Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008286.1 Hibiscus syriacus cultivar Beakdansim tig00110949_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: 504059
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:205300 original size:3 final size:3
Alignment explanation
Indices: 205294--205355 Score: 81
Period size: 3 Copynumber: 21.0 Consensus size: 3
205284 TATTTATTAT
* ** *
205294 TAA TAA TAA AAA T-A TAA TAA TAA TAA TAA TTT TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
205341 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
205356 AACGAGACAA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:206026 original size:16 final size:16
Alignment explanation
Indices: 205992--206035 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
205982 GTAAAAATTA
205992 AATTTAAAAAA-ATAT
1 AATTTAAAAAACATAT
206007 AATTTAAATAAACA-AT
1 AATTTAAA-AAACATAT
206023 AA-TTAAAAAACAT
1 AATTTAAAAAACAT
206036 CTTACTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 5 0.19
15 13 0.50
16 7 0.27
17 1 0.04
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (16 bp):
AATTTAAAAAACATAT
Found at i:206140 original size:18 final size:19
Alignment explanation
Indices: 206119--206158 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
206109 AAAAAAATAG
206119 TAATTAAAAA-AATTTCTT
1 TAATTAAAAATAATTTCTT
*
206137 TAATTAAAAATTATTTCTT
1 TAATTAAAAATAATTTCTT
206156 TAA
1 TAA
206159 AAAGAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
TAATTAAAAATAATTTCTT
Found at i:206571 original size:15 final size:17
Alignment explanation
Indices: 206536--206573 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
206526 AATCCTGAGG
*
206536 TAATTTTTTTATTTAGT
1 TAATTATTTTATTTAGT
206553 TAATTATTTT-TTT-GT
1 TAATTATTTTATTTAGT
206568 TAATTA
1 TAATTA
206574 ATTAATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 3 0.15
17 9 0.45
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (17 bp):
TAATTATTTTATTTAGT
Found at i:210872 original size:21 final size:20
Alignment explanation
Indices: 210848--210905 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 20
210838 TATATAGCCG
210848 TTGGGGATGTTTTGGAGCCAT
1 TTGGGGATGTTTTGGAG-CAT
210869 TTGGGGATGATTATTTTGGAGCAT
1 TTGGGGATG----TTTTGGAGCAT
210893 TTGGGGATGTTTT
1 TTGGGGATGTTTT
210906 TATACCCTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
20 4 0.12
21 9 0.27
24 12 0.36
25 8 0.24
ACGTcount: A:0.16, C:0.05, G:0.36, T:0.43
Consensus pattern (20 bp):
TTGGGGATGTTTTGGAGCAT
Found at i:210982 original size:22 final size:22
Alignment explanation
Indices: 210955--211033 Score: 115
Period size: 22 Copynumber: 3.6 Consensus size: 22
210945 TGTTTGAGCC
210955 TTCATAGGGGTATTGATACCCA
1 TTCATAGGGGTATTGATACCCA
* * *
210977 TGCATAGGGGTA-TCAGTACTCA
1 TTCATAGGGGTATTGA-TACCCA
210999 TTCATAGGGGTATTGATACCCA
1 TTCATAGGGGTATTGATACCCA
211021 TTCATAGGGGTAT
1 TTCATAGGGGTAT
211034 CGGTACCTCT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.04
22 45 0.92
23 2 0.04
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (22 bp):
