Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008319.1 Hibiscus syriacus cultivar Beakdansim tig00111022_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4819703
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 21
Found at i:4631234 original size:36 final size:37
Alignment explanation
Indices: 4631173--4631259 Score: 131
Period size: 36 Copynumber: 2.4 Consensus size: 37
4631163 TTGGCGTGAG
*
4631173 CTCTTCTTCTTCGTCAGCTATATTCAAGTGTTTGTATC
1 CTCTTCTTCTTC-TCAGCTATATTCAAGTGTTTATATC
*
4631211 CTCTTGTTCTTCT-AGCTATATTCAAGTGTTTATATC
1 CTCTTCTTCTTCTCAGCTATATTCAAGTGTTTATATC
*
4631247 TTCTTCTTCTTCT
1 CTCTTCTTCTTCT
4631260 TCTTCTTCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 33 0.73
37 1 0.02
38 11 0.24
ACGTcount: A:0.15, C:0.23, G:0.10, T:0.52
Consensus pattern (37 bp):
CTCTTCTTCTTCTCAGCTATATTCAAGTGTTTATATC
Found at i:4631253 original size:3 final size:3
Alignment explanation
Indices: 4631245--4631280 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
4631235 AGTGTTTATA
4631245 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
4631281 AGATACATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:4631330 original size:39 final size:39
Alignment explanation
Indices: 4631263--4631391 Score: 179
Period size: 39 Copynumber: 3.3 Consensus size: 39
4631253 TTCTTCTTCT
*
4631263 TCTTCTTCTTCTTCTTCTAGA-TACATGCAAGTGTTTATA
1 TCTTCTTCTTCTTCTTCTA-ACTATATGCAAGTGTTTATA
* * *
4631302 TCTTCTTCTTCTTCCTCTAACTGTATGCAATTGTTTATA
1 TCTTCTTCTTCTTCTTCTAACTATATGCAAGTGTTTATA
* * *
4631341 TCTTCTTCTTCTTCTTCTAGCTATATTCAAGTGTTTATG
1 TCTTCTTCTTCTTCTTCTAACTATATGCAAGTGTTTATA
4631380 TCTTCTTCTTCT
1 TCTTCTTCTTCT
4631392 CTTTTTCAGC
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
38 1 0.01
39 78 0.99
ACGTcount: A:0.16, C:0.22, G:0.09, T:0.53
Consensus pattern (39 bp):
TCTTCTTCTTCTTCTTCTAACTATATGCAAGTGTTTATA
Found at i:4631592 original size:2 final size:2
Alignment explanation
Indices: 4631585--4631617 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4631575 TCAACTAGTT
4631585 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4631618 TGTGTATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4644083 original size:4 final size:4
Alignment explanation
Indices: 4644060--4644101 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
4644050 GCAAACTCAA
* *
4644060 GTAT GCAT GTAT GCAT GTAT GTAT GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
4644102 CAAAATTACT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.24, C:0.05, G:0.26, T:0.45
Consensus pattern (4 bp):
GTAT
Found at i:4644812 original size:18 final size:18
Alignment explanation
Indices: 4644777--4644812 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4644767 TGTGTATAGA
*
4644777 GACACGCGCCACTTTCCG
1 GACACGCGCCACTATCCG
*
4644795 GACACGCGCCGCTATCCG
1 GACACGCGCCACTATCCG
4644813 CGGGGTTTGC
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:0.17, C:0.44, G:0.25, T:0.14
Consensus pattern (18 bp):
GACACGCGCCACTATCCG
Found at i:4644832 original size:16 final size:16
Alignment explanation
Indices: 4644813--4644845 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
4644803 CCGCTATCCG
4644813 CGGGGTTTGCTATAAA
1 CGGGGTTTGCTATAAA
*
4644829 CGGGGTTTGTTATAAA
1 CGGGGTTTGCTATAAA
4644845 C
1 C
4644846 TATAAAGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.12, G:0.30, T:0.33
Consensus pattern (16 bp):
CGGGGTTTGCTATAAA
Found at i:4651110 original size:22 final size:22
Alignment explanation
Indices: 4651082--4651125 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
4651072 TGTTCATCTT
*
4651082 CTAAAATTTTATAATTTAACCC
1 CTAAAATTTTATAAATTAACCC
4651104 CTAAAATTTTATAAATTAACCC
1 CTAAAATTTTATAAATTAACCC
4651126 ATAAGTATCT
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:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (22 bp):
CTAAAATTTTATAAATTAACCC
Found at i:4655343 original size:16 final size:16
Alignment explanation
Indices: 4655322--4655352 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4655312 CTCATTGTTT
4655322 TTTATTATTTTATCAA
1 TTTATTATTTTATCAA
*
4655338 TTTATTTTTTTATCA
1 TTTATTATTTTATCA
4655353 GTTAAATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTATTTTATCAA
Found at i:4655463 original size:132 final size:135
Alignment explanation
Indices: 4655233--4655474 Score: 312
Period size: 132 Copynumber: 1.8 Consensus size: 135
4655223 AATTATTAAG
* * * * * * *
4655233 TTTTATCTATTTTTCAGTCTCCTTTGAAACTATCATTTTTTATGTCTTTTGCAGTCACTTTAGAT
1 TTTTACCTATTTTTCAGTCTCCGTTGAAACCATCATTTTTTATGTCTTTTACAGTCACTCTAAAC
** *
4655298 ACTAATGAACTCGTCTCATTGTTTTTTATTATTTTATCAATTTATTTTTTTATCAGTTAAATTTA
66 ACTAATGAACTCGTCTCATTAATTTCTATTATTTTATCAATTTATTTTTTTATCAGTTAAATTTA
4655363 TGACT
131 TGACT
*
4655368 TTTTACCTA-TTTTCAGTCAT-CGTTGAAACCATCATTTTTT-T-TCTTTTACGGTCACTCTAAA
1 TTTTACCTATTTTTCAGTC-TCCGTTGAAACCATCATTTTTTATGTCTTTTACAGTCACTCTAAA
* * **
4655429 CATTAGTGAACTCGTCTTGTTAATTTCTATTATTTTATCAATTTAT
65 CACTAATGAACTCGTCTCATTAATTTCTATTATTTTATCAATTTAT
4655475 ATTCCTTTAA
Statistics
Matches: 91, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
132 54 0.59
133 1 0.01
134 27 0.30
135 9 0.10
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (135 bp):
TTTTACCTATTTTTCAGTCTCCGTTGAAACCATCATTTTTTATGTCTTTTACAGTCACTCTAAAC
ACTAATGAACTCGTCTCATTAATTTCTATTATTTTATCAATTTATTTTTTTATCAGTTAAATTTA
TGACT
Found at i:4661071 original size:15 final size:16
Alignment explanation
Indices: 4661040--4661074 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
4661030 AATATCACGA
4661040 ATTTTAATATGATTTT
1 ATTTTAATATGATTTT
*
4661056 ATTTTATTAT-ATTTT
1 ATTTTAATATGATTTT
4661071 ATTT
1 ATTT
4661075 GAATTTGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (16 bp):
ATTTTAATATGATTTT
Found at i:4667251 original size:27 final size:27
Alignment explanation
Indices: 4667212--4667272 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
4667202 AAAATTCTAA
*
4667212 AAAAAATCTTAAA-TTTCAGAAAATCTC
1 AAAAAATCCTAAATTTTCA-AAAATCTC
* *
4667239 AAAAACTCCTAAATTTTTAAAAATCTC
1 AAAAAATCCTAAATTTTCAAAAATCTC
4667266 AAAAAAT
1 AAAAAAT
4667273 ATAAAATCGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 25 0.86
28 4 0.14
ACGTcount: A:0.54, C:0.15, G:0.02, T:0.30
Consensus pattern (27 bp):
AAAAAATCCTAAATTTTCAAAAATCTC
Found at i:4667443 original size:29 final size:28
Alignment explanation
Indices: 4667354--4667443 Score: 83
Period size: 28 Copynumber: 3.1 Consensus size: 28
4667344 TTGAAATTAT
* * *
4667354 TAAAATTCCCAAAAAATATCTTAAATTC
1 TAAAAATCCCAAAAAAAATCATAAATTC
* * *
4667382 TAGAAAATCTC-AAAAAACTCCTAAATTCC
1 TA-AAAATCCCAAAAAAAATCATAAATT-C
*
4667411 TAAAAATCCCAAAAACAAATCATAAACTC
1 TAAAAATCCCAAAAA-AAATCATAAATTC
4667440 TAAA
1 TAAA
4667444 TCATAATCCC
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
28 22 0.45
29 18 0.37
30 9 0.18
ACGTcount: A:0.53, C:0.21, G:0.01, T:0.24
Consensus pattern (28 bp):
TAAAAATCCCAAAAAAAATCATAAATTC
Found at i:4667525 original size:154 final size:150
Alignment explanation
Indices: 4667198--4667488 Score: 388
Period size: 159 Copynumber: 1.9 Consensus size: 150
4667188 TCCATGAAAT
* **
4667198 TATTAAAATTCTAAAAAAAATCTTAAATTTCAGAAAATCTCAAAAACTCCTAAATTTTTAAAAAT
1 TATTAAAATTC-AAAAAATATCTTAAATTTCAGAAAATCTCAAAAACTCCTAAATTCCTAAAAAT
* * *
4667263 CTCAAAAAATATAAAATCGTAATCGTAATCTCTAAAAATCATAAGATTCATTTTTAGGGAGTTTA
