAAGTGAAAAAAT
4411409 ATCACCTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 7 0.26
32 20 0.74
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (31 bp):
AATAAAAAAAGAATTAAAAGTGAAAAAATTT
Found at i:4417882 original size:24 final size:23
Alignment explanation
Indices: 4417842--4417894 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
4417832 GAAAAAAAAT
*
4417842 CTTAAACTTAACTCGAT-TGAAGC
1 CTTAAACTGAACTCGATCTGAA-C
4417865 CTTAAACTCGAACTCGATCTGAAC
1 CTTAAACT-GAACTCGATCTGAAC
4417889 CTTAAA
1 CTTAAA
4417895 TACATGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 8 0.30
24 15 0.56
25 4 0.15
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.28
Consensus pattern (23 bp):
CTTAAACTGAACTCGATCTGAAC
Found at i:4425863 original size:29 final size:29
Alignment explanation
Indices: 4425820--4425902 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 29
4425810 CTCACCTAAC
*
4425820 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
* *
4425850 TAAATGAGGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
4425879 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
4425903 ATTTAGTTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 43 0.91
30 4 0.09
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:4429284 original size:15 final size:15
Alignment explanation
Indices: 4429264--4429293 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4429254 CTTTCTCATA
4429264 GTTGTTGTTGGAATT
1 GTTGTTGTTGGAATT
*
4429279 GTTGTTGTTGTAATT
1 GTTGTTGTTGGAATT
4429294 CCAGCCTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.30, T:0.57
Consensus pattern (15 bp):
GTTGTTGTTGGAATT
Found at i:4430615 original size:29 final size:29
Alignment explanation
Indices: 4430572--4430654 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 29
4430562 CTCACCTAAC
*
4430572 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
* *
4430602 TAAATGAGGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
4430631 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
4430655 ATTTAGTTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 43 0.91
30 4 0.09
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:4436985 original size:3 final size:3
Alignment explanation
Indices: 4436977--4437019 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
4436967 TATTTTTATT
*
4436977 TAA TAA TAA TAA TAA TAA TAA TGTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
4437020 AAGCATACTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 35 0.95
4 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:4437319 original size:45 final size:45
Alignment explanation
Indices: 4437238--4437341 Score: 111
Period size: 45 Copynumber: 2.3 Consensus size: 45
4437228 CTCAAAGGCT
* * ** *
4437238 TTTTGAAAACATCCTACACTATAGGTCTTATGGATGACCCGAAGG
1 TTTTGAAAACATCATACACTATAGGGCTTACAGATGACCCAAAGG
* *
4437283 TTTTGAAAACATCATGCACTGA-AGGGCTTACAGATGACCTAAAGG
1 TTTTGAAAACATCATACACT-ATAGGGCTTACAGATGACCCAAAGG
* *
4437328 ATTTGAAAATATCA
1 TTTTGAAAACATCA
4437342 AAAAGCTCCC
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 48 0.98
46 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (45 bp):
TTTTGAAAACATCATACACTATAGGGCTTACAGATGACCCAAAGG
Found at i:4437366 original size:75 final size:74
Alignment explanation
Indices: 4437275--4437416 Score: 230
Period size: 75 Copynumber: 1.9 Consensus size: 74
4437265 TTATGGATGA
* *
4437275 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCTAAAGGATTTGAAAATAT
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGATTTGAAAACAT
4437340 CAAAAAGCT
66 CAAAAAGCT
* * *
4437349 CCCGAAGGCTTTTGAAAACATTATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACA
1 CCCGAAGG-TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGATTTGAAAACA
4437414 TCA
65 TCA
4437417 TGCACTAAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
74 8 0.13
75 54 0.87
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (74 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGATTTGAAAACAT
CAAAAAGCT
Found at i:4437394 original size:120 final size:121
Alignment explanation
Indices: 4437172--4437461 Score: 370
Period size: 120 Copynumber: 2.4 Consensus size: 121
4437162 GAGGTCTTAT
* * * * * * * *
4437172 CATCTTGCACTGTAGGTCTTATAGATGACCCGGAGGCTTT-AAAACATCAAAAAGCTCTCAAAGG
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCTCCCAAAGG
* * **
4437236 CTTTTTGAAAACATCCTACACTATAGGTCTTATGGATGACCCGAAGGTTTTGAAAA
66 CTTTTTGAAAACATCATACACTATAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
** *
4437292 CATCATGCACTGAAGGGCTTACAGATGACCTAAAGGATTTGAAAATATCAAAAAGCTCCCGAAGG
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCTCCCAAAGG
* *
4437357 C-TTTTGAAAACATTATGCACTGA-AGGGCTTACAGATGACCCGAAGGTTTTGAAAA
66 CTTTTTGAAAACATCATACACT-ATAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
* * *
4437412 CATCATGCACTAAAGGGCTTACAGATGACCCGAGGGTTTTGAAAATATCA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTTGAAAATATCA
4437462 TGCACTGAAG
Statistics
Matches: 146, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
120 123 0.84
121 23 0.16
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (121 bp):
CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCTCCCAAAGG
CTTTTTGAAAACATCATACACTATAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
Found at i:4437414 original size:45 final size:45
Alignment explanation
Indices: 4437349--4437686 Score: 496
Period size: 45 Copynumber: 7.5 Consensus size: 45
4437339 TCAAAAAGCT
*
4437349 CCCGAAGGCTTTTGAAAACATTATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGG-TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
4437395 CCCGAAGGTTTTGAAAACATCATGCACTAAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* *
4437440 CCCGAGGGTTTTGAAAATATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* * *
4437485 CCCGGAGGCTTTGAAAATATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
4437530 CCCGAAGGTTTTGAAAACATCATGCACTGTAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* * * *
4437575 CCCGGAGGCTTTGAAAACATCATGCACTGTAGGTCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* * * *
4437620 CCCGGAGGTTTTAAAAACATCATGCACTGTAGGTCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* * *
4437665 CCCGGAGGCTTTGAAAATATCA
1 CCCGAAGGTTTTGAAAACATCA
4437687 AAAAGCTCCC
Statistics
Matches: 272, Mismatches: 20, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
45 264 0.97
46 8 0.03
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
Found at i:4437813 original size:74 final size:73
Alignment explanation
Indices: 4437628--4437825 Score: 288
Period size: 74 Copynumber: 2.7 Consensus size: 73
4437618 GACCCGGAGG
* * *
4437628 TTTTAAAAACATCATGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTGAAAATATCAAAAAGC
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGG-TTT-TAAATATCAAAAAGC
*
4437693 TCCCGAAGGC
64 TCACGAAGGC
* *
4437703 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTAAATATCAAAAAGCTC
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTAAATATCAAAAAGCTC
*
4437768 ACGAAGGAT
66 ACGAAGG-C
**
4437777 TTTTGAAAACATCATGCACTGTAGGTCTTATGGATGACCCGAAGGTTTT
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTT
4437826 GAAAACATCA
Statistics
Matches: 111, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
73 22 0.20
74 48 0.43
75 41 0.37
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.27
Consensus pattern (73 bp):
TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTAAATATCAAAAAGCTC
ACGAAGGC
Found at i:4437835 original size:45 final size:45
Alignment explanation
Indices: 4437777--4437870 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 45
4437767 CACGAAGGAT
* **
4437777 TTTTGAAAACATCATGCACTGTAGGTCTTATGGATGACCCGAAGG
1 TTTTGAAAACATCAAGCACTGTAGGTCTTACAGATGACCCGAAGG
*
4437822 TTTTGAAAACATCAAGCACTGTAGGTCTTACAGATGACCCGGAGG
1 TTTTGAAAACATCAAGCACTGTAGGTCTTACAGATGACCCGAAGG
4437867 TTTT
1 TTTT
4437871 AAATATCAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (45 bp):
TTTTGAAAACATCAAGCACTGTAGGTCTTACAGATGACCCGAAGG
Found at i:4437860 original size:119 final size:119
Alignment explanation
Indices: 4437694--4437972 Score: 452
Period size: 119 Copynumber: 2.3 Consensus size: 119
4437684 TCAAAAAGCT
* * *
4437694 CCCGAAGGCTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTAAATATC
1 CCCGAAGG-TTTTGAAAACATCAAGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTAAATATC
*
4437759 AAAAAGCTCAC-GAAGGATTTTTGAAAACATCATGCACTGTAGGTCTTATGGATGA
65 AAAAAGCTC-CTGAAGGACTTTTGAAAACATCATGCACTGTAGGTCTTATGGATGA
*
4437814 CCCGAAGGTTTTGAAAACATCAAGCACTGTAGGTCTTACAGATGACCCGGAGGTTTTAAATATCA
1 CCCGAAGGTTTTGAAAACATCAAGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTAAATATCA
* * *
4437879 AAAAGCTCCTGAAGGCCTTTTGAAAATATCCTGCACTGTAGGTCTTATGGATGA
66 AAAAGCTCCTGAAGGACTTTTGAAAACATCATGCACTGTAGGTCTTATGGATGA
*
4437933 CCCGAAGGTTTTGAAAACATCAAGCACTGTAGGTCATACA
1 CCCGAAGGTTTTGAAAACATCAAGCACTGTAGGTCTTACA
4437973 AATGTGGGAA
Statistics
Matches: 149, Mismatches: 9, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
118 1 0.01