TTCATAGGGGTATTGATACCCA
Found at i:211005 original size:44 final size:44
Alignment explanation
Indices: 210955--211039 Score: 152
Period size: 44 Copynumber: 1.9 Consensus size: 44
210945 TGTTTGAGCC
210955 TTCATAGGGGTATTGATACCCATGCATAGGGGTATCAGTACTCA
1 TTCATAGGGGTATTGATACCCATGCATAGGGGTATCAGTACTCA
* *
210999 TTCATAGGGGTATTGATACCCATTCATAGGGGTATCGGTAC
1 TTCATAGGGGTATTGATACCCATGCATAGGGGTATCAGTAC
211040 CTCTTAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (44 bp):
TTCATAGGGGTATTGATACCCATGCATAGGGGTATCAGTACTCA
Found at i:211288 original size:21 final size:19
Alignment explanation
Indices: 211254--211310 Score: 71
Period size: 18 Copynumber: 2.9 Consensus size: 19
211244 ATGTTTAATG
* *
211254 AAAAATATATCAATTGTTT
1 AAAAAGATACCAATTGTTT
211273 ACAAAAGGATACCAATTG-TT
1 A-AAAA-GATACCAATTGTTT
211293 AAAAAGATACCAATTGTT
1 AAAAAGATACCAATTGTT
211311 GGAAAATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 11 0.33
19 6 0.18
20 7 0.21
21 9 0.27
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (19 bp):
AAAAAGATACCAATTGTTT
Found at i:214054 original size:65 final size:64
Alignment explanation
Indices: 213922--214081 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 64
213912 TGCACTAAGA
* * *
213922 GTGCATCGATGCATGAAGTGCATTCGATG-TTTCAAAATAGCCTGAGTGCATCAATGCATGTCTT
1 GTGCATCGATGCAT-AAATGCATTCGATGTTTTCAAAATAACCTGAGTGCATCAATGCATGTCAT
*
213986 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-AACCTGAGTGCATCGATGCATGGT-
1 GTGCATCGATGCAT-AAATGCATTCGATGTTTTCA-AAATAACCTGAGTGCATCAATGCAT-GTC
214049 AT
63 AT
214051 GTGCATCGATGCATATAATGCATTCGATGTT
1 GTGCATCGATGCATA-AATGCATTCGATGTT
214082 CAATTTATTC
Statistics
Matches: 87, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
64 28 0.32
65 54 0.62
66 5 0.06
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATAAATGCATTCGATGTTTTCAAAATAACCTGAGTGCATCAATGCATGTCAT
Found at i:216821 original size:23 final size:23
Alignment explanation
Indices: 216788--216913 Score: 91
Period size: 23 Copynumber: 5.6 Consensus size: 23
216778 GCATGGCCTT
*
216788 GTGCATCGATGCATATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
* * *
216811 GTGCATTGATGCACCTTC-ATG-
1 GTGCATCGATGCACATTCAAGGA
* ***
216832 GTGTATCGATGCACATTC--CTT
1 GTGCATCGATGCACATTCAAGGA
* *
216853 GTGCATCGATTCATATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
*
216876 GTGCATTGATGCACATTCAAAGG-
1 GTGCATCGATGCACATTC-AAGGA
*
216899 GATGTATCGATGCAC
1 G-TGCATCGATGCAC
216914 TGTTCAGTGT
Statistics
Matches: 78, Mismatches: 20, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
21 30 0.38
22 2 0.03
23 31 0.40
24 15 0.19
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Found at i:216860 original size:21 final size:21
Alignment explanation
Indices: 216784--216862 Score: 59
Period size: 21 Copynumber: 3.7 Consensus size: 21
216774 CGATGCATGG
*
216784 CCTTGTGCATCGATGCATATT
1 CCTTGTGCATCGATGCACATT
*** * *
216805 CAAGGAGTGCATTGATGCACCTT
1 C--CTTGTGCATCGATGCACATT
* * *
216828 CATGGTGTATCGATGCACATT
1 CCTTGTGCATCGATGCACATT
216849 CCTTGTGCATCGAT
1 CCTTGTGCATCGAT