65 CCCAAAAAATATAAAATCGTAATCATAATCCCTAAAAATCATAAGATTCATTTTTAGGGAGTTTA
4667328 TTTCTAAAAAAACCCCTTGAAA
130 TTTCTAAAAAAACCCCTT-AAA
4667350 TTATTAAAATTCCCAAAAAATATCTTAAA-TTCTAGAAAATCTCAAAAAACTCCTAAATTCCTAA
1 -TATTAAAATT--CAAAAAATATCTTAAATTTC-AGAAAATCTC-AAAAACTCCTAAATTCCTAA
*
4667414 AAATCCCAAAAACAAATCATAAACTC-TAAATCATAATCCCTAAAAATCATAAGATTCATTTTTT
61 AAATCCC--AAA-AAAT-ATAAAATCGT-AATCATAATCCCTAAAAATCATAAGATTCA-TTTTT
4667478 AGGGAGTTTAT
120 AGGGAGTTTAT
4667489 AATTTTTTGA
Statistics
Matches: 121, Mismatches: 7, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
153 13 0.11
154 24 0.20
155 25 0.21
157 3 0.02
158 5 0.04
159 35 0.29
160 16 0.13
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (150 bp):
TATTAAAATTCAAAAAATATCTTAAATTTCAGAAAATCTCAAAAACTCCTAAATTCCTAAAAATC
CCAAAAAATATAAAATCGTAATCATAATCCCTAAAAATCATAAGATTCATTTTTAGGGAGTTTAT
TTCTAAAAAAACCCCTTAAA
Found at i:4667698 original size:28 final size:29
Alignment explanation
Indices: 4667650--4667711 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
4667640 GAGTTTATGA
*
4667650 TTTTTGAGATTTTTAGAAATTT-AGGAGT
1 TTTTTGAGATTTCTAGAAATTTAAGGAGT
* *
4667678 TTTTTGAGACTTTCT-GGAATTTAAGGTGT
1 TTTTTGAGA-TTTCTAGAAATTTAAGGAGT
4667707 TTTTT
1 TTTTT
4667712 TTAGAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 15 0.52
29 14 0.48
ACGTcount: A:0.23, C:0.03, G:0.21, T:0.53
Consensus pattern (29 bp):
TTTTTGAGATTTCTAGAAATTTAAGGAGT
Found at i:4675184 original size:14 final size:14
Alignment explanation
Indices: 4675167--4675212 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
4675157 ATAATAGTAA
4675167 TAAATAAATAAAAC
1 TAAATAAATAAAAC
* *
4675181 TAAAAAAAAAAAAC
1 TAAATAAATAAAAC
4675195 TAAAATAAATAATAAC
1 T-AAATAAATAA-AAC
4675211 TA
1 TA
4675213 TAATCAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 13 0.50
15 9 0.35
16 4 0.15
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.20
Consensus pattern (14 bp):
TAAATAAATAAAAC
Found at i:4675461 original size:129 final size:130
Alignment explanation
Indices: 4675339--4675577 Score: 324
Period size: 131 Copynumber: 1.8 Consensus size: 130
4675329 AATATATTAT
4675339 TAAATAAAACAAATGAATAGAA-ATAA-ATATACAGATAATAATAAAA-GAAAAAAAATATGTTT
1 TAAATAAAACAAATGAA-A-AATA-AAGATATACAGATAATAATAAAAGGAAAAAAAATATGTTT
* *
4675401 ATATACGCTATCAA-AATACTTAAAATAATAAATTAACGATGGTTATGTATAGAGATAAATAAAA
63 ATATACGCTATCAATAATACTTAAAATAATAAAAT-ACGATGATTATGTATAGAGATAAATAAAA
4675465 TAAA
127 TAAA
* ** ** *
4675469 TACATAAAGTAAATGAAAAATAAAGATATACCTATAATAATAAAAGGGAAAAAATATATGTTTAT
1 TAAATAAAACAAATGAAAAATAAAGATATACAGATAATAATAAAA-GGAAAAAAAATATGTTTAT
*
4675534 ATACGCTATCAATGATACTTAAAATAATAAAATACGATGATTAT
65 ATACGCTATCAATAATACTTAAAATAATAAAATACGATGATTAT
4675578 ATGTATATAT
Statistics
Matches: 95, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
128 4 0.04
129 20 0.21
130 14 0.15
131 39 0.41
132 18 0.19
ACGTcount: A:0.56, C:0.06, G:0.10, T:0.28
Consensus pattern (130 bp):
TAAATAAAACAAATGAAAAATAAAGATATACAGATAATAATAAAAGGAAAAAAAATATGTTTATA
TACGCTATCAATAATACTTAAAATAATAAAATACGATGATTATGTATAGAGATAAATAAAATAAA
Found at i:4675657 original size:34 final size:36
Alignment explanation
Indices: 4675584--4675658 Score: 84
Period size: 34 Copynumber: 2.1 Consensus size: 36
4675574 TTATATGTAT
* *
4675584 ATATATATGTATAATAAATAAAATGAAATACATAAA
1 ATATATATATATAATAAATAAAATGAAATAAATAAA
* *
4675620 ATATATATATAT-ATAGAAT-AAA-GGAATAAATATA
1 ATATATATATATAATA-AATAAAATGAAATAAATAAA
4675654 ATATA
1 ATATA
4675659 ATGAAAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
34 14 0.41
35 6 0.18
36 14 0.41
ACGTcount: A:0.60, C:0.01, G:0.07, T:0.32
Consensus pattern (36 bp):
ATATATATATATAATAAATAAAATGAAATAAATAAA
Found at i:4677542 original size:105 final size:105
Alignment explanation
Indices: 4676984--4677542 Score: 971
Period size: 105 Copynumber: 5.3 Consensus size: 105
4676974 CCTTGACTTG
4676984 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-AAATTGGAGAAATGTTTGGTGACAACCAGCG
1 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GAGAAATGTTTGGTGACAACCAGCG
4677048 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
65 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
*
4677089 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-AAATTTGAGAAATGTTTGGTGACAACCAGCG
1 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA-TTGAGAAATGTTTGGTGACAACCAGCG
4677153 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
65 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
*
4677194 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGG
1 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGGTGACAACCAGCGG
* *
4677259 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGCAGTCC
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* * *
4677299 AATATCTTTCGTTTTGAAATTGAAATTGGCTCTG-AATTGGAGAAATGTTTGGTGACAACCAGCG
1 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GAGAAATGTTTGGTGACAACCAGCG
*
4677363 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCGGGAGTCC
65 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* *
4677404 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGAAAACCAGCGG
1 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGGTGACAACCAGCGG
*
4677469 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCC
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
4677509 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
4677543 GGTAAAACCT
Statistics
Matches: 431, Mismatches: 19, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
104 4 0.01
105 418 0.97
106 9 0.02
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (105 bp):
AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGGTGACAACCAGCGG
TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
Found at i:4678331 original size:13 final size:13
Alignment explanation
Indices: 4678313--4678354 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
4678303 ACCCTAAGCG
4678313 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
4678326 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
**
4678339 TTTTTCATTTTTT
1 TTTTTTGTTTTTT
4678352 TTT
1 TTT
4678355 CAACTTAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.02, C:0.02, G:0.05, T:0.90
Consensus pattern (13 bp):
TTTTTTGTTTTTT
Found at i:4687799 original size:20 final size:20
Alignment explanation
Indices: 4687760--4687803 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
4687750 ATGGTTAGTA
*
4687760 AAATAAAAATAAATGAAAAT
1 AAATAAAAATAAAAGAAAAT
4687780 AAATAAAAATAACAAG-AAAT
1 AAATAAAAATAA-AAGAAAAT
4687800 AAAT
1 AAAT
4687804 GGCAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (20 bp):
AAATAAAAATAAAAGAAAAT
Found at i:4689137 original size:17 final size:17
Alignment explanation
Indices: 4689091--4689148 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
4689081 ATATAATAGT
4689091 AATAAATAAATAA--AA
1 AATAAATAAATAACTAA
* * *
4689106 ACTAAAAAAAAAACTAA
1 AATAAATAAATAACTAA
*
4689123 AATAAATAAATAACTAT
1 AATAAATAAATAACTAA
4689140 AATCAAATA
1 AAT-AAATA
4689149 TGTACGTATA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
15 10 0.30
17 18 0.55
18 5 0.15
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (17 bp):
AATAAATAAATAACTAA
Found at i:4689393 original size:132 final size:135
Alignment explanation
Indices: 4689248--4689492 Score: 329
Period size: 133 Copynumber: 1.8 Consensus size: 135
4689238 AAAACTATAT
* * * *