119 140 0.94
120 8 0.05
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (119 bp):
CCCGAAGGTTTTGAAAACATCAAGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTAAATATCA
AAAAGCTCCTGAAGGACTTTTGAAAACATCATGCACTGTAGGTCTTATGGATGA
Found at i:4439155 original size:54 final size:54
Alignment explanation
Indices: 4439040--4439283 Score: 310
Period size: 54 Copynumber: 4.5 Consensus size: 54
4439030 CACTGATTCA
* * * * * *
4439040 TAAAACATTTGACAACACGTTCATCCTTTCCT-CGGCTTCTGTCCAGAGGTTCG
1 TAAAACATTTGACAACACATTCATCATTTCATGTGGCTTCTGCCCAGATGTTCG
* * *
4439093 TAAAACATTTGACAACGCATTCATCATTTCATGTGGCTTCTGCCTAGATGTTCA
1 TAAAACATTTGACAACACATTCATCATTTCATGTGGCTTCTGCCCAGATGTTCG
* * * *
4439147 TAAAACATTTGACAACACATTCATCTTTTTATGTGGATTCTTCCCAGATGTTCG
1 TAAAACATTTGACAACACATTCATCATTTCATGTGGCTTCTGCCCAGATGTTCG
* * * *
4439201 TAAAGCATTTGACAACACATTCATCATTTCCTGTGGCTTCTACCCAGATTTTCG
1 TAAAACATTTGACAACACATTCATCATTTCATGTGGCTTCTGCCCAGATGTTCG
* *
4439255 TAAAGCATTTGACAATACATTCATCATTT
1 TAAAACATTTGACAACACATTCATCATTT
4439284 TCTATGTTTG
Statistics
Matches: 166, Mismatches: 24, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
53 28 0.17
54 138 0.83
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (54 bp):
TAAAACATTTGACAACACATTCATCATTTCATGTGGCTTCTGCCCAGATGTTCG
Found at i:4442393 original size:134 final size:137
Alignment explanation
Indices: 4442151--4442422 Score: 435
Period size: 134 Copynumber: 2.0 Consensus size: 137
4442141 AGCTTTATTG
4442151 ACATTAGCCTTCATTGGACTAATTAAACAGTTCAACTCATCATAAATGTCTTCGACTTAACAATC
1 ACATTAGCCTTCATTGGACTAATTAAACAGTTCAACTCATCATAAATGTCTTCGACTTAACAATC
* **
4442216 ACAGTGGAGCAAACACCGAACTGCCAAATACCCGATCAAGGTCATGCTTTAAATATATGACTCT-
66 ACAGTGGAGCAAACACCGAACTACCAAATACCCGATCAAGGTCATGCTTTAAATATACAACTCTC
4442280 TTTTTTT
131 TTTTTTT
* * * *
4442287 ACATTAGCCTTCATTGGACTAATTAAA-GGTTCAACTCATCA-CAATGTCTTTGACTTGACAATC
1 ACATTAGCCTTCATTGGACTAATTAAACAGTTCAACTCATCATAAATGTCTTCGACTTAACAATC
*
4442350 ACAGTGGAGCAAACACCGAACTACCAAATATCCC-ATCAAGGTCATGCTTTGAATATACAACTCT
66 ACAGTGGAGCAAACACCGAACTACCAAATA-CCCGATCAAGGTCATGCTTTAAATATACAACTCT
4442414 CTTTTTTT
130 CTTTTTTT
4442422 A
1 A
4442423 AGAATAACTT
Statistics
Matches: 126, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
134 75 0.60
135 24 0.19
136 27 0.21
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.31
Consensus pattern (137 bp):
ACATTAGCCTTCATTGGACTAATTAAACAGTTCAACTCATCATAAATGTCTTCGACTTAACAATC
ACAGTGGAGCAAACACCGAACTACCAAATACCCGATCAAGGTCATGCTTTAAATATACAACTCTC
TTTTTTT
Found at i:4443318 original size:12 final size:12
Alignment explanation
Indices: 4443301--4443326 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4443291 GTATTGTCGG
4443301 TGCCTCTTATCC
1 TGCCTCTTATCC
4443313 TGCCTCTTATCC
1 TGCCTCTTATCC
4443325 TG
1 TG
4443327 TCATTCTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.38, G:0.12, T:0.42
Consensus pattern (12 bp):
TGCCTCTTATCC
Found at i:4444723 original size:35 final size:34
Alignment explanation
Indices: 4444664--4444733 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 34
4444654 ACAAATATGC
* *
4444664 AAATTCAAAAATGAAAATGTAAATACAAACGTAA
1 AAATGCAAAAATGAAAATGCAAATACAAACGTAA
* *
4444698 AAATGCAAAGATGCAAAATGCAAATACAAATGTAA
1 AAATGCAAAAATG-AAAATGCAAATACAAACGTAA
4444733 A
1 A
4444734 TATGTGAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 11 0.35
35 20 0.65
ACGTcount: A:0.60, C:0.10, G:0.11, T:0.19
Consensus pattern (34 bp):
AAATGCAAAAATGAAAATGCAAATACAAACGTAA
Found at i:4444828 original size:7 final size:7
Alignment explanation
Indices: 4444793--4444833 Score: 59
Period size: 6 Copynumber: 6.0 Consensus size: 7
4444783 ATAAAAGTAC
4444793 AAATGCA
1 AAATGCA
4444800 AAATG-A
1 AAATGCA
4444806 AAATGCA
1 AAATGCA
4444813 AATATGCA
1 AA-ATGCA
4444821 AAATGC-
1 AAATGCA
4444827 AAATGCA
1 AAATGCA
4444834 TGTATCAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
6 12 0.39
7 12 0.39
8 7 0.23
ACGTcount: A:0.56, C:0.12, G:0.15, T:0.17
Consensus pattern (7 bp):
AAATGCA
Found at i:4444992 original size:43 final size:43
Alignment explanation
Indices: 4444911--4444993 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
4444901 TGTATCAAAC
** *
4444911 AAAACTTTACATATAGGGGACAACTTTTAGTCCCAACTTCAAT
1 AAAACTTTACATATAGGGGACAACTTCCACTCCCAACTTCAAT
* * *
4444954 AAAACTTTACATATAGGGGATAACTTCCCCTCCTAACTTC
1 AAAACTTTACATATAGGGGACAACTTCCACTCCCAACTTC
4444994 TCTAAAGCCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (43 bp):
AAAACTTTACATATAGGGGACAACTTCCACTCCCAACTTCAAT
Found at i:4445511 original size:36 final size:36
Alignment explanation
Indices: 4445447--4445515 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
4445437 TCTTACCGTA
* *
4445447 GAATGCTTTTGGTATAAATCTAACAGGATCTTTATG
1 GAATACTTTTGGTATAAATATAACAGGATCTTTATG
* *
4445483 GAATACTTTTGGTATTAATATAATAGGATCTTT
1 GAATACTTTTGGTATAAATATAACAGGATCTTT
4445516 GTGTGCATAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (36 bp):
GAATACTTTTGGTATAAATATAACAGGATCTTTATG
Found at i:4448835 original size:3 final size:3
Alignment explanation
Indices: 4448829--4448855 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4448819 TATTTTTATT
4448829 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
4448856 AAGCAAACTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:4450671 original size:23 final size:23
Alignment explanation
Indices: 4450645--4450704 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
4450635 ATAGAAGTAG
4450645 AAGAATACGCGTCATAGAGGCAT
1 AAGAATACGCGTCATAGAGGCAT
*
4450668 AAGAATA--CATACTATAGAGGCAT
1 AAGAATACGCGT-C-ATAGAGGCAT
*
4450691 AAGAATACGTGTCA
1 AAGAATACGCGTCA
4450705 AAAGACATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 2 0.07
22 1 0.03
23 25 0.83
24 1 0.03
25 1 0.03
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.20
Consensus pattern (23 bp):
AAGAATACGCGTCATAGAGGCAT
Found at i:4452357 original size:31 final size:31
Alignment explanation
Indices: 4452322--4452389 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
4452312 TAATTAGATT
* *
4452322 ACTAAAATAAAATAATGAGAATAATTGAGTG
1 ACTAAAACAAAATAATAAGAATAATTGAGTG
4452353 ACTAAAACAAAATAATAAGAATAATTGAGTG
1 ACTAAAACAAAATAATAAGAATAATTGAGTG
4452384 ACTAAA
1 ACTAAA
4452390 TATATAGCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.57, C:0.06, G:0.13, T:0.24
Consensus pattern (31 bp):
ACTAAAACAAAATAATAAGAATAATTGAGTG
Found at i:4456633 original size:2 final size:2
Alignment explanation
Indices: 4456626--4456650 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4456616 CAGCTGGTTC
4456626 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 A
4456651 GGCTTAAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4458713 original size:57 final size:57
Alignment explanation
Indices: 4458625--4458732 Score: 173
Period size: 57 Copynumber: 1.9 Consensus size: 57
4458615 GAATACTTAA
* *
4458625 AAGGTTTTAAATCTCTTTAAAAAAGCTGCATAAACAACTTTTAATTAAGTAAACTCG
1 AAGGTCTTAAATCTCTTTAAAAAAGATGCATAAACAACTTTTAATTAAGTAAACTCG
*
4458682 AAGGTCTTAAATCTC-TTAAAAATAGATGCATAAACAACTTTTGATTAAGTA
1 AAGGTCTTAAATCTCTTTAAAAA-AGATGCATAAACAACTTTTAATTAAGTA
4458733 TCTCTTAGAG
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
56 7 0.15
57 40 0.85
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (57 bp):
AAGGTCTTAAATCTCTTTAAAAAAGATGCATAAACAACTTTTAATTAAGTAAACTCG
Found at i:4471293 original size:20 final size:20
Alignment explanation
Indices: 4471268--4471315 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
4471258 TGAAAATCGA
4471268 GTTGCGATTTTCCATTTCGC
1 GTTGCGATTTTCCATTTCGC
4471288 GTTGCGATTTTCCATTTCGC
1 GTTGCGATTTTCCATTTCGC
4471308 GTTGCGAT
1 GTTGCGAT
4471316 AGTCTACAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.44
Consensus pattern (20 bp):
GTTGCGATTTTCCATTTCGC
Found at i:4471335 original size:22 final size:22
Alignment explanation
Indices: 4471307--4471378 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
4471297 TTCCATTTCG
4471307 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
4471329 CGTTGCGAT--TTTTCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
4471348 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
4471370 CGTTGCGAT
1 CGTTGCGAT
4471379 TTTTCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 19 0.49
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:4471336 original size:42 final size:40
Alignment explanation
Indices: 4471287--4471400 Score: 165
Period size: 41 Copynumber: 2.8 Consensus size: 40
4471277 TTCCATTTCG
* *
4471287 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCAAATT--CGTTGCGATAGTCTACAGTTGT
4471329 CGTTGCGATTTTTCAAATTCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGA-TTTTCAAATTCGTTGCGATAGTCTACAGTTGT
*
4471370 CGTTGCGATTTTTCAAATTCGTTGTGATAGT
1 CGTTGCGA-TTTTCAAATTCGTTGCGATAGT
4471401 TAAAAAAAAG
Statistics
Matches: 68, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
41 52 0.76
42 8 0.12
43 8 0.12
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.42
Consensus pattern (40 bp):
CGTTGCGATTTTCAAATTCGTTGCGATAGTCTACAGTTGT
Found at i:4471352 original size:19 final size:19