216863 TCATATTCAA
Statistics
Matches: 41, Mismatches: 15, Indels: 4
0.68 0.25 0.07
Matches are distributed among these distances:
21 26 0.63
23 15 0.37
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.33
Consensus pattern (21 bp):
CCTTGTGCATCGATGCACATT
Found at i:216875 original size:65 final size:67
Alignment explanation
Indices: 216784--216913 Score: 210
Period size: 65 Copynumber: 2.0 Consensus size: 67
216774 CGATGCATGG
* *
216784 CCTTGTGCATCGATGCATATTCAAGGAGTGCATTGATGCACCTTC-ATGG-TGTATCGATGCACA
1 CCTTGTGCATCGATGCATATTCAAGGAGTGCATTGATGCACATTCAAGGGATGTATCGATGCACA
216847 TT
66 TT
*
216849 CCTTGTGCATCGATTCATATTCAAGGAGTGCATTGATGCACATTCAAAGGGATGTATCGATGCAC
1 CCTTGTGCATCGATGCATATTCAAGGAGTGCATTGATGCACATTC-AAGGGATGTATCGATGCAC
216914 TGTTCAGTGT
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
65 43 0.73
67 3 0.05
68 13 0.22
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (67 bp):
CCTTGTGCATCGATGCATATTCAAGGAGTGCATTGATGCACATTCAAGGGATGTATCGATGCACA
TT
Found at i:222812 original size:65 final size:65
Alignment explanation
Indices: 222683--222839 Score: 194
Period size: 65 Copynumber: 2.4 Consensus size: 65
222673 ACTAAGAGTA
* * * * *
222683 CATCGTTGCATGAAGTGCATTCGATG-TTTCAAAATAACATGAGTGTATCGATGCATGTCTTGTG
1 CATCGATGCATAAAATGCATTCGATGTTTTCAAAATAACATGAGTGCATCGATGCATGTCATGTG
* * *
222747 CATCGATGCATAAAATGCATTCAATGTTTTCATAAA-AACCTGAGTGCATTGATGCATGGT-ATG
1 CATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAACATGAGTGCATCGATGCAT-GTCATG
222810 TG
64 TG
*
222812 CATCGATGCATATAATGCATTCGATGTT
1 CATCGATGCATAAAATGCATTCGATGTT
222840 CAATTTATTC
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 22 0.28
65 53 0.66
66 5 0.06
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (65 bp):
CATCGATGCATAAAATGCATTCGATGTTTTCAAAATAACATGAGTGCATCGATGCATGTCATGTG
Found at i:223860 original size:22 final size:22
Alignment explanation
Indices: 223829--223892 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
223819 TGTTTGAGCC
*
223829 TTCATAGGGGTATCGGTACCCA
1 TTCATAGGGGTATCGATACCCA
* *
223851 TTTATAGGGGTATCAATACCCA
1 TTCATAGGGGTATCGATACCCA
*
223873 TTCATAAGGGTATCGATACC
1 TTCATAGGGGTATCGATACC
223893 TCTTAATATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (22 bp):
TTCATAGGGGTATCGATACCCA
Found at i:226154 original size:17 final size:17
Alignment explanation
Indices: 226134--226189 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
226124 ATATTGCAAC
226134 GAGAGTGGCACTGCGAG
1 GAGAGTGGCACTGCGAG
** ** *
226151 GAGAGCAGCGTTGCGAT
1 GAGAGTGGCACTGCGAG
*
226168 GTGAGTGGCACTGCGAG
1 GAGAGTGGCACTGCGAG
226185 GAGAG
1 GAGAG
226190 CAACGTTGTG
Statistics
Matches: 27, Mismatches: 12, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.23, C:0.16, G:0.46, T:0.14
Consensus pattern (17 bp):
GAGAGTGGCACTGCGAG
Found at i:226157 original size:34 final size:34
Alignment explanation
Indices: 226117--226193 Score: 100
Period size: 34 Copynumber: 2.3 Consensus size: 34
226107 GTGGCACAAC
*
226117 GAGAGCAATATTGCAACGAGAGTGGCACTGCGAG
1 GAGAGCAACATTGCAACGAGAGTGGCACTGCGAG