4689248 ATAAATAACAAATATAT-TATTAA-TAAAACAATGAATAGAAATAAATATACAGATAATAATAAA
1 ATAAATAACAAATAAATACATAAAGTAAAACAA-AAATAGAAA-AAATATACAGATAATAATAAA
4689311 -AGAAAAAAATATGTTTATATACGCTATCAATAATACTT-AAATAATAAATTAACGATGGTTATG
64 GAGAAAAAAATATGTTTATATACGCTATCAATAATACTTAAAATAATAAATTAACGATGGTTATG
4689374 TATAGAG
129 TATAGAG
** * * ** *
4689381 ATAAATAA-AAATAAATACATAAAGTAAATGAAAAATATAAAGAATATACCTATAATAATAAAGG
1 ATAAATAACAAATAAATACATAAAGTAAAACAAAAATAGAAAAAATATACAGATAATAATAAAGA
*
4689445 GAAAAAAATATGTTTATATACGCTATCAATGATACTTAAAATAATAAA
66 GAAAAAAATATGTTTATATACGCTATCAATAATACTTAAAATAATAAA
4689493 AATACGATGA
Statistics
Matches: 96, Mismatches: 12, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
132 25 0.26
133 55 0.57
134 16 0.17
ACGTcount: A:0.57, C:0.06, G:0.09, T:0.29
Consensus pattern (135 bp):
ATAAATAACAAATAAATACATAAAGTAAAACAAAAATAGAAAAAATATACAGATAATAATAAAGA
GAAAAAAATATGTTTATATACGCTATCAATAATACTTAAAATAATAAATTAACGATGGTTATGTA
TAGAG
Found at i:4689561 original size:133 final size:130
Alignment explanation
Indices: 4689286--4689586 Score: 317
Period size: 133 Copynumber: 2.3 Consensus size: 130
4689276 CAATGAATAG
* *
4689286 AAATAAATATACAGATAATAATAAAAGAAAAAAATATGTTTATATACGCTATCAATAATACTTAA
1 AAAT-AATATAC-TATAATAATAAAGGAAAAAAATATGTTTATATACGCTATCAATAATACTTAA
* * *
4689351 ATAATAAATTAACGATGGTTATGTATAGAGATAAATAAAAATAAATACATAAAGTAAATGAAAAA
64 ATAATAAAATAACGATGATTA-GTATAGAGATAAATAAAAATAAATACATAAAATAAATGAAAAA
*
4689416 TAT
128 CAT
* *
4689419 AAAGAATATACCTATAATAATAAAGGGAAAAAAATATGTTTATATACGCTATCAATGATACTTAA
1 AAATAATATA-CTATAATAATAAA-GGAAAAAAATATGTTTATATACGCTATCAATAATACTT-A
* * * * **
4689484 AATAATAAAA-ATACGATGATTA-TAT-G-TATATATATATATGTATA-ATAAAATAAAATGAAA
63 AATAATAAAATA-ACGATGATTAGTATAGAGATAAATAAAAATAAATACATAAAAT-AAATG-AA
4689544 TAAACAT
125 -AAACAT
*
4689551 AAATATATATA-TATATATAATAAAGGAATAAAATAT
1 AAATA-ATATACTATA-ATAATAAAGGAAAAAAATAT
4689587 AATAATAATG
Statistics
Matches: 143, Mismatches: 16, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
129 6 0.04
130 17 0.12
131 18 0.13
132 37 0.26
133 46 0.32
134 19 0.13
ACGTcount: A:0.56, C:0.05, G:0.09, T:0.30
Consensus pattern (130 bp):
AAATAATATACTATAATAATAAAGGAAAAAAATATGTTTATATACGCTATCAATAATACTTAAAT
AATAAAATAACGATGATTAGTATAGAGATAAATAAAAATAAATACATAAAATAAATGAAAAACAT
Found at i:4689612 original size:21 final size:21
Alignment explanation
Indices: 4689559--4689616 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
4689549 ATAAATATAT
*
4689559 ATATATATATAATAAAGGAATA
1 ATATATATATAAT-AATGAATA
*
4689581 AAATATA-ATAATAATGAA-A
1 ATATATATATAATAATGAATA
4689600 ATATAGTATATAATAAT
1 ATATA-TATATAATAAT
4689617 AGTAGGGACT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 5 0.16
20 7 0.23
21 13 0.42
22 6 0.19
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (21 bp):
ATATATATATAATAATGAATA
Found at i:4693194 original size:15 final size:15
Alignment explanation
Indices: 4693174--4693203 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4693164 GAGTCAGATA
4693174 GCACATCATTAATAC
1 GCACATCATTAATAC
4693189 GCACATCATTAATAC
1 GCACATCATTAATAC
4693204 ACACTTGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.27
Consensus pattern (15 bp):
GCACATCATTAATAC
Found at i:4698577 original size:30 final size:31
Alignment explanation
Indices: 4698541--4698601 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
4698531 TTGATTTTGA
*
4698541 AAAAACTTACTCCCC-TTACTATAGCACATC
1 AAAAACTTACTCCCCTTTACTATAACACATC
4698571 AAAAACTTACTCCCCTTTACTATAACACATC
1 AAAAACTTACTCCCCTTTACTATAACACATC
4698602 TTAAATTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 15 0.52
31 14 0.48
ACGTcount: A:0.38, C:0.33, G:0.02, T:0.28
Consensus pattern (31 bp):
AAAAACTTACTCCCCTTTACTATAACACATC
Found at i:4704207 original size:22 final size:21
Alignment explanation
Indices: 4704181--4704227 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
4704171 AAGGTCAAAA
*
4704181 ATCAAATTGTTTGAAAATTG-AT
1 ATCAAATGGTTT-AAAA-TGAAT
4704203 ATC-AATGGTTTAAAATGAAT
1 ATCAAATGGTTTAAAATGAAT
4704223 ATCAA
1 ATCAA
4704228 TTACGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 2 0.09
20 9 0.41
21 8 0.36
22 3 0.14
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (21 bp):
ATCAAATGGTTTAAAATGAAT
Found at i:4708335 original size:61 final size:61
Alignment explanation
Indices: 4708240--4708361 Score: 208
Period size: 61 Copynumber: 2.0 Consensus size: 61
4708230 CAAACATAAA
*
4708240 ACATAAGCTTGGGAAGCTCTGCTCTGCTTCACAATAAACTGAAATAAAATAGGAATACATT
1 ACATAAGCTTGGGAAGCTCTGCTATGCTTCACAATAAACTGAAATAAAATAGGAATACATT
* * *
4708301 ACATAAGCTTGGGATGCTCTGCTATGCTTCACAATAACCTGAAATAGAATAGGAATACATT
1 ACATAAGCTTGGGAAGCTCTGCTATGCTTCACAATAAACTGAAATAAAATAGGAATACATT
4708362 TTCAGGCTGT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (61 bp):
ACATAAGCTTGGGAAGCTCTGCTATGCTTCACAATAAACTGAAATAAAATAGGAATACATT
Found at i:4711475 original size:2 final size:2
Alignment explanation
Indices: 4711462--4711500 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
4711452 CATCTTATTT
*
4711462 TA TA TA TT 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
4711501 CCATTTATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:4714680 original size:2 final size:2
Alignment explanation
Indices: 4714675--4714724 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
4714665 AGTGTGTGTG
4714675 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4714717 TA TA TA TA
1 TA TA TA TA
4714725 AGAAGAATAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4715787 original size:21 final size:21
Alignment explanation
Indices: 4715764--4715802 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4715754 TGTTTAATGA
4715764 AAAAT-ATACCAATTGTTAAC
1 AAAATGATACCAATTGTTAAC
*
4715784 AAAATGATATCAATTGTTA
1 AAAATGATACCAATTGTTA
4715803 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (21 bp):
AAAATGATACCAATTGTTAAC
Found at i:4724035 original size:2 final size:2
Alignment explanation
Indices: 4724028--4724057 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4724018 ATTTTATTAA
4724028 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
4724058 CAGTCAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4724790 original size:43 final size:44
Alignment explanation
Indices: 4724743--4724879 Score: 133
Period size: 43 Copynumber: 3.2 Consensus size: 44
4724733 TTACAACATA
*
4724743 TAGCGGCGATTGT-TCA-ACAAACGCCGCAAAAGGTATTGATATT
1 TAGCGGCGATT-TATCATACAAACGCCGCAATAGGTATTGATATT
*
4724786 TAGCGGCG-TTTATCATTA-AAACGCCGCAATAGGTTTTGATATT
1 TAGCGGCGATTTATCA-TACAAACGCCGCAATAGGTATTGATATT
* ** * * *
4724829 TAACGGC-ATTTGGCAGACAAACGCCGCAATA-GTCGTTGATGTT
1 TAGCGGCGATTTATCATACAAACGCCGCAATAGGT-ATTGATATT
4724872 TAGCGGCG
1 TAGCGGCG
4724880 TTCCGTAGTA
Statistics
Matches: 78, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
41 1 0.01
42 8 0.10
43 68 0.87
44 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (44 bp):
TAGCGGCGATTTATCATACAAACGCCGCAATAGGTATTGATATT
Found at i:4725357 original size:23 final size:21
Alignment explanation
Indices: 4725311--4725370 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
4725301 ATATATTACT
* *
4725311 TCTCTCTGTTCTGCCGCTGCC
1 TCTCTCTGTGCTGCCGCTACC
*
4725332 TCTCTCTGTGCTGCCGCTACT
1 TCTCTCTGTGCTGCCGCTACC
* *
4725353 TCTCTCTCTGCTTCCGCT
1 TCTCTCTGTGCTGCCGCT
4725371 GCTGCTCTAG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.02, C:0.42, G:0.17, T:0.40