Alignment explanation
Indices: 4471328--4471393 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
4471318 TCTACAGTTG
4471328 TCGTTGCGATTTTTCAAAT
1 TCGTTGCGATTTTTCAAAT
* * **
4471347 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTTCAAAT
4471368 GTCGTTGCGATTTTTCAAAT
1 -TCGTTGCGATTTTTCAAAT
4471388 TCGTTG
1 TCGTTG
4471394 TGATAGTTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 16 0.44
20 5 0.14
21 5 0.14
22 10 0.28
ACGTcount: A:0.18, C:0.17, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGTTGCGATTTTTCAAAT
Found at i:4471359 original size:41 final size:41
Alignment explanation
Indices: 4471307--4471400 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
4471297 TTCCATTTCG
4471307 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTTCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTTCAAATT
4471348 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTTCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTTCAAATT
*
4471389 CGTTGTGATAGT
1 CGTTGCGATAGT
4471401 TAAAAAAAAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.41
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTTCAAATT
Found at i:4471502 original size:13 final size:13
Alignment explanation
Indices: 4471484--4471517 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
4471474 TATTACCACG
4471484 ACCACGACGTATT
1 ACCACGACGTATT
4471497 ACCACGACGTATT
1 ACCACGACGTATT
4471510 ACCACGAC
1 ACCACGAC
4471518 CACGACCACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.32, C:0.35, G:0.15, T:0.18
Consensus pattern (13 bp):
ACCACGACGTATT
Found at i:4483305 original size:21 final size:21
Alignment explanation
Indices: 4483281--4483327 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
4483271 AAATATATAA
*
4483281 AAAAATAAATATAAAACTACT
1 AAAAATAAAAATAAAACTACT
* *
4483302 AAAAATAAAAATTAAATTACT
1 AAAAATAAAAATAAAACTACT
4483323 AAAAA
1 AAAAA
4483328 AATTATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAATAAAAATAAAACTACT
Found at i:4484796 original size:25 final size:25
Alignment explanation
Indices: 4484735--4484798 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
4484725 TATATGAAAC
*
4484735 ATATTAATTTA-AATTATAATAAAA
1 ATATAAATTTATAATTATAATAAAA
** *
4484759 ATATAAAAATATAATTATAATAAAG
1 ATATAAATTTATAATTATAATAAAA
**
4484784 ATATATTTTTATAAT
1 ATATAAATTTATAAT
4484799 AACTCATTAT
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
24 8 0.26
25 23 0.74
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
ATATAAATTTATAATTATAATAAAA
Found at i:4489110 original size:45 final size:45
Alignment explanation
Indices: 4489061--4489150 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 45
4489051 TATAAAATGA
**
4489061 TTTTAAAGTTAAATTTAAAAAAAATATTTAAAACATATACTAATT
1 TTTTAAAGTTAAACATAAAAAAAATATTTAAAACATATACTAATT
* **
4489106 TTTTAAAGTTAAACATATACTAAATATTTAAAACATATACTAATT
1 TTTTAAAGTTAAACATAAAAAAAATATTTAAAACATATACTAATT
4489151 ATGTTTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (45 bp):
TTTTAAAGTTAAACATAAAAAAAATATTTAAAACATATACTAATT
Found at i:4489112 original size:20 final size:20
Alignment explanation
Indices: 4489085--4489152 Score: 73
Period size: 20 Copynumber: 3.1 Consensus size: 20
4489075 TTAAAAAAAA
4489085 TATTTAAAACATATACTAAT
1 TATTTAAAACATATACTAAT
* *
4489105 TTTTTAAAGTTAAACATATACTAAA
1 TATTT--A---AAACATATACTAAT
4489130 TATTTAAAACATATACTAAT
1 TATTTAAAACATATACTAAT
4489150 TAT
1 TAT
4489153 GTTTTTTTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
20 20 0.51
22 1 0.03
23 1 0.03
25 17 0.44
ACGTcount: A:0.49, C:0.09, G:0.01, T:0.41
Consensus pattern (20 bp):
TATTTAAAACATATACTAAT
Found at i:4489221 original size:26 final size:21
Alignment explanation
Indices: 4489154--4489222 Score: 104
Period size: 21 Copynumber: 3.3 Consensus size: 21
4489144 ACTAATTATG
4489154 TTTT-TTTTCAAAATAAATTTA
1 TTTTATTTT-AAAATAAATTTA
4489175 TTTTATTTTAAAATAAATTTA
1 TTTTATTTTAAAATAAATTTA
* *
4489196 TTTTATTTTAAAATAAATGTC
1 TTTTATTTTAAAATAAATTTA
4489217 TTTTAT
1 TTTTAT
4489223 AAATCGAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
21 41 0.91
22 4 0.09
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (21 bp):
TTTTATTTTAAAATAAATTTA
Found at i:4491382 original size:20 final size:20
Alignment explanation
Indices: 4491354--4491422 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
4491344 TGTTGTTCAT
* *
4491354 TACTGTTCACACAGTATCGG
1 TACTATTCACATAGTATCGG
* ***
4491374 TACTATTCATATAGTATTAA
1 TACTATTCACATAGTATCGG
*
4491394 TACTATTCAGATAGTATCGG
1 TACTATTCACATAGTATCGG
4491414 TACTATTCA
1 TACTATTCA
4491423 TACAATACAT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (20 bp):
TACTATTCACATAGTATCGG
Found at i:4491874 original size:48 final size:48
Alignment explanation
Indices: 4491811--4492141 Score: 339
Period size: 48 Copynumber: 7.0 Consensus size: 48
4491801 TTACATAAGT
* * * *
4491811 AACGTTAGACATGCTAGGTACCATTGATAGTGGCACCACCGTCACA-A
1 AACGTCAGACGTGCTAGGTACCATTAATAGTAGCACCACCGTCACACA
4491858 AGACGTCCA-ACGTGCTAGGTACCATTAATAGTAGCACCACCGTCACACA
1 A-ACGT-CAGACGTGCTAGGTACCATTAATAGTAGCACCACCGTCACACA
* * *
4491907 AACATCAGACGTGCTAGGTACCATTAATAGTAGTACCATCGTCACACA
1 AACGTCAGACGTGCTAGGTACCATTAATAGTAGCACCACCGTCACACA
*
4491955 AACGTCAGACGTGTTAGGTACCATT-A-A-TAGCACCACCGTCACACA
1 AACGTCAGACGTGCTAGGTACCATTAATAGTAGCACCACCGTCACACA
* * * * ** * *
4492000 TACGTCAGGCATGTTAATTATCATTAATAGTAGCACCACCGTCACACG
1 AACGTCAGACGTGCTAGGTACCATTAATAGTAGCACCACCGTCACACA
* * ** * * *
4492048 GACGTCAGACGTGATATTTATCATTAATAGTAGCACCATCATCACACA
1 AACGTCAGACGTGCTAGGTACCATTAATAGTAGCACCACCGTCACACA
* * * * ** *
4492096 GATGTTAGATGTGCTATTTATCATTAATAGTAGCACCACCGTCACA
1 AACGTCAGACGTGCTAGGTACCATTAATAGTAGCACCACCGTCACA
4492142 AAAGTGATGT
Statistics
Matches: 245, Mismatches: 32, Indels: 13
0.84 0.11 0.04
Matches are distributed among these distances:
45 35 0.14
46 2 0.01
47 5 0.02
48 200 0.82
49 3 0.01
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (48 bp):
AACGTCAGACGTGCTAGGTACCATTAATAGTAGCACCACCGTCACACA
Found at i:4492121 original size:141 final size:144
Alignment explanation
Indices: 4491811--4492141 Score: 364
Period size: 141 Copynumber: 2.3 Consensus size: 144
4491801 TTACATAAGT
* * * * * * * * *
4491811 AACGTTAGACATGCTAGGTACCATTGATAGTGGCACCACCGTCACAAAGACGTCCA-ACGTGCTA
1 AACGTCAGACGTGCTAGGTACCATTAATAGTAGCACCACCGTCACACATACGT-CAGGCATGTTA
** * *
4491875 GGTACCATTAATAGTAGCACCACCGTCACACAAACATCAGACGTGCTAGGTACCATTAATAGTAG
65 ATTATCATTAATAGTAGCACCACCGTCACACAAACATCAGACGTGATAGGTACCATTAATAGTAG
* *
4491940 TACCATCGTCACACA
130 CACCATCATCACACA
*
4491955 AACGTCAGACGTGTTAGGTACCATT-A-A-TAGCACCACCGTCACACATACGTCAGGCATGTTAA
1 AACGTCAGACGTGCTAGGTACCATTAATAGTAGCACCACCGTCACACATACGTCAGGCATGTTAA
** * ** *
4492017 TTATCATTAATAGTAGCACCACCGTCACACGGACGTCAGACGTGATATTTATCATTAATAGTAGC
66 TTATCATTAATAGTAGCACCACCGTCACACAAACATCAGACGTGATAGGTACCATTAATAGTAGC
4492082 ACCATCATCACACA
131 ACCATCATCACACA
* * * * ** *
4492096 GATGTTAGATGTGCTATTTATCATTAATAGTAGCACCACCGTCACA
1 AACGTCAGACGTGCTAGGTACCATTAATAGTAGCACCACCGTCACA
4492142 AAAGTGATGT
Statistics
Matches: 154, Mismatches: 29, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
140 2 0.01
141 110 0.71
142 2 0.01
143 2 0.01
144 38 0.25
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (144 bp):
AACGTCAGACGTGCTAGGTACCATTAATAGTAGCACCACCGTCACACATACGTCAGGCATGTTAA
TTATCATTAATAGTAGCACCACCGTCACACAAACATCAGACGTGATAGGTACCATTAATAGTAGC
ACCATCATCACACA
Found at i:4492324 original size:52 final size:52
Alignment explanation
Indices: 4492228--4492329 Score: 134
Period size: 52 Copynumber: 2.0 Consensus size: 52
4492218 AAATCATTTG
*
4492228 TCATTCACTTATCAAAATCTTTTCAAACATCATCACAATAAAGTATCATATA
1 TCATTCACTTATCAAAATCTTTTCAAACATCATCAAAATAAAGTATCATATA
* * * * *
4492280 TCATTCACTTATCATAATCTTTTTAAATATTGA-CAAAATCAAGTATCATA
1 TCATTCACTTATCAAAATCTTTTCAAACA-TCATCAAAATAAAGTATCATA
4492330 CAATATAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
52 41 0.95
53 2 0.05
ACGTcount: A:0.41, C:0.19, G:0.03, T:0.37
Consensus pattern (52 bp):
TCATTCACTTATCAAAATCTTTTCAAACATCATCAAAATAAAGTATCATATA
Found at i:4495765 original size:253 final size:249
Alignment explanation
Indices: 4495318--4495920 Score: 903
Period size: 253 Copynumber: 2.4 Consensus size: 249
4495308 TTTATTCATA
*
4495318 TATTGAATAAAAAT-ATTTTTTTATTATTTCAGGTCGGGTCGGGTTTCTAATTCATATATTCAGG
1 TATTGAATAAAAATAATTTTTTTATTA-TT----TCGGGTCGGGTTTCTAATTCATATATTCGGG
* *
4495382 TCGGGTCGGGTTAAACTTTATTTTTGGTCGGGTC-GGTCGGTTATTTTAAGTGTGATATTCGGGT
61 TCGGGTCGGGTGAAACTTTA-TTTTGGTCGGGTCGGGTCGGTTATTTTAAGTGTGATAATCGGGT
* *
4495446 CGAGTTCGGGTTTAGGGTGAAAAATACTCGACCAAAATATATATATATATTTACCTTATATATTT
125 CGAGTTCGGGTTTAGGGTGAAAAATACCCGACCAAAAAATATATATATATTTACCTTATATATTT
* *
4495511 AGGAATAATTATAATAATATCCCTCTATATATAA-TTTTTTTCAATTAAGTCATTGTTTT
190 AGGAATAATTATAATAATACCCCTCTATATATAATTTTTTTTCAATTAAGTCACTGTTTT
4495570 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGG
1 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGG
** * * * *
4495635 TATGGTGAAACTTTATTTTAGTCGGGTCGGGTCGATTTTTTTTAAGTGTGATAATCGGGTCGGGT