* * * * *
226151 GAGAGCAGCGTTGCGATGTGAGTGGCACTGCGAG
1 GAGAGCAACATTGCAACGAGAGTGGCACTGCGAG
226185 GAGAGCAAC
1 GAGAGCAAC
226194 GTTGTGATGG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.29, C:0.18, G:0.39, T:0.14
Consensus pattern (34 bp):
GAGAGCAACATTGCAACGAGAGTGGCACTGCGAG
Found at i:226197 original size:34 final size:33
Alignment explanation
Indices: 226136--226212 Score: 118
Period size: 34 Copynumber: 2.3 Consensus size: 33
226126 ATTGCAACGA
*
226136 GAGTGGCACTGCGAGGAGAGCAGCGTTGCGATG
1 GAGTGGCACTGCGAGGAGAGCAACGTTGCGATG
*
226169 TGAGTGGCACTGCGAGGAGAGCAACGTTGTGATG
1 -GAGTGGCACTGCGAGGAGAGCAACGTTGCGATG
226203 GAAGTGGCAC
1 G-AGTGGCAC
226213 AACAAGGAGG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
33 1 0.03
34 39 0.98
ACGTcount: A:0.23, C:0.17, G:0.43, T:0.17
Consensus pattern (33 bp):
GAGTGGCACTGCGAGGAGAGCAACGTTGCGATG
Found at i:226221 original size:34 final size:34
Alignment explanation
Indices: 226149--226221 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
226139 TGGCACTGCG
* ** *
226149 AGGAGAGCAGCGTTGCGATGTGAGTGGCACTGCG
1 AGGAGAGCAACGTTGCGATGTGAGTGGCACAACA
*
226183 AGGAGAGCAACGTTGTGATG-GAAGTGGCACAACA
1 AGGAGAGCAACGTTGCGATGTG-AGTGGCACAACA
226217 AGGAG
1 AGGAG
226222 GACGATTTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
33 1 0.03
34 32 0.97
ACGTcount: A:0.29, C:0.15, G:0.41, T:0.15
Consensus pattern (34 bp):
AGGAGAGCAACGTTGCGATGTGAGTGGCACAACA
Found at i:227004 original size:161 final size:160
Alignment explanation
Indices: 226832--227156 Score: 632
Period size: 161 Copynumber: 2.0 Consensus size: 160
226822 CTAATATAAT
226832 TCTTTGGATATGGTGCTAGATTTGTAATGTTTAGGTTATTCATTGTGAATTGTTTTTGGAAGACA
1 TCTTTGGATATGGTGCTAGATTTGTAATGTTTAGGTTATTCATTGTGAATTGTTTTTGGAAGACA
226897 GTGCAAGGGTGTGATGTTTTGGGCCAATATGTTTAGTAATTGATTCTTCTATGATATTTTATCCT
66 GTGCAAGGGTGTGATGTTTTGGGCCAATATGTTTAGTAATTGATTCTTCTATGATA-TTTATCCT
226962 ATAGTTTAAGTTGTCTATCCAAGTCAATTCA
130 ATAGTTTAAGTTGTCTATCCAAGTCAATTCA
*
226993 TCTTTGGATATGGTGCTAGATTTGTAATGTTTAGGTTATTCATTGTGAATTGTTTTTGGAAGATA
1 TCTTTGGATATGGTGCTAGATTTGTAATGTTTAGGTTATTCATTGTGAATTGTTTTTGGAAGACA
227058 GTGCAAGGGTGTGATGTTTTGGGCCAATATGTTTAGTAATTGATTCTTCTATGATATTTATCCTA
66 GTGCAAGGGTGTGATGTTTTGGGCCAATATGTTTAGTAATTGATTCTTCTATGATATTTATCCTA
227123 TAGTTTAAGTTGTCTATCCAAGTCAATTCA
131 TAGTTTAAGTTGTCTATCCAAGTCAATTCA
227153 TCTT
1 TCTT
227157 AATTTGTTTG
Statistics
Matches: 163, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
160 43 0.26
161 120 0.74
ACGTcount: A:0.24, C:0.10, G:0.22, T:0.45
Consensus pattern (160 bp):
TCTTTGGATATGGTGCTAGATTTGTAATGTTTAGGTTATTCATTGTGAATTGTTTTTGGAAGACA
GTGCAAGGGTGTGATGTTTTGGGCCAATATGTTTAGTAATTGATTCTTCTATGATATTTATCCTA
TAGTTTAAGTTGTCTATCCAAGTCAATTCA
Found at i:233237 original size:23 final size:23
Alignment explanation
Indices: 233210--233257 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
233200 TATGTTCGTT
*
233210 AATATATAAACGAACATTAAACG
1 AATATATAAACGAACACTAAACG
**
233233 AATATATTCACGAACACTAAACG
1 AATATATAAACGAACACTAAACG
233256 AA
1 AA