Consensus pattern (21 bp):
TCTCTCTGTGCTGCCGCTACC
Found at i:4725415 original size:21 final size:21
Alignment explanation
Indices: 4725324--4725409 Score: 93
Period size: 21 Copynumber: 4.1 Consensus size: 21
4725314 CTCTGTTCTG
* *
4725324 CCGCTGCCT-CTCTCTGTGCTG
1 CCGCTG-CTGCTCTCTCTGCTT
* *
4725345 CCGCTACTTCTCTCTCTGCTT
1 CCGCTGCTGCTCTCTCTGCTT
**
4725366 CCGCTGCTGCTCTAGCTGCTT
1 CCGCTGCTGCTCTCTCTGCTT
*
4725387 CCGCTGCTGCTCTCTCTGTTT
1 CCGCTGCTGCTCTCTCTGCTT
4725408 CC
1 CC
4725410 CTTGCTTCAT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
20 2 0.04
21 52 0.96
ACGTcount: A:0.02, C:0.42, G:0.19, T:0.37
Consensus pattern (21 bp):
CCGCTGCTGCTCTCTCTGCTT
Found at i:4735202 original size:41 final size:41
Alignment explanation
Indices: 4735136--4735296 Score: 213
Period size: 41 Copynumber: 4.0 Consensus size: 41
4735126 CGTTTATACA
4735136 AAAAAACGCCACTATTGATTA-CACTATT-CTGGCGTTTGTT
1 AAAAAACGCCACTATTGATTATCACTATTGC-GGCGTTTGTT
4735176 AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTT-TT
1 AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTTGTT
* * * **
4735216 CTAAAAACGCCATTATTGATTAACACTATTATGGCGTTTGTCT
1 -AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTTGT-T
*
4735259 -AAAAACACCACTATTGATTATCACTATTGCGGCGTTTG
1 AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTTG
4735297 AGGAATAAAC
Statistics
Matches: 106, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
40 23 0.22
41 80 0.75
42 2 0.02
43 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (41 bp):
AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTTGTT
Found at i:4735254 original size:82 final size:81
Alignment explanation
Indices: 4735137--4735295 Score: 266
Period size: 82 Copynumber: 2.0 Consensus size: 81
4735127 GTTTATACAA
* *
4735137 AAAAACGCCACTATTGATTACACTATTCTGGCGTTTGT-TAAAAAACGCCACTATTGATTATCAC
1 AAAAACGCCACTATTGATTACACTATTATGGCGTTTGTCT-AAAAACACCACTATTGATTATCAC
4735201 TATTGCGGCGTTTTTCT
65 TATTGCGGCGTTTTTCT
*
4735218 AAAAACGCCATTATTGATTAACACTATTATGGCGTTTGTCTAAAAACACCACTATTGATTATCAC
1 AAAAACGCCACTATTGATT-ACACTATTATGGCGTTTGTCTAAAAACACCACTATTGATTATCAC
4735283 TATTGCGGCGTTT
65 TATTGCGGCGTTT
4735296 GAGGAATAAA
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
81 18 0.25
82 54 0.74
83 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.35
Consensus pattern (81 bp):
AAAAACGCCACTATTGATTACACTATTATGGCGTTTGTCTAAAAACACCACTATTGATTATCACT
ATTGCGGCGTTTTTCT
Found at i:4735442 original size:41 final size:42
Alignment explanation
Indices: 4735325--4735458 Score: 157
Period size: 42 Copynumber: 3.2 Consensus size: 42
4735315 ATGTGTAATA
* *
4735325 TATTGCGGCGTTTGTGGTATAAACGCCACGAATTTACCACTC
1 TATTGCGGCGTTTGTGGTATAAACGCCGCAAATTTACCACTC
* * *
4735367 TATTGCGGCGTTT-TGGCT-CAATCGCCGCAAAATTTA-TACTC
1 TATTGCGGCGTTTGTGG-TATAAACGCCGC-AAATTTACCACTC
* * *
4735408 TATTGTGGCGTTTGTGGTATAAACGCCGCTAATTTACCACCC
1 TATTGCGGCGTTTGTGGTATAAACGCCGCAAATTTACCACTC
4735450 TATTGCGGC
1 TATTGCGGC
4735459 ATTTTTTGTA
Statistics
Matches: 75, Mismatches: 12, Indels: 10
0.77 0.12 0.10
Matches are distributed among these distances:
41 33 0.44
42 42 0.56
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.33
Consensus pattern (42 bp):
TATTGCGGCGTTTGTGGTATAAACGCCGCAAATTTACCACTC
Found at i:4736680 original size:16 final size:15
Alignment explanation
Indices: 4736652--4736683 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
4736642 AGTGGAAGCT
4736652 GAAGAAGAAGAGGAG
1 GAAGAAGAAGAGGAG
4736667 GAAGAAGCAAGAGGAG
1 GAAGAAG-AAGAGGAG
4736683 G
1 G
4736684 CGCTGCGGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (15 bp):
GAAGAAGAAGAGGAG
Found at i:4737528 original size:21 final size:21
Alignment explanation
Indices: 4737495--4737562 Score: 118
Period size: 21 Copynumber: 3.2 Consensus size: 21
4737485 GATTCTTAAC
*
4737495 GCGAACTTCGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
*
4737516 GCGAGCTTGGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
4737537 GCGAACTTGGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
4737558 GCGAA
1 GCGAA
4737563 TATGTAAATC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (21 bp):
GCGAACTTGGACTATCGCAAT
Found at i:4739347 original size:28 final size:29
Alignment explanation
Indices: 4739311--4739367 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
4739301 ATAGGTAGAT
* *
4739311 ATAATTAAT-GTGAGTATAATATATATATA
1 ATAATTAATAGT-AATAAAATATATATATA
4739340 ATAA-TAATAGTAATAAAATATATATATA
1 ATAATTAATAGTAATAAAATATATATATA
4739368 CAACGACGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 19 0.76
29 6 0.24
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (29 bp):
ATAATTAATAGTAATAAAATATATATATA
Found at i:4739424 original size:23 final size:23
Alignment explanation
Indices: 4739396--4739459 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 23
4739386 AAAATAGAGA
4739396 ATAAATATAATAGTAAAAATATAT
1 ATAAATATAATA-TAAAAATATAT
4739420 A-AAAT-TAA-ATGAAAAATATAT
1 ATAAATATAATAT-AAAAATATAT
* *
4739441 ATATACATAATATTAAAAA
1 ATAAATATAATA-TAAAAA
4739460 ATAATTACGT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
20 1 0.03
21 12 0.36
22 5 0.15
23 7 0.21
24 7 0.21
25 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (23 bp):
ATAAATATAATATAAAAATATAT
Found at i:4741086 original size:105 final size:105
Alignment explanation
Indices: 4740934--4741708 Score: 1451
Period size: 105 Copynumber: 7.4 Consensus size: 105
4740924 GTATTGTTCC
*
4740934 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
*
4740999 CAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
4741039 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
*
4741104 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
4741144 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
4741209 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
4741249 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
*
4741314 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
4741354 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
4741419 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
4741459 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATATTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
* *
4741524 CAACGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
4741564 GAGTCCAATATCCTTCGTTGTGAAGTTGAGATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
4741629 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
4741669 GAGTCCAATATCCTTCGTTGTGAAGTTGAGATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
4741709 GGTAAAACCT
Statistics
Matches: 653, Mismatches: 17, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 653 1.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:4742477 original size:8 final size:8
Alignment explanation
Indices: 4742464--4742507 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
4742454 TTGTTTTCTC
*
4742464 TTCTTTTG
1 TTCTTTTT
4742472 TTCTTTTT
1 TTCTTTTT
*
4742480 TTCTCTTT
1 TTCTTTTT
*
4742488 TTCTTTTC
1 TTCTTTTT
4742496 TT-TTTTT
1 TTCTTTTT
4742503 TTCTT
1 TTCTT
4742508 CAATTTAGGG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (8 bp):
TTCTTTTT
Found at i:4742481 original size:11 final size:10
Alignment explanation
Indices: 4742457--4742507 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
4742447 ACCCCCATTG
*
4742457 TTTTCTCTTCT