66 TCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCG-GTTATTTTAAGTGTGATAATCGGGTCGAGT
4495700 TCGGGTTTAGGGTGAAAAATACCCGACCCGACCCAAAAA-ATATATA-ATTTTACCTTATATATT
130 TCGGGTTTAGGGTGAAAAATACCCGA-CC-A---AAAAATATATATATA-TTTACCTTATATATT
*
4495763 TAGGAATAATTATAATGATACCCCTCTATATATAATTTTTTTTCAATTAAGTCACTGTTTT
189 TAGGAATAATTATAATAATACCCCTCTATATATAATTTTTTTTCAATTAAGTCACTGTTTT
*
4495824 TATTGAATAAAAATAA-TTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGATCGGG
1 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGG
*
4495888 TCGGGTGAAACTTTATTTTGGTTGGGTCGGGTC
66 TCGGGTGAAACTTTATTTTGGTCGGGTCGGGTC
4495921 TCGGATGGAG
Statistics
Matches: 322, Mismatches: 19, Indels: 19
0.89 0.05 0.05
Matches are distributed among these distances:
247 12 0.04
248 52 0.16
249 51 0.16
250 2 0.01
251 1 0.00
252 17 0.05
253 143 0.44
254 44 0.14
ACGTcount: A:0.27, C:0.11, G:0.19, T:0.42
Consensus pattern (249 bp):
TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGG
TCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTATTTTAAGTGTGATAATCGGGTCGAGTT
CGGGTTTAGGGTGAAAAATACCCGACCAAAAAATATATATATATTTACCTTATATATTTAGGAAT
AATTATAATAATACCCCTCTATATATAATTTTTTTTCAATTAAGTCACTGTTTT
Found at i:4496297 original size:17 final size:18
Alignment explanation
Indices: 4496275--4496321 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
4496265 TATGGAGTTG
*
4496275 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
*
4496292 GATTCCAATTCCTTCATA
1 GATTCCAATTCCTTCACA
4496310 GATTCCAATTCC
1 GATTCCAATTCC
4496322 CTCAGAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.34
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:4519357 original size:16 final size:16
Alignment explanation
Indices: 4519336--4519366 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
4519326 TTGAAAAGTA
4519336 AAATTAAAAAAATATG
1 AAATTAAAAAAATATG
4519352 AAATTAAAAAAATAT
1 AAATTAAAAAAATAT
4519367 AATAAAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
AAATTAAAAAAATATG
Found at i:4519393 original size:20 final size:19
Alignment explanation
Indices: 4519352--4519391 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
4519342 AAAAAATATG
*
4519352 AAATTAAAAAAATATAATA
1 AAATGAAAAAAATATAATA
*
4519371 AAATGAAAAGAA-ATAATA
1 AAATGAAAAAAATATAATA
4519389 AAA
1 AAA
4519392 AACGTGATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (19 bp):
AAATGAAAAAAATATAATA
Found at i:4530965 original size:65 final size:64
Alignment explanation
Indices: 4530892--4531013 Score: 183
Period size: 65 Copynumber: 1.9 Consensus size: 64
4530882 GTGCATTGGT
*
4530892 CATCGATGCATAAAATACATTCGATGTTTCAAATAAGCCTA-GAGTGCATCGATGCATGGTATGT
1 CATCGATGCATAAAATACATTCGATG-CTCAAATAA-CCTAGGAGTGCATCGATGCATGGTATGT
4530956 G
64 G
* **
4530957 CATCGATGCATAAAATACATTCGATGCTCAAATTATTTAGGAGTGCATCGATGCATG
1 CATCGATGCATAAAATACATTCGATGCTCAAATAACCTAGGAGTGCATCGATGCATG
4531014 CCTTGTGCAT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
63 2 0.04
64 24 0.46
65 26 0.50
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (64 bp):
CATCGATGCATAAAATACATTCGATGCTCAAATAACCTAGGAGTGCATCGATGCATGGTATGTG
Found at i:4531021 original size:64 final size:65
Alignment explanation
Indices: 4530892--4531025 Score: 184
Period size: 64 Copynumber: 2.1 Consensus size: 65
4530882 GTGCATTGGT
* *
4530892 CATCGATGCATAAAATACATTCGATGTTTCAAATAAGCCTAGAGTGCATCGATGCATGGTATGTG
1 CATCGATGCATAAAATACATTCGATGTCTCAAATAAGCCTAGAGTGCATCGATGCATGCTATGTG
* **
4530957 CATCGATGCATAAAATACATTCGATG-CTCAAATTA-TTTAGGAGTGCATCGATGCATGCCT-TG
1 CATCGATGCATAAAATACATTCGATGTCTCAAATAAGCCTA-GAGTGCATCGATGCATG-CTATG
4531019 TG
64 TG
4531021 CATCG
1 CATCG
4531026 GTACACAAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
63 2 0.03
64 33 0.53
65 27 0.44
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (65 bp):
CATCGATGCATAAAATACATTCGATGTCTCAAATAAGCCTAGAGTGCATCGATGCATGCTATGTG
Found at i:4531036 original size:64 final size:65
Alignment explanation
Indices: 4530933--4531096 Score: 165
Period size: 64 Copynumber: 2.5 Consensus size: 65
4530923 AATAAGCCTA
* * * ** *
4530933 GAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAAT-ACATTCGATGCTCAAATTATT-TA
1 GAGTGCATCGATGCATGCTATGTGCATCGATACACAAAATGA-ATTCGAAACTCAAATTATTCAA
4530996 G
65 G
* * *
4530997 GAGTGCATCGATGCATGCCT-TGTGCATCGGTACACAAAATGAATTCGAAATTCAATTTATTCAA
1 GAGTGCATCGATGCATG-CTATGTGCATCGATACACAAAATGAATTCGAAACTCAAATTATTCAA
4531061 G
65 G
** *
4531062 G-GTGCATCGATGCATTATATAGTGCATCGGTACAC
1 GAGTGCATCGATGCATGCTAT-GTGCATCGATACAC
4531097 TACTCTGAAA
Statistics
Matches: 84, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
63 1 0.01
64 64 0.76
65 19 0.23
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (65 bp):
GAGTGCATCGATGCATGCTATGTGCATCGATACACAAAATGAATTCGAAACTCAAATTATTCAAG
Found at i:4533260 original size:16 final size:16
Alignment explanation
Indices: 4533239--4533281 Score: 79
Period size: 15 Copynumber: 2.8 Consensus size: 16
4533229 TGTGCAAATC
4533239 CGGGTACCCGGATTTT
1 CGGGTACCCGGATTTT
4533255 CGGGTACCC-GATTTT
1 CGGGTACCCGGATTTT
4533270 CGGGTACCCGGA
1 CGGGTACCCGGA
4533282 ACTTCCGGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.14, C:0.28, G:0.33, T:0.26
Consensus pattern (16 bp):
CGGGTACCCGGATTTT
Found at i:4533376 original size:17 final size:17
Alignment explanation
Indices: 4533344--4533375 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4533334 ACTCGGTAAT
4533344 CGGGTACCCGGATTTTG
1 CGGGTACCCGGATTTTG
4533361 CGGGTACCCGG-TTTT
1 CGGGTACCCGGATTTT
4533376 TAATTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.09, C:0.25, G:0.34, T:0.31
Consensus pattern (17 bp):
CGGGTACCCGGATTTTG
Found at i:4534275 original size:21 final size:21
Alignment explanation
Indices: 4534203--4534299 Score: 90
Period size: 23 Copynumber: 4.5 Consensus size: 21
4534193 CGACGGGTAT
*
4534203 ATCGATGCACA-AC-AGAGTGC
1 ATCGATGCACATTCAAG-GTGC
4534223 ATCGATGCACATTCAAGACGTGC
1 ATCGATGCACATTCAAG--GTGC
* * * *
4534246 ATCGGTGCACCTTCATGGTGA
1 ATCGATGCACATTCAAGGTGC
4534267 ATCGATGCACATTCAAGGGATGC
1 ATCGATGCACATTCAA-GG-TGC
4534290 ATCGATGCAC
1 ATCGATGCAC
4534300 TAGGTAGTGT
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
20 11 0.18
21 17 0.27
22 4 0.06
23 30 0.48
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.22
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGC
Found at i:4537998 original size:20 final size:21
Alignment explanation
Indices: 4537959--4537998 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
4537949 GAAGCTTTAA
* *
4537959 GATCATCAATTTATTTTTGAT
1 GATCATCAATTTACTCTTGAT
4537980 GATCATC-ATTTACTCTTGA
1 GATCATCAATTTACTCTTGA
4537999 AAGTAAGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.47
Consensus pattern (21 bp):
GATCATCAATTTACTCTTGAT
Found at i:4538147 original size:21 final size:21
Alignment explanation
Indices: 4538108--4538150 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
4538098 AGACTATTTT
4538108 CATTTTTTCAATTTTAAAATAA
1 CATTTTTT-AATTTTAAAATAA
4538130 CATTTTTT-ATTTTGAAAATAA
1 CATTTTTTAATTTT-AAAATAA
4538151 AGTCTTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 7 0.35
22 8 0.40
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (21 bp):
CATTTTTTAATTTTAAAATAA
Found at i:4538428 original size:165 final size:165
Alignment explanation
Indices: 4538156--4538487 Score: 664
Period size: 165 Copynumber: 2.0 Consensus size: 165
4538146 AATAAAGTCT
4538156 TATAATTCGAATCCAACCCATTATACTCCTCTAATAACTCATCATAAGATAAATCATCTGAATTA
1 TATAATTCGAATCCAACCCATTATACTCCTCTAATAACTCATCATAAGATAAATCATCTGAATTA
4538221 AATGAGTTAGAGGTTACCTGAGAGTTTTCCCCGATGGCCATTAAGCACAAGTTAGCAACTTCTTG
66 AATGAGTTAGAGGTTACCTGAGAGTTTTCCCCGATGGCCATTAAGCACAAGTTAGCAACTTCTTG
4538286 TTCCTCTTCATCGGAACCTTCTTCATCGCTCCATG
131 TTCCTCTTCATCGGAACCTTCTTCATCGCTCCATG
4538321 TATAATTCGAATCCAACCCATTATACTCCTCTAATAACTCATCATAAGATAAATCATCTGAATTA
1 TATAATTCGAATCCAACCCATTATACTCCTCTAATAACTCATCATAAGATAAATCATCTGAATTA
4538386 AATGAGTTAGAGGTTACCTGAGAGTTTTCCCCGATGGCCATTAAGCACAAGTTAGCAACTTCTTG
66 AATGAGTTAGAGGTTACCTGAGAGTTTTCCCCGATGGCCATTAAGCACAAGTTAGCAACTTCTTG
4538451 TTCCTCTTCATCGGAACCTTCTTCATCGCTCCATG
131 TTCCTCTTCATCGGAACCTTCTTCATCGCTCCATG
4538486 TA
1 TA
4538488 ACTACATGAG
Statistics
Matches: 167, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
165 167 1.00
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (165 bp):
TATAATTCGAATCCAACCCATTATACTCCTCTAATAACTCATCATAAGATAAATCATCTGAATTA
AATGAGTTAGAGGTTACCTGAGAGTTTTCCCCGATGGCCATTAAGCACAAGTTAGCAACTTCTTG
TTCCTCTTCATCGGAACCTTCTTCATCGCTCCATG
Found at i:4540359 original size:64 final size:63
Alignment explanation
Indices: 4540227--4540428 Score: 190
Period size: 64 Copynumber: 3.1 Consensus size: 63
4540217 TACACTAGGG
* * ** * *
4540227 GTGCATCGATGCATAAAATACATTCGATGTTTCAAATAAGCCTGGGGTGCATTGATGCATGGTAT
1 GTGCATCGATGCATAAAATGCATTCGATG-TTCAAATTA-TTTAGGGTGCATTGATGCATGCTAT
4540292 GTGCATCGATGCATAAAATGCATTCGATGTTCAAATTATTTAGGAGTGCATTGATGCATGCCT-T
1 GTGCATCGATGCATAAAATGCATTCGATGTTCAAATTATTTAGG-GTGCATTGATGCATG-CTAT
* * * * ** * * * **