233258 CAAACATGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.54, C:0.17, G:0.08, T:0.21
Consensus pattern (23 bp):
AATATATAAACGAACACTAAACG
Found at i:235846 original size:14 final size:14
Alignment explanation
Indices: 235823--235858 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
235813 TTTTTACATT
235823 TTATTATTATTATA
1 TTATTATTATTATA
* *
235837 TTATTGTTATTTTA
1 TTATTATTATTATA
235851 TTATTATT
1 TTATTATT
235859 TTACTTTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (14 bp):
TTATTATTATTATA
Found at i:235858 original size:11 final size:11
Alignment explanation
Indices: 235826--235870 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
235816 TTACATTTTA
*
235826 TTATTATTATA
1 TTATTATTATT
*
235837 TTATTGTTATT
1 TTATTATTATT
235848 TTATTATTATT
1 TTATTATTATT
*
235859 TTACT-TTATT
1 TTATTATTATT
235869 TT
1 TT
235871 TTGCAGGCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
10 7 0.23
11 23 0.77
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (11 bp):
TTATTATTATT
Found at i:235871 original size:22 final size:22
Alignment explanation
Indices: 235826--235870 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
235816 TTACATTTTA
*
235826 TTATTATTATATTATTGTTATT
1 TTATTATTATATTACTGTTATT
*
235848 TTATTATTATTTTACT-TTATT
1 TTATTATTATATTACTGTTATT
235869 TT
1 TT
235871 TTGCAGGCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (22 bp):
TTATTATTATATTACTGTTATT
Found at i:237642 original size:16 final size:16
Alignment explanation
Indices: 237623--237666 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
237613 TTTATAACAA
*
237623 TATTAGTTTAATATTT
1 TATTATTTTAATATTT
*
237639 TATTTATTTTAGTATTT
1 TA-TTATTTTAATATTT
*
237656 CATTATTTTAA
1 TATTATTTTAA
237667 GTAATATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (16 bp):
TATTATTTTAATATTT
Found at i:237654 original size:17 final size:17
Alignment explanation
Indices: 237629--237682 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
237619 ACAATATTAG
*
237629 TTTAATATTTTATTTAT
1 TTTAGTATTTTATTTAT
*
237646 TTTAGTATTTCA-TTAT
1 TTTAGTATTTTATTTAT
* *
237662 TTTAAGTAATATATTTAT
1 TTT-AGTATTTTATTTAT
237680 TTT
1 TTT
237683 TCATATTATG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 7 0.23
17 16 0.53
18 7 0.23
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAGTATTTTATTTAT
Found at i:240534 original size:21 final size:22
Alignment explanation
Indices: 240484--240537 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
240474 GAATGAACAA
240484 TATCGATACCATAAGGAAGGAG
1 TATCGATACCATAAGGAAGGAG
* *
240506 TATTGATACCATTATGG-AGG-G
1 TATCGATACCA-TAAGGAAGGAG
240527 TATCGATACCA
1 TATCGATACCA
240538 GGTAACATCG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.39
22 13 0.46
23 4 0.14
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (22 bp):
TATCGATACCATAAGGAAGGAG
Found at i:248524 original size:22 final size:22
Alignment explanation
Indices: 248496--248547 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
248486 GAACAATATC
248496 GATACCATAAGGAAGGAGTATT
1 GATACCATAAGGAAGGAGTATT