1 TTTTTTCTT-T
*
4742468 TTTGTTCTTT
1 TTTTTTCTTT
*
4742478 TTTTCTCTTT
1 TTTTTTCTTT
4742488 TTCTTTTCTTT
1 TT-TTTTCTTT
4742499 TTTTTTCTT
1 TTTTTTCTT
4742508 CAATTTAGGG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
10 18 0.53
11 16 0.47
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:4742481 original size:21 final size:22
Alignment explanation
Indices: 4742457--4742508 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
4742447 ACCCCCATTG
4742457 TTTTCTCTTCTTT-TGTTCTTT
1 TTTTCTCTTCTTTCTGTTCTTT
*
4742478 TTTTCTCTT-TTTCTTTTCTTT
1 TTTTCTCTTCTTTCTGTTCTTT
*
4742499 TTTTTTCTTC
1 TTTTCTCTTC
4742509 AATTTAGGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 3 0.11
21 24 0.89
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (22 bp):
TTTTCTCTTCTTTCTGTTCTTT
Found at i:4742586 original size:15 final size:15
Alignment explanation
Indices: 4742553--4742586 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4742543 CGTTTTTCTC
4742553 TTTTTGTTTTTTTTG
1 TTTTTGTTTTTTTTG
*
4742568 TTTTTGTTTTGTTT-
1 TTTTTGTTTTTTTTG
4742582 TTTTT
1 TTTTT
4742587 CCAACTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (15 bp):
TTTTTGTTTTTTTTG
Found at i:4750610 original size:387 final size:387
Alignment explanation
Indices: 4749891--4750667 Score: 1509
Period size: 387 Copynumber: 2.0 Consensus size: 387
4749881 CTTGCTAGGC
*
4749891 CGTGAAGATGACGGGCTACTTTTTGCACTTGATCTAGGAAATCTCGGATGGTTGCATCTCGGGCC
1 CGTGAAGATGACGGGCTACTTTTTGCACTTAATCTAGGAAATCTCGGATGGTTGCATCTCGGGCC
4749956 CTCACCCTTCGTTGTGCTTGCTCCCAACGAAAATGCCATTGTAATCCTCCGTCGAAGGGCACCAT
66 CTCACCCTTCGTTGTGCTTGCTCCCAACGAAAATGCCATTGTAATCCTCCGTCGAAGGGCACCAT
4750021 CTGAAGCTCGTTTGCTTGCCTCTTGAACCCATCTACAATAGCCTCTAACTCAGCTATTGTCTTGC
131 CTGAAGCTCGTTTGCTTGCCTCTTGAACCCATCTACAATAGCCTCTAACTCAGCTATTGTCTTGC
*
4750086 CATCTTTCTCATGCTGTTTTTCTAAGTCAGCTACCCGAACTCTCAAGCGCTGGTTCTGATATTGA
196 CATCTTTCTCATGCTGTTTTTCTAAGTCAGCTACCCGAACTCTCAAGCACTGGTTCTGATATTGA
*
4750151 CTATCTGCCAAGCGTATTTGGGCAATCTTCATCTTTTCCTTCCAAGCTTTCTCATCAGGCCCCTC
261 CTATCTGCCAAGCGTATTTGGGCAATCTTCATCTGTTCCTTCCAAGCTTTCTCATCAGGCCCCTC
4750216 AAACTTCCTTTTCAGGCTATGAGCTTCGTCTTTCCAGTATTCAGAGGTTACCTTCAATTTGG
326 AAACTTCCTTTTCAGGCTATGAGCTTCGTCTTTCCAGTATTCAGAGGTTACCTTCAATTTGG
*
4750278 CGTGGAGATGACGGGCTACTTTTTGCACTTAATCTAGGAAATCTCGGATGGTTGCATCTCGGGCC
1 CGTGAAGATGACGGGCTACTTTTTGCACTTAATCTAGGAAATCTCGGATGGTTGCATCTCGGGCC
4750343 CTCACCCTTCGTTGTGCTTGCTCCCAACGAAAATGCCATTGTAATCCTCCGTCGAAGGGCACCAT
66 CTCACCCTTCGTTGTGCTTGCTCCCAACGAAAATGCCATTGTAATCCTCCGTCGAAGGGCACCAT
4750408 CTGAAGCTCGTTTGCTTGCCTCTTGAACCCATCTACAATAGCCTCTAACTCAGCTATTGTCTTGC
131 CTGAAGCTCGTTTGCTTGCCTCTTGAACCCATCTACAATAGCCTCTAACTCAGCTATTGTCTTGC
4750473 CATCTTTCTCATGCTGTTTTTCTAAGTCAGCTACCCGAACTCTCAAGCACTGGTTCTGATATTGA
196 CATCTTTCTCATGCTGTTTTTCTAAGTCAGCTACCCGAACTCTCAAGCACTGGTTCTGATATTGA
*
4750538 CTATCTGCCAAGCGTCTTTGGGCAATCTTCATCTGTTCCTTCCAAGCTTTCTCATCAGGCCCCTC
261 CTATCTGCCAAGCGTATTTGGGCAATCTTCATCTGTTCCTTCCAAGCTTTCTCATCAGGCCCCTC
4750603 AAACTTCCTTTTCAGGCTATGAGCTTCGTCTTTCCAGTATTCAGAGGTTACCTTCAATTTGG
326 AAACTTCCTTTTCAGGCTATGAGCTTCGTCTTTCCAGTATTCAGAGGTTACCTTCAATTTGG
4750665 CGT
1 CGT
4750668 TATCCTTGAC
Statistics
Matches: 385, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
387 385 1.00
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.33
Consensus pattern (387 bp):
CGTGAAGATGACGGGCTACTTTTTGCACTTAATCTAGGAAATCTCGGATGGTTGCATCTCGGGCC
CTCACCCTTCGTTGTGCTTGCTCCCAACGAAAATGCCATTGTAATCCTCCGTCGAAGGGCACCAT
CTGAAGCTCGTTTGCTTGCCTCTTGAACCCATCTACAATAGCCTCTAACTCAGCTATTGTCTTGC
CATCTTTCTCATGCTGTTTTTCTAAGTCAGCTACCCGAACTCTCAAGCACTGGTTCTGATATTGA
CTATCTGCCAAGCGTATTTGGGCAATCTTCATCTGTTCCTTCCAAGCTTTCTCATCAGGCCCCTC
AAACTTCCTTTTCAGGCTATGAGCTTCGTCTTTCCAGTATTCAGAGGTTACCTTCAATTTGG
Found at i:4752307 original size:10 final size:10
Alignment explanation
Indices: 4752288--4752321 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
4752278 AAGGTTAATA
*
4752288 AAATAGAAAT
1 AAATAAAAAT
4752298 AAATAAAAAT
1 AAATAAAAAT
*
4752308 AAAAAAAAAT
1 AAATAAAAAT
4752318 AAAT
1 AAAT
4752322 GGTAAAGGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:4752308 original size:16 final size:16
Alignment explanation
Indices: 4752287--4752320 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4752277 AAAGGTTAAT
* *
4752287 AAAATAGAAATAAATA
1 AAAATAAAAAAAAATA
4752303 AAAATAAAAAAAAATA
1 AAAATAAAAAAAAATA
4752319 AA
1 AA
4752321 TGGTAAAGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (16 bp):
AAAATAAAAAAAAATA
Found at i:4753421 original size:11 final size:11
Alignment explanation
Indices: 4753402--4753431 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4753392 ATAGTGAAAG
*
4753402 AATGATAAATA
1 AATGCTAAATA
4753413 AATGCTAAATA
1 AATGCTAAATA
4753424 AATGCTAA
1 AATGCTAA
4753432 GACGAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.57, C:0.07, G:0.10, T:0.27
Consensus pattern (11 bp):
AATGCTAAATA
Found at i:4753666 original size:23 final size:23
Alignment explanation
Indices: 4753638--4753701 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 23
4753628 AAAATAGAGA
4753638 ATAAATATAATAGTAAAAATATAT
1 ATAAATATAATA-TAAAAATATAT
4753662 A-AAAT-TAA-ATGAAAAATATAT
1 ATAAATATAATAT-AAAAATATAT
* *
4753683 ATATACATAATATTAAAAA
1 ATAAATATAATA-TAAAAA
4753702 ATAATTACGT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
20 1 0.03
21 12 0.36
22 5 0.15
23 7 0.21
24 7 0.21
25 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (23 bp):
ATAAATATAATATAAAAATATAT
Found at i:4756179 original size:14 final size:14
Alignment explanation
Indices: 4756160--4756192 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
4756150 TGTCGCACAC
4756160 AGTCAAAATTATTT
1 AGTCAAAATTATTT
4756174 AGTCAAAATTATTT
1 AGTCAAAATTATTT
4756188 AGTCA
1 AGTCA
4756193 TTGCGATCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.39
Consensus pattern (14 bp):
AGTCAAAATTATTT
Found at i:4757678 original size:14 final size:14
Alignment explanation
Indices: 4757659--4757691 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
4757649 GATGGAGCTG
*
4757659 TTTTATGTGAATAT
1 TTTTATATGAATAT
4757673 TTTTATATGAATAT
1 TTTTATATGAATAT
4757687 TTTTA
1 TTTTA
4757692 GTGGTATGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (14 bp):
TTTTATATGAATAT
Found at i:4767464 original size:27 final size:27
Alignment explanation
Indices: 4767434--4767511 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 27
4767424 GTATGCATCT
4767434 TTCTGAAGAATAAATCATATATATTGC
1 TTCTGAAGAATAAATCATATATATTGC
* * *
4767461 TTCT---CAAT---TGAGT-TATA-TGT
1 TTCTGAAGAATAAATCA-TATATATTGC
4767481 TTCTGAAGAATAAATCATATATATTGC
1 TTCTGAAGAATAAATCATATATATTGC
4767508 TTCT
1 TTCT
4767512 CAATTGAGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 18
0.60 0.10 0.30
Matches are distributed among these distances:
20 6 0.17
21 6 0.17
22 1 0.03
23 3 0.08
24 3 0.08
25 1 0.03
26 6 0.17
27 10 0.28
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (27 bp):
TTCTGAAGAATAAATCATATATATTGC
Found at i:4767502 original size:47 final size:47
Alignment explanation
Indices: 4767433--4767526 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
4767423 AGTATGCATC
4767433 TTTCTGAAGAATAAATCATATATATTGCTTCTCAATTGAGTTATATG
1 TTTCTGAAGAATAAATCATATATATTGCTTCTCAATTGAGTTATATG
*
4767480 TTTCTGAAGAATAAATCATATATATTGCTTCTCAATTGAGTTCTATG
1 TTTCTGAAGAATAAATCATATATATTGCTTCTCAATTGAGTTATATG