4540356 GTGCATCGGTACACAAAATGCATTTGAAATTCAATTTATTCAAGGGTGCATCGATGCATTATAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTCAAATTATT-TAGGGTGCATTGATGCATGCTAT
4540420 AGTGCATCG
1 -GTGCATCG
4540429 GTACACTACT
Statistics
Matches: 115, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
63 4 0.03
64 71 0.62
65 40 0.35
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTCAAATTATTTAGGGTGCATTGATGCATGCTAT
Found at i:4553552 original size:16 final size:15
Alignment explanation
Indices: 4553531--4553560 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
4553521 TCTAATATTG
4553531 AATTAGATTAAGATTA
1 AATTAGATT-AGATTA
4553547 AATTAGATTAGATT
1 AATTAGATTAGATT
4553561 GTTGATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (15 bp):
AATTAGATTAGATTA
Found at i:4556616 original size:29 final size:29
Alignment explanation
Indices: 4556574--4556650 Score: 147
Period size: 29 Copynumber: 2.7 Consensus size: 29
4556564 TTTTATATGT
4556574 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
4556602 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
4556631 TCATGTAGCTCATGTCATTT
1 TCATGTAGCTCATGTCATTT
4556651 TCTCATATCA
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.15
29 41 0.85
ACGTcount: A:0.18, C:0.21, G:0.16, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:4557436 original size:2 final size:2
Alignment explanation
Indices: 4557429--4557467 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4557419 CTATTAAAAG
4557429 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4557468 TAAAATATAG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4557542 original size:14 final size:16
Alignment explanation
Indices: 4557522--4557559 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
4557512 ATAATATACG
*
4557522 TATATAATAAT-AATA
1 TATATAAAAATAAATA
4557537 -ATATAAAAATAAATA
1 TATATAAAAATAAATA
4557552 TATATAAA
1 TATATAAA
4557560 TGAGTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 9 0.45
15 4 0.20
16 7 0.35
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TATATAAAAATAAATA
Found at i:4557704 original size:15 final size:14
Alignment explanation
Indices: 4557645--4557718 Score: 64
Period size: 15 Copynumber: 5.1 Consensus size: 14
4557635 TGTAAACCAA
4557645 ATAAAGAGTAATAAT
1 ATAAA-AGTAATAAT
4557660 ATAAAAGTAA-AAT
1 ATAAAAGTAATAAT
4557673 ATGAAATACGT-AT-AT
1 AT-AAA-A-GTAATAAT
4557688 ATATAAAGTAATAAT
1 ATA-AAAGTAATAAT
*
4557703 ATTAAAAATAATAAT
1 A-TAAAAGTAATAAT
4557718 A
1 A
4557719 ACGATTATAA
Statistics
Matches: 50, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
13 7 0.14
14 12 0.24
15 27 0.54
16 4 0.08
ACGTcount: A:0.61, C:0.01, G:0.08, T:0.30
Consensus pattern (14 bp):
ATAAAAGTAATAAT
Found at i:4559198 original size:45 final size:45
Alignment explanation
Indices: 4559132--4559236 Score: 124
Period size: 45 Copynumber: 2.3 Consensus size: 45
4559122 GCACTACTTG
* **
4559132 TGCATCGGTGCA-TAAAATGCATTCGAT-GTTTTATTATTAATGGAA
1 TGCATCGATGCACT-AAATGCATTCGATCGTTTTATT-TTAAAAGAA
* * *
4559177 TGCATCGATGCACTAATTGCATTCGATCTTTTTATTTTAAAAGAG
1 TGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAGAA
4559222 TGCATCGATGCACTA
1 TGCATCGATGCACTA
4559237 CTGTGCATCG
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
45 44 0.85
46 8 0.15
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (45 bp):
TGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAGAA
Found at i:4561342 original size:196 final size:197
Alignment explanation
Indices: 4561008--4561394 Score: 749
Period size: 196 Copynumber: 2.0 Consensus size: 197
4560998 CTTATCCATG
4561008 GAGAAATCAGTTCGTACCGAAATAAAATGGGATGACTTAGTCAATCTATCTACGATCACCCAGAT
1 GAGAAATCAGTTCGTACCGAAATAAAATGGGATGACTTAGTCAATCTATCTACGATCACCCAGAT
4561073 TGAATCCTTTTTGTTCGGAGTTAAAGGCAACCCCGTCACAAAATCCATCGTTATGTTTTCCAATT
66 TGAATCCTTTTTGTTCGGAGTTAAAGGCAACCCCGTCACAAAATCCATCGTTATGTTTTCCAATT
*
4561138 TCCATTGAGGAATTGAAATTGGCTGTAACAATCCTGACGGAACCTGATG-CTCAGCTTTGACTTG
131 TCCATTGAGGAATTGAAATTGGCTGTAACAATCCTGACGGAACCTGATGTATCAGCTTTGACTTG
4561202 TT
196 TT
4561204 GAGAAATCAGTTCGTACCGAAATAAAATGGGATGACTTAGTCAATCTATCTACGATCACCCAGAT
1 GAGAAATCAGTTCGTACCGAAATAAAATGGGATGACTTAGTCAATCTATCTACGATCACCCAGAT
4561269 TGAATCCTTTTTGTTCGGAGTTAAAGGCAACCCCGTCACAAAATCCATCGTTATGTTTTCCAATT
66 TGAATCCTTTTTGTTCGGAGTTAAAGGCAACCCCGTCACAAAATCCATCGTTATGTTTTCCAATT
*
4561334 TCCATTGAGGAATTGAAATTGGCTGTAACAATCTTGACGGAACCTGATGTATCAGCTTTGA
131 TCCATTGAGGAATTGAAATTGGCTGTAACAATCCTGACGGAACCTGATGTATCAGCTTTGA
4561395 TACAAATTTC
Statistics
Matches: 188, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
196 178 0.95
197 10 0.05
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (197 bp):
GAGAAATCAGTTCGTACCGAAATAAAATGGGATGACTTAGTCAATCTATCTACGATCACCCAGAT
TGAATCCTTTTTGTTCGGAGTTAAAGGCAACCCCGTCACAAAATCCATCGTTATGTTTTCCAATT
TCCATTGAGGAATTGAAATTGGCTGTAACAATCCTGACGGAACCTGATGTATCAGCTTTGACTTG
TT
Found at i:4562489 original size:12 final size:12
Alignment explanation
Indices: 4562472--4562504 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
4562462 TGTCTCATAA
4562472 AATCTGTAAAAC
1 AATCTGTAAAAC
4562484 AATCTGTAAAAC
1 AATCTGTAAAAC
4562496 AATCTGTAA
1 AATCTGTAA
4562505 GTGTGAACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.48, C:0.15, G:0.09, T:0.27
Consensus pattern (12 bp):
AATCTGTAAAAC
Found at i:4565769 original size:29 final size:29
Alignment explanation
Indices: 4565726--4565802 Score: 138
Period size: 29 Copynumber: 2.7 Consensus size: 29
4565716 TTTTATATGT
4565726 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
4565754 TCATGTAGGTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
4565783 TCATGTAGCTCATGTCATTT
1 TCATGTAGCTCATGTCATTT
4565803 TCTCATATCA
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
28 7 0.15
29 39 0.85
ACGTcount: A:0.18, C:0.19, G:0.17, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:4566254 original size:64 final size:63
Alignment explanation
Indices: 4566185--4566341 Score: 165
Period size: 64 Copynumber: 2.5 Consensus size: 63
4566175 TAATGAAGGT
* **
4566185 ATGCATCGATGCATTACTTGTGCATCGGTGCA-TAAAATGCATTCGAT-GTTTTATTATTAATGG
1 ATGCATCGATGCATTACTTGTGCATCGATGCACT-AAATGCATTCGATCGTTTTATT-TTAA-AA
4566248 G
63 G
* ** * * *
4566249 ATGCATCGATACATGCCTTATGCATCGATGCACTAATTGCATTCGATCTTTTTATTTTAAAAG
1 ATGCATCGATGCATTACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
* *
4566312 AGTGCATCGATGCACTACATGTGCATCGAT
1 A-TGCATCGATGCATTACTTGTGCATCGAT
4566342 ACACATTCAA
Statistics
Matches: 75, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
63 2 0.03
64 65 0.87
65 8 0.11
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (63 bp):
ATGCATCGATGCATTACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
Found at i:4572980 original size:28 final size:27
Alignment explanation
Indices: 4572927--4572980 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
4572917 AAATTAGTTG
* *
4572927 CTATATTTTCTTTTTTTATTTTAATCT
1 CTATATTTTCTTTTTATATTATAATCT
4572954 CTATATTTTACTTTATTATA-TATAATC
1 CTATATTTT-CTTT-TTATATTATAATC
4572981 CCTTAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 9 0.39
28 10 0.43
29 4 0.17
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (27 bp):
CTATATTTTCTTTTTATATTATAATCT
Found at i:4573230 original size:2 final size:2
Alignment explanation
Indices: 4573223--4573256 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
4573213 AACCTAAGTG
*
4573223 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4573257 AAAATTATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:4575212 original size:29 final size:29
Alignment explanation
Indices: 4575157--4575212 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
4575147 CCCGTTGACC
* *
4575157 GGTGACATATTAGTAATTATTTTGAAACT
1 GGTGACATATTAGTAATTAATTCGAAACT
4575186 GGTGACATATTGAG-AATTAATTCGAAA
1 GGTGACATATT-AGTAATTAATTCGAAA
4575213 AGAGTGTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.92
30 2 0.08
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.36
Consensus pattern (29 bp):
GGTGACATATTAGTAATTAATTCGAAACT
Found at i:4575343 original size:29 final size:30
Alignment explanation
Indices: 4575288--4575345 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
4575278 TTTAGTAAAT
4575288 ATTTTGAAAATGGTGCTATATTGGTAATTA
1 ATTTTGAAAATGGTGCTATATTGGTAATTA
* *
4575318 ATTTT-AAAATGGTGCTATTTTTGTAATT
1 ATTTTGAAAATGGTGCTATATTGGTAATT
4575346 TTGAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.48
Consensus pattern (30 bp):
ATTTTGAAAATGGTGCTATATTGGTAATTA
Found at i:4582705 original size:29 final size:30
Alignment explanation
Indices: 4582650--4582707 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
4582640 TTTAGTAAAT
4582650 ATTTTGAAAATGGTGCTATATTGGTAATTA
1 ATTTTGAAAATGGTGCTATATTGGTAATTA
* *
4582680 ATTTT-AAAATGGTGCTATTTTTGTAATT
1 ATTTTGAAAATGGTGCTATATTGGTAATT
4582708 TTGAAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.48
Consensus pattern (30 bp):
ATTTTGAAAATGGTGCTATATTGGTAATTA
Found at i:4593462 original size:10 final size:10
Alignment explanation
Indices: 4593443--4593484 Score: 66