248518 GATACCATAAGGAAGGAGTATT
1 GATACCATAAGGAAGGAGTATT
248540 GATACCAT
1 GATACCAT
248548 TATAGAGGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (22 bp):
GATACCATAAGGAAGGAGTATT
Found at i:252867 original size:23 final size:23
Alignment explanation
Indices: 252815--252859 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
252805 TTAAGGACTG
* *
252815 CATATAATTGTCCCGAAGGACCA
1 CATAGAATTGTCCCAAAGGACCA
252838 CATAGAATTGTCCCAAAGGACC
1 CATAGAATTGTCCCAAAGGACC
252860 GCGTAGAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.20
Consensus pattern (23 bp):
CATAGAATTGTCCCAAAGGACCA
Found at i:260319 original size:33 final size:33
Alignment explanation
Indices: 260281--260347 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
260271 GCGAGTTTGA
260281 GATAGTCTCTCTTACTGAAGGTTATAGCGACAT
1 GATAGTCTCTCTTACTGAAGGTTATAGCGACAT
* *
260314 GATAGTCTCTCTTACTGAAGGTTGTAGCGCCAT
1 GATAGTCTCTCTTACTGAAGGTTATAGCGACAT
260347 G
1 G
260348 GCTACAAGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (33 bp):
GATAGTCTCTCTTACTGAAGGTTATAGCGACAT
Found at i:273556 original size:19 final size:19
Alignment explanation
Indices: 273534--273576 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
273524 TAAACTAAAG
273534 TAATAAATTATTAATATAA
1 TAATAAATTATTAATATAA
* * * *
273553 TAATATATTTTTATTTTAA
1 TAATAAATTATTAATATAA
273572 TAATA
1 TAATA
273577 TATAATAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATAAATTATTAATATAA
Found at i:273623 original size:14 final size:13
Alignment explanation
Indices: 273603--273636 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
273593 ATAATAATAT
273603 TTATTAAGAATTA
1 TTATTAAGAATTA
*
273616 TTAGTTAATAATTA
1 TTA-TTAAGAATTA
273630 TTATTAA
1 TTATTAA
273637 TTTGCTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (13 bp):
TTATTAAGAATTA
Found at i:273789 original size:3 final size:3
Alignment explanation
Indices: 273783--273838 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
273773 GGGTTCTCAT
273783 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
273831 TTA TTA TT
1 TTA TTA TT
273839 TTAACAATAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:275442 original size:321 final size:323
Alignment explanation
Indices: 274858--275497 Score: 892
Period size: 321 Copynumber: 2.0 Consensus size: 323
274848 TATATATATA
*
274858 TCTTTCAAACGAGGAAATGAAACAAATGAGAAGAGGAAGTTTACCTACCTCGACGCTCATCAGTC
1 TCTTTCAAACGAGGAAATGAAACAAATGAGAAGAGGAAGTTTACCTACCTCAACGCTCATCAGTC
* * ** *
274923 ATCTCGACGGTCACCGAAGTCAAAGAAACCGAAGGGTTTTTCCTATATCTATTTTTTAGGGACCT
66 ATCTCAACGGTCACCGAAGTCAAAGAAACCGAAGGGTTTTTCCTAGATCTACGTTTTAAGGACCT
* * * *
274988 TTTTTTGGTTAAAAGAAGCTCGGATCCTCGATCAGGGTGAGGAGACACTTTGAACGACCTATTTT
131 TTTTTTGGTTAAAAGAAGCTCGGATCCTCGATCAAGGTGAGGAGACACTTCGAACAACCAATTTT
* * *
275053 TCTCACTTCAACGGCTCTGACGAATGGCGGTGACCGCCGGTCAACGACGGTCGATGTAGCGGAGG
196 TCTCACTTCAACGGCTCTGACGAACGGCGATGACCGCCGGTCAACGACGGCCGATGTAGCGGAGG
* *
275118 CCCACCGAATTCT-AGAACTCGGCTTCCGATTGAAGCTTTTGAGAGATATCTCTCTCTCTCTC
261 CCCACCGAATTCTGAAAACTCGACTTCCGATTGAAGCTTTTGAGAGATATCTCTCTCTCTCTC