4767527 CAAAGAATCT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.43
Consensus pattern (47 bp):
TTTCTGAAGAATAAATCATATATATTGCTTCTCAATTGAGTTATATG
Found at i:4776123 original size:31 final size:31
Alignment explanation
Indices: 4776085--4776161 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
4776075 TCCACAATTT
* *
4776085 TATTTAAATAATATTAATCAAATCATTTAAC
1 TATTTAAATGATATTAATCAAACCATTTAAC
* *
4776116 TATTTAAACGATATTAATTAAACCATTTAAC
1 TATTTAAATGATATTAATCAAACCATTTAAC
4776147 TATTTAAATGATATT
1 TATTTAAATGATATT
4776162 GTATGTAGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (31 bp):
TATTTAAATGATATTAATCAAACCATTTAAC
Found at i:4777627 original size:2 final size:2
Alignment explanation
Indices: 4777616--4777645 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4777606 AAATTTATTA
4777616 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4777646 ATAATTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4784150 original size:20 final size:20
Alignment explanation
Indices: 4784127--4784178 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
4784117 AACGCGATCC
4784127 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
4784147 CCAGAATCGTAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
4784167 CCAAAATCGCAA
1 CCAGAATCGCAA
4784179 CGCGATTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.23
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:4784259 original size:20 final size:20
Alignment explanation
Indices: 4784234--4784427 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
4784224 GATTTTCCAT
* *
4784234 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
4784254 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
4784274 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
4784294 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
4784314 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
4784334 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
4784354 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
4784374 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
4784395 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
4784415 AATCGCAACGCGA
1 AATCGCAACGCGA
4784428 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:4784279 original size:40 final size:39
Alignment explanation
Indices: 4784230--4784427 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
4784220 TTGCGATTTT
* ** *
4784230 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
4784268 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
4784309 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
4784349 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
4784388 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
4784428 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:4784317 original size:60 final size:60
Alignment explanation
Indices: 4784234--4784426 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
4784224 GATTTTCCAT
* ** * *
4784234 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
4784294 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
4784354 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
4784415 AATCGCAACGCG
1 AATCGCAACGCG
4784427 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:4784847 original size:33 final size:33
Alignment explanation
Indices: 4784808--4784878 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
4784798 TTCACTTAGA
*
4784808 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
4784841 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
4784874 TTTCA
1 TTTCA
4784879 AGTTAGTATT
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:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:4785018 original size:14 final size:14
Alignment explanation
Indices: 4784999--4785053 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
4784989 AGAATGACTG
4784999 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
4785013 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
4785032 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
4785046 TCGCAACG
1 TCGCAACG
4785054 CCTAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:4785065 original size:33 final size:33
Alignment explanation
Indices: 4784999--4785069 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
4784989 AGAATGACTG
* **
4784999 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCCAAACCAAAA
*
4785032 TCGCAACGAGAGAATCGCAACGCCTAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCCAAACCAAAA
4785065 TCGCA
1 TCGCA
4785070 TTGCGATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.42, C:0.27, G:0.21, T:0.10
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCCAAACCAAAA
Found at i:4785087 original size:19 final size:19
Alignment explanation
Indices: 4785065--4785162 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
4785055 CTAACCAAAA
*
4785065 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
4785084 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
4785098 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
4785117 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
4785131 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
4785150 TCGCGTTGCGATT
1 TCGCGTTGCGATT
4785163 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:4785106 original size:14 final size:14
Alignment explanation
Indices: 4785087--4785176 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
4785077 TTTCATTTCG
4785087 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
4785101 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
4785120 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
4785134 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
4785151 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
4785167 CGTTGCGATT
1 CGTTGCGATT
4785177 TTCATTTCAA
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:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:4785112 original size:33 final size:33
Alignment explanation
Indices: 4785070--4785184 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
4785060 CAAAATCGCA
4785070 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
4785103 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
4785136 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
4785169 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
4785185 AACCAAAAGA
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:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:4787113 original size:185 final size:186
Alignment explanation
Indices: 4786883--4787540 Score: 1293
Period size: 185 Copynumber: 3.5 Consensus size: 186
4786873 TAGATTGCTT
*
4786883 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4786948 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
4787013 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
4787068 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4787133 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
4787198 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
4787254 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4787318 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
4787383 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
4787439 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4787504 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