Period size: 10 Copynumber: 4.1 Consensus size: 10
4593433 ATTATGCTTG
*
4593443 AAGAAGAAAA
1 AAGAAAAAAA
4593453 AAGAAAAAAA
1 AAGAAAAAAA
4593463 AAGAAAAAAA
1 AAGAAAAAAA
4593473 AAGAAAGAAAA
1 AAGAAA-AAAA
4593484 A
1 A
4593485 TAATAATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
10 25 0.83
11 5 0.17
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:4593870 original size:18 final size:18
Alignment explanation
Indices: 4593847--4593883 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4593837 TCCAAGTTTA
4593847 TCTTTTCGAAATTCAATT
1 TCTTTTCGAAATTCAATT
**
4593865 TCTTTTTTAAATTCAATT
1 TCTTTTCGAAATTCAATT
4593883 T
1 T
4593884 ATTCTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.14, G:0.03, T:0.57
Consensus pattern (18 bp):
TCTTTTCGAAATTCAATT
Found at i:4595810 original size:2 final size:2
Alignment explanation
Indices: 4595805--4595833 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4595795 ATTCACATAA
4595805 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4595834 ATTCATTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4596245 original size:21 final size:21
Alignment explanation
Indices: 4596203--4596246 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
4596193 ATCACATTGT
**
4596203 GATTTTCCAAATTCGCGTTGC
1 GATTTTCCAAATTCGCAATGC
*
4596224 GATTTTCCTAATTCGCAATGC
1 GATTTTCCAAATTCGCAATGC
4596245 GA
1 GA
4596247 ATACGTAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (21 bp):
GATTTTCCAAATTCGCAATGC
Found at i:4596261 original size:20 final size:20
Alignment explanation
Indices: 4596236--4596348 Score: 181
Period size: 20 Copynumber: 5.7 Consensus size: 20
4596226 TTTTCCTAAT
4596236 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
4596256 TCGCAATGCAAATACGTAAA
1 TCGCAATGCGAATACGTAAA
4596276 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
4596296 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
4596316 TCGCAATACGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
* *
4596336 TTGCAACGCGAAT
1 TCGCAATGCGAAT
4596349 CTGACTATCG
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 86 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:4596570 original size:22 final size:22
Alignment explanation
Indices: 4596545--4596610 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
4596535 GGCGACATCC
4596545 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
4596567 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* * *
4596589 GTCTCCGTCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
4596611 TTCACGATCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.23, C:0.39, G:0.17, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:4596989 original size:20 final size:19
Alignment explanation
Indices: 4596957--4597066 Score: 104
Period size: 20 Copynumber: 5.9 Consensus size: 19
4596947 GTTGTGGTTT
4596957 TCATTTCGCGTTGCGATAG
1 TCATTTCGCGTTGCGATAG
* **
4596976 TCATTTTCGTGTTGCGATTT
1 TCA-TTTCGCGTTGCGATAG
*
4596996 TCATTTCGCCTTGCGAT--
1 TCATTTCGCGTTGCGATAG
4597013 TC--TT-GCGTTGCGATAG
1 TCATTTCGCGTTGCGATAG
*
4597029 TCAAATTCGCGTTGCGATAG
1 TC-ATTTCGCGTTGCGATAG
*
4597049 TCATTTTCGTGTTGCGAT
1 TCA-TTTCGCGTTGCGAT
4597067 TTTAAGTTTC
Statistics
Matches: 75, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
14 9 0.12
15 2 0.03
16 2 0.03
17 2 0.03
19 18 0.24
20 42 0.56
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.42
Consensus pattern (19 bp):
TCATTTCGCGTTGCGATAG
Found at i:4598928 original size:20 final size:20
Alignment explanation
Indices: 4598903--4599015 Score: 65
Period size: 20 Copynumber: 6.3 Consensus size: 20
4598893 AGAATAGTTT
4598903 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
4598923 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
4598939 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
4598956 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
*
4598972 A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
4598990 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
4599010 ACTATC
1 ACTATC
4599016 ACAACGAAAG
Statistics
Matches: 74, Mismatches: 5, Indels: 28
0.69 0.05 0.26
Matches are distributed among these distances:
14 14 0.19
16 10 0.14
17 8 0.11
18 5 0.07
19 7 0.09
20 30 0.41
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:4598949 original size:34 final size:34
Alignment explanation
Indices: 4598906--4598999 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 34
4598896 ATAGTTTACT
* * *
4598906 ATCGCAATGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGACTATCGCAACAACAAA
**
4598940 ATCGCAATGCG-AAATGAAAATCGCAACAACAAA
1 ATCGCAATGCGAAAATGACTATCGCAACAACAAA
*
4598973 ATCGCAACGCGAAAATGACTATCGCAA
1 ATCGCAATGCGAAAATGACTATCGCAA
4599000 TGCGAATTTG
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 27 0.53
34 24 0.47
ACGTcount: A:0.45, C:0.22, G:0.19, T:0.14
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGACTATCGCAACAACAAA
Found at i:4599168 original size:20 final size:20
Alignment explanation
Indices: 4599066--4599162 Score: 131
Period size: 20 Copynumber: 4.8 Consensus size: 20
4599056 GATTCTCTCG
* ** *
4599066 TTGCAATAGTCAAATTCGTA
1 TTGCGATAGTCATTTTCGCA
**
4599086 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
4599106 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
4599126 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
4599146 TTGCGATAGTCATTTTC
1 TTGCGATAGTCATTTTC
4599163 ACGTTGTGAT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 72 1.00
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:4599747 original size:21 final size:21
Alignment explanation
Indices: 4599656--4599760 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 21
4599646 GACTCACCTG
*
4599656 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
* *
4599678 T-ATCGTTTAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
4599698 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
4599719 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
4599740 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
4599761 CTAGCATTCT
Statistics
Matches: 61, Mismatches: 21, Indels: 3
0.72 0.25 0.04
Matches are distributed among these distances:
20 3 0.05
21 57 0.93
22 1 0.02
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:4599760 original size:42 final size:43
Alignment explanation
Indices: 4599653--4599761 Score: 109
Period size: 42 Copynumber: 2.6 Consensus size: 43
4599643 CCCGACTCAC
* * *
4599653 CTGTCATCGTTCAAGAGG--CCTCCCCTATCGTTTAAGAGGCCC
1 CTGTCATCGTTCAAGAGGTCCCT-CCCTACCGTTCAAGAGGCCA
* **
4599695 CTATCATCCCTCAAGA-GTCCCCTCCC-ACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGGT-CCCTCCCTACCGTTCAAGAGGCCA
*
4599737 CTGTCATCGTTGAAGAGGTCCCTCC
1 CTGTCATCGTTCAAGAGGTCCCTCC
4599762 TAGCATTCTA
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
41 1 0.02
42 44 0.83
43 5 0.09
44 3 0.06
ACGTcount: A:0.20, C:0.37, G:0.19, T:0.24
Consensus pattern (43 bp):
CTGTCATCGTTCAAGAGGTCCCTCCCTACCGTTCAAGAGGCCA
Found at i:4601163 original size:14 final size:14
Alignment explanation
Indices: 4601144--4601179 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
4601134 ATTGTTTAAT
4601144 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
4601158 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
4601172 TGATTTGT
1 TGATTTGT
4601180 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:4601373 original size:34 final size:33
Alignment explanation
Indices: 4601285--4601380 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
4601275 AAAACAGACT
* ** *
4601285 ATCGCAACGCGGAAATGACTATCGCAACAAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
4601319 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
4601352 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
4601381 CGAAACTAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:4601376 original size:20 final size:19
Alignment explanation
Indices: 4601318--4601385 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 19
4601308 GCAACAAGAG
4601318 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
4601337 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
4601351 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
4601371 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
4601386 CTAAATTCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
19 12 0.30
20 13 0.32
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:4601420 original size:20 final size:19
Alignment explanation
Indices: 4601391--4601457 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
4601381 CGAAACTAAA
*
4601391 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCA-T
4601411 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
4601427 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
4601444 TTCGCATTGCGATT
1 TTCGCATTGCGATT
4601458 CTCTCGTTGC
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
14 6 0.15
16 7 0.18
17 4 0.10
18 3 0.08
19 8 0.21
20 11 0.28
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:4601436 original size:14 final size:14