* * * *
275180 TCTTTCAAACGAGGAAATGAGACAAATGAGAAGAGGAGGTTTACCTACCTCAACGCTCGTCGGTC
1 TCTTTCAAACGAGGAAATGAAACAAATGAGAAGAGGAAGTTTACCTACCTCAACGCTCATCAGTC
* * * * * ** *
275245 ATCTCAACGGTTATCGGAGTTAAATAAATTGAAGGGTTTTTCTTAGATCTACGTTTTAAGGACC-
66 ATCTCAACGGTCACCGAAGTCAAAGAAACCGAAGGGTTTTTCCTAGATCTACGTTTTAAGGACCT
*
275309 TTTTTTGGTTAAAAGAAGCTTGGATCCTCGATCAAGGTGAGGAGACACTTCGAACAACCAATTTT
131 TTTTTTGGTTAAAAGAAGCTCGGATCCTCGATCAAGGTGAGGAGACACTTCGAACAACCAATTTT
* * * * *
275374 TCTCACTTCAACGGCT-TCGGCGAACGGCGATGGCCGTCGGTCAACGACGGCC-AGTGTGGCGTA
196 TCTCACTTCAACGGCTCT-GACGAACGGCGATGACCGCCGGTCAACGACGGCCGA-TGTAGCGGA
* * * *
275437 GGCCCACTGTATTCTGGAAAACTCGACTTCTGGTTGAAGCTTTTGAGAGATATCTCTCTCT
259 GGCCCACCGAATTCT-GAAAACTCGACTTCCGATTGAAGCTTTTGAGAGATATCTCTCTCT
275498 TTCAAATGAG
Statistics
Matches: 277, Mismatches: 37, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
320 2 0.01
321 124 0.45
322 111 0.40
323 40 0.14
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (323 bp):
TCTTTCAAACGAGGAAATGAAACAAATGAGAAGAGGAAGTTTACCTACCTCAACGCTCATCAGTC
ATCTCAACGGTCACCGAAGTCAAAGAAACCGAAGGGTTTTTCCTAGATCTACGTTTTAAGGACCT
TTTTTTGGTTAAAAGAAGCTCGGATCCTCGATCAAGGTGAGGAGACACTTCGAACAACCAATTTT
TCTCACTTCAACGGCTCTGACGAACGGCGATGACCGCCGGTCAACGACGGCCGATGTAGCGGAGG
CCCACCGAATTCTGAAAACTCGACTTCCGATTGAAGCTTTTGAGAGATATCTCTCTCTCTCTC
Found at i:282556 original size:52 final size:50
Alignment explanation
Indices: 282471--282594 Score: 140
Period size: 52 Copynumber: 2.4 Consensus size: 50
282461 TTTTGCAATT
*** * * *
282471 GCACTTAACACATACTTACATTGGTGTAAGTGAATAAAATAAAAAAATTGTA
1 GCACTTAACACATACTTACACCAGTATAAGTGAATAAAAT--AAAAAGTATA
* *
282523 GCACTTAACACATACTTACACCATTATATGTGAATAAAATAAAAAGTATA
1 GCACTTAACACATACTTACACCAGTATAAGTGAATAAAATAAAAAGTATA
* *
282573 ACACTTAACATATACTTACACC
1 GCACTTAACACATACTTACACC
282595 GGTGTAAGCA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
50 28 0.45
52 34 0.55
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.28
Consensus pattern (50 bp):
GCACTTAACACATACTTACACCAGTATAAGTGAATAAAATAAAAAGTATA
Found at i:282825 original size:37 final size:37
Alignment explanation
Indices: 282740--282849 Score: 87
Period size: 37 Copynumber: 3.0 Consensus size: 37
282730 TATTCATAGC
* * * * *
282740 CAACAACAGTAACCCCTACATCAATGAAGTTGATATC
1 CAACAGCACTAACCCCTAAATCAATGAAGTTCATATA
**
282777 CAACATTACTAACCCCTAAATCAATGGAA-TTCATATA
1 CAACAGCACTAACCCCTAAATCAAT-GAAGTTCATATA
* ** * * *
282814 CAATAGCACTAATTCATAAATTAATGAATTTCATAT
1 CAACAGCACTAACCCCTAAATCAATGAAGTTCATAT
282850 CCAAAAACAC
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
36 3 0.05
37 52 0.90
38 3 0.05
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.28
Consensus pattern (37 bp):
CAACAGCACTAACCCCTAAATCAATGAAGTTCATATA
Found at i:283816 original size:83 final size:83
Alignment explanation
Indices: 283665--283827 Score: 229
Period size: 83 Copynumber: 2.0 Consensus size: 83
283655 TGTATATCTA
* * * * *
283665 TTTAATGTTTTAAATTTCAAAGACATTATTATCTGTTTAAATTTAGATATTAAAAGATATATTGT