4787541 ATCCATTCAA
Statistics
Matches: 470, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
185 339 0.72
186 131 0.28
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:4787197 original size:93 final size:93
Alignment explanation
Indices: 4786883--4787540 Score: 1293
Period size: 93 Copynumber: 7.1 Consensus size: 93
4786873 TAGATTGCTT
*
4786883 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4786948 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
4786976 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4787040 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
4787068 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4787133 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
4787161 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4787226 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
4787254 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4787318 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
4787346 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4787411 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
4787439 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4787504 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
4787532 AGTAAATTT
1 AGTAAATTT
4787541 ATCCATTCAA
Statistics
Matches: 562, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
92 184 0.33
93 378 0.67
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:4787380 original size:278 final size:278
Alignment explanation
Indices: 4786883--4787540 Score: 1307
Period size: 278 Copynumber: 2.4 Consensus size: 278
4786873 TAGATTGCTT
*
4786883 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4786948 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
4787013 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
131 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
4787078 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
196 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
4787143 TTTTGTCTTTTGGTTGAA
261 TTTTGTCTTTTGGTTGAA
4787161 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4787226 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
4787291 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
131 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
4787356 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
196 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
4787421 TTTTGTCTTTTGGTTGAA
261 TTTTGTCTTTTGGTTGAA
4787439 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4787504 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
4787541 ATCCATTCAA
Statistics
Matches: 379, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
278 379 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (278 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
TTTTGTCTTTTGGTTGAA
Found at i:4787624 original size:19 final size:19
Alignment explanation
Indices: 4787584--4787712 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
4787574 TAGTTTACTT
* *
4787584 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
4787604 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
4787623 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
4787642 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
4787656 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
4787675 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
4787689 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
4787708 TCGCA
1 TCGCA
4787713 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:4787663 original size:33 final size:32
Alignment explanation
Indices: 4787620--4787712 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
4787610 CGCGAAACCA
**
4787620 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
4787652 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
4787685 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
4787713 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:4787710 original size:52 final size:52
Alignment explanation
Indices: 4787584--4787712 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
4787574 TAGTTTACTT
**
4787584 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
4787636 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
4787689 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
4787713 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:4787730 original size:19 final size:18
Alignment explanation
Indices: 4787708--4787826 Score: 110
Period size: 19 Copynumber: 6.8 Consensus size: 18
4787698 GAAACCAAAA
*
4787708 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTC-TT
4787727 TCGCGTTGCGA--TTCTT
1 TCGCGTTGCGATTTTCTT
*
4787743 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTT-CTT
*
4787760 TCGCGTTGCGA--TTCTG
1 TCGCGTTGCGATTTTCTT
4787776 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTC-TT
*
4787793 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTT-CTT
4787812 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
4787827 AAGTTTCGTG
Statistics
Matches: 83, Mismatches: 6, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
14 16 0.19
16 10 0.12
17 10 0.12
19 47 0.57
ACGTcount: A:0.08, C:0.19, G:0.25, T:0.47
Consensus pattern (18 bp):
TCGCGTTGCGATTTTCTT
Found at i:4787749 original size:14 final size:14
Alignment explanation
Indices: 4787730--4787786 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
4787720 TTTCATTTCG
4787730 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
*
4787744 CGTTGCGATTTTGGTTT
1 CGTTGCGA--TT-CTTT
*
4787761 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
4787777 CGTTGCGATT
1 CGTTGCGATT
4787787 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 18 0.51
16 4 0.11
17 5 0.14
19 8 0.23
ACGTcount: A:0.07, C:0.19, G:0.28, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:4787755 original size:33 final size:33
Alignment explanation
Indices: 4787713--4787805 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
4787703 CAAAATCGCA
*
4787713 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
**
4787746 TTGCGATTTTGGTTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
4787779 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
4787806 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.09, C:0.19, G:0.25, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:4787834 original size:20 final size:19
Alignment explanation
Indices: 4787708--4787842 Score: 105
Period size: 19 Copynumber: 7.6 Consensus size: 19
4787698 GAAACCAAAA
*
4787708 TCGCATTGCGATTTTCA-TT
1 TCGCGTTGCGATTTT-AGTT
*
4787727 TCGCGTTGCGA--TT-CTT
1 TCGCGTTGCGATTTTAGTT
*
4787743 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTAGTT
*
4787760 TCGCGTTGCGATTCT-G--
1 TCGCGTTGCGATTTTAGTT
4787776 T--CGTTGCGATTTTCA-TT
1 TCGCGTTGCGATTTT-AGTT
*
4787793 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTAGTT
4787812 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTT-AGTT
*
4787832 TCGTGTTGCGA
1 TCGCGTTGCGA
4787843 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 7, Indels: 27
0.74 0.05 0.21
Matches are distributed among these distances:
14 19 0.20
16 6 0.06
17 6 0.06
18 1 0.01
19 50 0.53
20 13 0.14
ACGTcount: A:0.10, C:0.19, G:0.26, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTAGTT
Found at i:4789767 original size:14 final size:14