Alignment explanation
Indices: 4601417--4601470 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
4601407 CATTTTCGCA
4601417 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
4601431 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
4601448 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
4601464 TTGCGAT
1 TTGCGAT
4601471 AGTCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:4601438 original size:34 final size:34
Alignment explanation
Indices: 4601395--4601490 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 34
4601385 ACTAAATTCG
4601395 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
4601429 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
** * *
4601462 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
4601491 AGTCATTTCC
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:4601487 original size:20 final size:20
Alignment explanation
Indices: 4601462--4601530 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
4601452 GCGATTCTCT
4601462 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
4601482 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
4601502 TGTTACGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
4601522 CGTTGCGAT
1 CGTTGCGAT
4601531 TTCCGCGTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:4603306 original size:24 final size:24
Alignment explanation
Indices: 4603272--4603325 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
4603262 CTGAAAAATC
4603272 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
* *
4603296 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
4603320 ATCAAA
1 ATCAAA
4603326 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.24
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTGACCAAG
Found at i:4603339 original size:24 final size:24
Alignment explanation
Indices: 4603272--4603339 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
4603262 CTGAAAAATC
* * *
4603272 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAGTCTGAATACTGACCAAG
** *
4603296 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAGTCTGAATACTGACCAAG
* *
4603320 ATCAAATTTTGAATACTGAC
1 ATCAAAGTCTGAATACTGAC
4603340 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (24 bp):
ATCAAAGTCTGAATACTGACCAAG
Found at i:4603789 original size:11 final size:11
Alignment explanation
Indices: 4603775--4603850 Score: 66
Period size: 11 Copynumber: 6.6 Consensus size: 11
4603765 AAAATTCAAG
4603775 AGCTCGATTGA
1 AGCTCGATTGA
*
4603786 AGCTCGAGACTCG-
1 AGCTC--GA-TTGA
4603799 AGCTCGATTGA
1 AGCTCGATTGA
4603810 AGCTCGATTTTG-
1 AGCTCGA--TTGA
*
4603822 AGCTCGATTCA
1 AGCTCGATTGA
*
4603833 AGCTCGATTAA
1 AGCTCGATTGA
4603844 AGCTCGA
1 AGCTCGA
4603851 ACTCAAACTC
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
10 4 0.07
11 31 0.57
12 7 0.13
13 10 0.19
14 2 0.04
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.26
Consensus pattern (11 bp):
AGCTCGATTGA
Found at i:4603828 original size:23 final size:23
Alignment explanation
Indices: 4603774--4603841 Score: 91
Period size: 23 Copynumber: 2.9 Consensus size: 23
4603764 AAAAATTCAA
**
4603774 GAGCTCGATTGAAGCTCGAGACTC
1 GAGCTCGATTGAAGCTCGA-TTTC
*
4603798 GAGCTCGATTGAAGCTCGATTTT
1 GAGCTCGATTGAAGCTCGATTTC
*
4603821 GAGCTCGATTCAAGCTCGATT
1 GAGCTCGATTGAAGCTCGATT
4603842 AAAGCTCGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 21 0.52
24 19 0.47
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (23 bp):
GAGCTCGATTGAAGCTCGATTTC
Found at i:4604263 original size:26 final size:26
Alignment explanation
Indices: 4604227--4604313 Score: 138
Period size: 26 Copynumber: 3.3 Consensus size: 26
4604217 CCTGCAGACA
4604227 CACAAAACAAGGGACAGAGCACCAAG
1 CACAAAACAAGGGACAGAGCACCAAG
4604253 CACAAAACAAGGGACAGAGCACCAAG
1 CACAAAACAAGGGACAGAGCACCAAG
* * *
4604279 CAAAAAACAAGGGACAGAGAACCAAA
1 CACAAAACAAGGGACAGAGCACCAAG
4604305 CACCAAAAC
1 CA-CAAAAC
4604314 CAATACTAGG
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
26 51 0.91
27 5 0.09
ACGTcount: A:0.54, C:0.26, G:0.20, T:0.00
Consensus pattern (26 bp):
CACAAAACAAGGGACAGAGCACCAAG
Found at i:4606012 original size:21 final size:21
Alignment explanation
Indices: 4605988--4606081 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
4605978 TGGTATAACT
4605988 TAAACCCTAACACATAAACCC
1 TAAACCCTAACACATAAACCC
*
4606009 TAAACCTTAACACATAAACCC
1 TAAACCCTAACACATAAACCC
* * * *
4606030 TAAACTCTAA-ACTTTAAATCT
1 TAAACCCTAACAC-ATAAACCC
* * *
4606051 TAAATCCTATCACATAAACTC
1 TAAACCCTAACACATAAACCC
*
4606072 TAAATCCTAA
1 TAAACCCTAA
4606082 ACCCTAAACC
Statistics
Matches: 57, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
20 2 0.04
21 53 0.93
22 2 0.04
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAACCCTAACACATAAACCC
Found at i:4606372 original size:14 final size:14
Alignment explanation
Indices: 4606355--4606395 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
4606345 TTTATTCATC
4606355 AATAATGTATTTTT
1 AATAATGTATTTTT
4606369 AAT-A--TATTTTT
1 AATAATGTATTTTT
*
4606380 AATAATGTAATTTT
1 AATAATGTATTTTT
4606394 AA
1 AA
4606396 AAAATATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 1 0.04
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:4607264 original size:20 final size:20
Alignment explanation
Indices: 4607183--4607265 Score: 121
Period size: 20 Copynumber: 4.2 Consensus size: 20
4607173 AAATTCAGTA
*
4607183 TTGCGATAGTCAGAATCGCA
1 TTGCGATAGTCAGAATCGCG
* *
4607203 TTGCGATAGTCAAAATTGCG
1 TTGCGATAGTCAGAATCGCG
*
4607223 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
4607243 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
4607263 TTG
1 TTG
4607266 TGATTTACAA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:4607279 original size:20 final size:20
Alignment explanation
Indices: 4607256--4607328 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
4607246 CGATAGTCAG
* *
4607256 ATTCGCGTTGTGATTTACAA
1 ATTCGCATTGCGATTTACAA
**
4607276 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACAA
**
4607296 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACAA
4607316 ATTCGCATTGCGA
1 ATTCGCATTGCGA
4607329 ATTAGGAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACAA
Found at i:4608203 original size:21 final size:21
Alignment explanation
Indices: 4608179--4608244 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 21
4608169 GCAAATTCGC
4608179 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
4608200 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
4608220 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
4608241 GTTG
1 GTTG
4608245 AAATCGCAAC
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 15 0.44
21 19 0.56
ACGTcount: A:0.17, C:0.18, G:0.27, T:0.38
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:4608251 original size:20 final size:20
Alignment explanation
Indices: 4608187--4608251 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
4608177 GCGTTGCATT
4608187 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTG-AAA
* * **
4608208 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTT-GAAA
4608228 TCGCGTTGCGATAGTTGAAA
1 TCGCGTTGCGATAGTTGAAA
4608248 TCGC
1 TCGC
4608252 AACGCGATCT
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
20 20 0.59
21 14 0.41
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (20 bp):
TCGCGTTGCGATAGTTGAAA
Found at i:4608322 original size:101 final size:100
Alignment explanation
Indices: 4608154--4608342 Score: 326
Period size: 101 Copynumber: 1.9 Consensus size: 100
4608144 AATTCGCATT
*
4608154 GCGATCTCCACTATCGCAAATTCGCGTTGCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGA
1 GCGATCTCCACTATCGCAAATTCGCGTTGCATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGA
*
4608219 TTTTCC-ATTTCGCGTTGCGATAGTTGAAATCGCAAC
66 TTTTCCAAATT--CGTTGCGATAGTTGAAATCGCAAC
*
4608255 GCGATCTCCACTATCGCAAATTCGCGTTGCATTTCGCATTGCTATAGTTGAAAATCGCGTTGCGA
1 GCGATCTCCACTATCGCAAATTCGCGTTGCATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGA
4608320 TTTTCCAAATTCGTTGCGATAGT
66 TTTTCCAAATTCGTTGCGATAGT
4608343 CTACAGTTGT
Statistics
Matches: 84, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
100 12 0.14
101 69 0.82
102 3 0.04
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (100 bp):
GCGATCTCCACTATCGCAAATTCGCGTTGCATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGA
TTTTCCAAATTCGTTGCGATAGTTGAAATCGCAAC
Found at i:4608376 original size:22 final size:22
Alignment explanation
Indices: 4608313--4608376 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
4608303 TGAAAATCGC
*
4608313 GTTGCGATTTTCCAAATTC---
1 GTTGCGATTTTCTAAATTCGTT
** *
4608332 GTTGCGATAGTCTACAGTT-GTT
1 GTTGCGATTTTCTA-AATTCGTT
4608354 GTTGCGATTTTCTAAATTCGTT
1 GTTGCGATTTTCTAAATTCGTT
4608376 G
1 G
4608377 AAAAAAAAGA
Statistics
Matches: 33, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
19 11 0.33
20 3 0.09
21 3 0.09
22 16 0.48
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.44
Consensus pattern (22 bp):
GTTGCGATTTTCTAAATTCGTT
Found at i:4608463 original size:6 final size:6