Alignment explanation
Indices: 4789748--4789783 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
4789738 ATTGTTTAAT
4789748 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
4789762 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
4789776 TGATTTGT
1 TGATTTGT
4789784 GTAATTGATG
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:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:4789906 original size:19 final size:19
Alignment explanation
Indices: 4789890--4789991 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
4789880 AAAAATGACT
4789890 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
4789909 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4789928 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
4789942 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
4789961 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
4789981 ATCGCAATGCG
1 ATCGCAATGCG
4789992 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:4790044 original size:19 final size:19
Alignment explanation
Indices: 4790020--4790345 Score: 407
Period size: 19 Copynumber: 18.4 Consensus size: 19
4790010 GATTATCTCG
4790020 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4790039 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4790058 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4790077 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
4790091 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4790110 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4790129 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
4790148 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
4790167 TTGCGA--TTC-TGTT-G--
1 TTGCGATTTTCAT-TTCGCA
4790181 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4790200 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
4790219 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
4790233 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4790252 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
4790271 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
4790285 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
4790305 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
4790319 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
4790338 TTGCGATT
1 TTGCGATT
4790346 GTATTTTCCG
Statistics
Matches: 271, Mismatches: 8, Indels: 56
0.81 0.02 0.17
Matches are distributed among these distances:
14 35 0.13
16 31 0.11
17 27 0.10
18 3 0.01
19 163 0.60
20 12 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:4790060 original size:52 final size:52
Alignment explanation
Indices: 4789998--4790317 Score: 434
Period size: 52 Copynumber: 6.0 Consensus size: 52
4789988 TGCGTTTATA
4789998 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
4790050 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
* *
4790102 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTA
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
* * *
4790159 ATTTCGCATTGCGATTCTGTTGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
4790211 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
4790263 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
4790316 AT
1 AT
4790318 GTTGGGATTT
Statistics
Matches: 249, Mismatches: 8, Indels: 21
0.90 0.03 0.08
Matches are distributed among these distances:
52 174 0.70
53 17 0.07
54 13 0.05
55 15 0.06
57 30 0.12
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:4790077 original size:71 final size:71
Alignment explanation
Indices: 4789998--4790278 Score: 430
Period size: 71 Copynumber: 4.0 Consensus size: 71
4789988 TGCGTTTATA
4789998 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
4790063 ATTTTC
66 ATTTTC
* *
4790069 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
4790134 ATTTTC
66 ATTTTC
*
4790140 ATTTCGCATTGCGATTTTAATTTCGCATTGCGA--TTC-TGTT-G--TTGCGATTTTCATTTCGC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTCAT-TTCGCATTGCGATTTTCATTTCGC
4790199 ATTGCGATTTTC
60 ATTGCGATTTTC
*
4790211 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
4790276 ATT
66 ATT
4790279 CTCTCGTTGC
Statistics
Matches: 193, Mismatches: 5, Indels: 24
0.87 0.02 0.11
Matches are distributed among these distances:
66 6 0.03
68 9 0.05
69 4 0.02
71 154 0.80
73 4 0.02
74 10 0.05
76 6 0.03
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (71 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTTTC
Found at i:4790289 original size:33 final size:33
Alignment explanation
Indices: 4790110--4790345 Score: 192
Period size: 33 Copynumber: 6.8 Consensus size: 33
4790100 TCATTTCGCA
*
4790110 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * *
4790146 CATTGCGATTTTAATTTCGCATTGCGATTCTGTTG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
4790181 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
4790217 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
4790252 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
4790285 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
4790319 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
4790346 GTATTTTCCG
Statistics
Matches: 165, Mismatches: 20, Indels: 31
0.76 0.09 0.14
Matches are distributed among these distances:
31 9 0.05
32 5 0.03
33 61 0.37
34 29 0.18
35 9 0.05
36 6 0.04
37 2 0.01
38 32 0.19
39 3 0.02
40 9 0.05
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:4792849 original size:24 final size:24
Alignment explanation
Indices: 4792815--4792861 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
4792805 CTGAAACATC
4792815 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
4792839 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
4792862 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:4793572 original size:20 final size:20
Alignment explanation
Indices: 4793544--4793912 Score: 467
Period size: 20 Copynumber: 18.4 Consensus size: 20
4793534 AAATTTCAGT
* * * *
4793544 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
4793564 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
4793584 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
4793604 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
4793624 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
4793644 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
4793664 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
4793684 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
4793704 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
4793724 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
4793744 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
4793764 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
4793784 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
4793804 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
4793824 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
4793844 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
4793864 GTTGCGATTTACGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
4793884 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
4793904 GTTGCGATT
1 GTTGCGATT
4793913 ATGGAAAATC
Statistics
Matches: 311, Mismatches: 30, Indels: 16
0.87 0.08 0.04
Matches are distributed among these distances:
19 5 0.02
20 301 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Done.