Alignment explanation
Indices: 4608452--4608488 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
4608442 GACACGTATT
*
4608452 ACCACG ACCACG ACCACG ACCACG ACCATG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
4608489 GACGGACGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.35, C:0.46, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:4608976 original size:5 final size:5
Alignment explanation
Indices: 4608962--4608996 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
4608952 CCACCGCCGC
4608962 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT C
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT C
4608997 AGGTCGTGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.00, C:0.43, G:0.20, T:0.37
Consensus pattern (5 bp):
CGTCT
Found at i:4609009 original size:6 final size:6
Alignment explanation
Indices: 4608998--4609024 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4608988 TCTCGTCTCA
4608998 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
4609025 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:4609133 original size:19 final size:19
Alignment explanation
Indices: 4609109--4609193 Score: 98
Period size: 19 Copynumber: 4.3 Consensus size: 19
4609099 TTAACTATCA
4609109 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * **
4609128 CAACGACAACTGTAGACTATCG
1 CAACG--AA-TTTGGAAAATCG
4609150 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
*
4609169 CAATGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
4609188 CAACGA
1 CAACGA
4609194 CAACTGTAGA
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
19 36 0.68
20 2 0.04
21 2 0.04
22 13 0.25
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.20
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:4609159 original size:41 final size:41
Alignment explanation
Indices: 4609102--4609338 Score: 182
Period size: 41 Copynumber: 5.8 Consensus size: 41
4609092 TTTTTTTTTA
*
4609102 ACTATCACAACGAATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
* * *
4609143 ACTATCGCAACGAATTTGGAAAATCGCAATG--AA-TTTGG
1 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
** * * ** *
4609181 AAAATCGCAACGACAACTGTAGACTATCGCAACG-CGAAATG--G
1 ACTATCGCAACG--AA-TTTGGAAAATCGCAACGAC-AACTGTAG
** * ** *
4609223 AAAATCGCAACGCGATTTTCAACTATCGCAACGACAACTGTAG
1 ACTATCGCAACG-AATTTGGAA-AATCGCAACGACAACTGTAG
*
4609266 ACGATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
*
4609307 ACTATCGCAACGCGAA-ATGGAAAATCGCAACG
1 ACTATCGCAA--CGAATTTGGAAAATCGCAACG
4609339 CGGTTTTCAA
Statistics
Matches: 158, Mismatches: 26, Indels: 23
0.76 0.13 0.11
Matches are distributed among these distances:
38 13 0.08
39 2 0.01
40 5 0.03
41 85 0.54
42 35 0.22
43 17 0.11
44 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
Found at i:4609206 original size:60 final size:60
Alignment explanation
Indices: 4609109--4609297 Score: 272
Period size: 60 Copynumber: 3.1 Consensus size: 60
4609099 TTAACTATCA
4609109 CAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGAATTTGGAAAATCG
* *
4609169 CAATGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAA-ATGGAAAATCG
1 CAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAA--CGAATTTGGAAAATCG
* ** * *
4609230 CAACGCGATTTTCAACTATCGCAACGACAACTGTAGACGATCGCAACGAATTTGGAAAATCG
1 CAACG-AATTTGGAA-AATCGCAACGACAACTGTAGACTATCGCAACGAATTTGGAAAATCG
4609292 CAACGA
1 CAACGA
4609298 CAACTGTAGA
Statistics
Matches: 114, Mismatches: 10, Indels: 9
0.86 0.08 0.07
Matches are distributed among these distances:
60 43 0.38
61 18 0.16
62 25 0.22
63 28 0.25
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (60 bp):
CAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGAATTTGGAAAATCG
Found at i:4609293 original size:104 final size:104
Alignment explanation
Indices: 4609165--4609358 Score: 370
Period size: 104 Copynumber: 1.9 Consensus size: 104
4609155 AATTTGGAAA
*
4609165 ATCGCAATGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGGAAAATCG
1 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGGAAAATCG
4609230 CAACGCGATTTTCAACTATCGCAACGACAACTGTAGACG
66 CAACGCGATTTTCAACTATCGCAACGACAACTGTAGACG
4609269 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGGAAAATCG
1 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGGAAAATCG
*
4609334 CAACGCGGTTTTCAACTATCGCAAC
66 CAACGCGATTTTCAACTATCGCAAC
4609359 TCGATTTTCA
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 88 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (104 bp):
ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGGAAAATCG
CAACGCGATTTTCAACTATCGCAACGACAACTGTAGACG
Found at i:4609356 original size:21 final size:21
Alignment explanation
Indices: 4609330--4609383 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
4609320 GAAATGGAAA
*
4609330 ATCGCAACGCGGTTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
4609351 ATCGCAACTCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
4609372 ATCGCAACGCGA
1 ATCGCAACGCGA
4609384 AATGCAACGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:4609818 original size:2 final size:2
Alignment explanation
Indices: 4609811--4609848 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4609801 ATAACATTAC
4609811 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
4609849 TTCATACCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4609928 original size:15 final size:15
Alignment explanation
Indices: 4609895--4609926 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4609885 TATTTTTCTT
4609895 ATTT-AGATTTTATG
1 ATTTAAGATTTTATG
4609909 ATTTAAGATTTTAT-
1 ATTTAAGATTTTATG
4609923 ATTT
1 ATTT
4609927 TAGGATTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.59
Consensus pattern (15 bp):
ATTTAAGATTTTATG
Found at i:4612205 original size:2 final size:2
Alignment explanation
Indices: 4612198--4612226 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4612188 TAATAATAAC
4612198 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4612227 GTTGAACTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4613369 original size:28 final size:28
Alignment explanation
Indices: 4613311--4613369 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
4613301 TATAAAGTTA
* *
4613311 TCTAAACCAGAAGGGATAACTAATGTTC
1 TCTAAACCAGAAGGGATAACTAATATAC
**
4613339 TCTAAACCAGAAGGGATAACTGTTATAC
1 TCTAAACCAGAAGGGATAACTAATATAC
4613367 TCT
1 TCT
4613370 CTATCATTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (28 bp):
TCTAAACCAGAAGGGATAACTAATATAC
Found at i:4614160 original size:17 final size:17
Alignment explanation
Indices: 4614129--4614162 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4614119 TAACTTGAGC
*
4614129 ACACAAAGTGCTATCAT
1 ACACAAAGTACTATCAT
*
4614146 ACACAAAGTATTATCAT
1 ACACAAAGTACTATCAT
4614163 GATACTTGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.26
Consensus pattern (17 bp):
ACACAAAGTACTATCAT
Found at i:4614674 original size:2 final size:2
Alignment explanation
Indices: 4614667--4614693 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4614657 AACAAATCGT
4614667 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4614694 TCAAACTTGC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4626799 original size:2 final size:2
Alignment explanation
Indices: 4626792--4626823 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4626782 TTGTATGTGA
4626792 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4626824 GTAGATGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4630277 original size:60 final size:62
Alignment explanation
Indices: 4630183--4630315 Score: 209
Period size: 60 Copynumber: 2.2 Consensus size: 62
4630173 TCTAAATTAG
* * *
4630183 TCCCCAAACTAAGATCTTAATTCTAAATTGGTCCCCAAAC-TTTTTGAACATTTCAA-TTCA
1 TCCCCAAACTATGATATTAATTCTAAATTAGTCCCCAAACTTTTTTGAACATTTCAATTTCA
*
4630243 TCCCCAAACTATGATATTCATTCTAAATTAGTCCCCAAACTTTTTTGAACATTTCAATTTCA
1 TCCCCAAACTATGATATTAATTCTAAATTAGTCCCCAAACTTTTTTGAACATTTCAATTTCA
4630305 T-CCCAAACTAT
1 TCCCCAAACTAT
4630316 ACATATATAC
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
60 36 0.54
61 26 0.39
62 5 0.07
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (62 bp):
TCCCCAAACTATGATATTAATTCTAAATTAGTCCCCAAACTTTTTTGAACATTTCAATTTCA
Found at i:4630281 original size:31 final size:31
Alignment explanation
Indices: 4630152--4630283 Score: 114
Period size: 31 Copynumber: 4.3 Consensus size: 31
4630142 TATAATTCCA
* *
4630152 TCCCTAAATTATG-TATATCATTCTAAATTAG
1 TCCCCAAACTATGATAT-TCATTCTAAATTAG
* * * *
4630183 TCCCCAAACTAAGATCTTAATTCTAAATTGG
1 TCCCCAAACTATGATATTCATTCTAAATTAG
* *
4630214 TCCCCAAACTTTTTGA-A--CATT-TCAATTCA-
1 TCCCCAAAC--TATGATATTCATTCTAAATT-AG
4630243 TCCCCAAACTATGATATTCATTCTAAATTAG
1 TCCCCAAACTATGATATTCATTCTAAATTAG
4630274 TCCCCAAACT
1 TCCCCAAACT
4630284 TTTTTGAACA
Statistics
Matches: 78, Mismatches: 14, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
27 4 0.05
28 1 0.01
29 14 0.18
30 8 0.10
31 46 0.59
32 2 0.03
33 3 0.04
ACGTcount: A:0.34, C:0.24, G:0.06, T:0.36
Consensus pattern (31 bp):
TCCCCAAACTATGATATTCATTCTAAATTAG
Done.