1 TTTAATATTTTAAATTTAAAAGACATTATTATCTGTTTAAATTTAAATATTAAAAGAGATATTAT
*
283730 TGGAGTAAATTTCTCAGG
66 TGGAGTAAATCTCTCAGG
* *
283748 TTTAATATTTTAAATTTAAAAGATATTATTATTTGTTTAAATTTAAATATTAAAAGAGAT-TTAA
1 TTTAATATTTTAAATTTAAAAGACATTATTATCTGTTTAAATTTAAATATTAAAAGAGATATT-A
*
283812 TTGGAGTTAATCTCTC
65 TTGGAGTAAATCTCTC
283828 TTGAAATTCC
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
82 2 0.03
83 68 0.97
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.46
Consensus pattern (83 bp):
TTTAATATTTTAAATTTAAAAGACATTATTATCTGTTTAAATTTAAATATTAAAAGAGATATTAT
TGGAGTAAATCTCTCAGG
Found at i:288135 original size:20 final size:20
Alignment explanation
Indices: 288110--288159 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
288100 GGAAAAGAAC
288110 TTAATTTATGATTGAGTCAA
1 TTAATTTATGATTGAGTCAA
* *
288130 TTAATTTATGCTTGAGTCAT
1 TTAATTTATGATTGAGTCAA
288150 TTAATTTATG
1 TTAATTTATG
288160 TCATAGTAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.30, C:0.06, G:0.14, T:0.50
Consensus pattern (20 bp):
TTAATTTATGATTGAGTCAA
Found at i:288720 original size:4 final size:4
Alignment explanation
Indices: 288692--289476 Score: 385
Period size: 4 Copynumber: 198.8 Consensus size: 4
288682 ATTATGGGCG
* * * * *
288692 TACA TACG TACC TACG TATA TACA TACA T--A TACA TACA TATA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
288738 TACA TACC TACA TACA T--A TACA TACA TACA TACA TACA TACA -ACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
** * * * * * *
288783 TATG TACA TACA TATA TATA TATA TACA TACA TAAA TACA TATA TAAA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * ** * * *
288831 TACA CATA TACA TATA TACA TACA TATT TATA TACA TATA TATA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * *
288879 TACA TACA TACA TACA TACA TATA TACA T--A TATA TATA TATA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * *
288925 TACA TACA TACA TACA TGCA TACA TATA TACA TACA TACA TATA TATA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * * **
288973 TGCA TACA TACA TATA TATA TACA TATA TATA TACA TACA TACGTA TGTA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC--A TACA
** * * * * * * * * * *
289023 TGTA TATA TATA TACG TACG TACGTA TATA TATA TATA TATA TATA TATA
1 TACA TACA TACA TACA TACA TAC--A TACA TACA TACA TACA TACA TACA
* * * * * * * **
289073 TATA TATA TGCA TACA TATA TATA TACG TATA TACA TACA TACA TGTA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * *
289121 TACA TACA TACG TACG TATA TACA TACA TACA TATA TATA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * *
289169 T--A TATA TATA TACA TACA TACA TACA TACA T--A TATA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * * * *
289213 TACA TACA TACA T--A TATA TATA TATA TACG TATTA TACG TACA TACG
1 TACA TACA TACA TACA TACA TACA TACA TACA TA-CA TACA TACA TACA
* * * * * * * * * * * *
289260 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * * * * * ** * *
289308 TATA TATA TATA TATA TATA TATA TATA TATA TATG TACG TACG TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * ** *
289356 TATA TACT TACA TACA TATA TACA TGCA TACA TATG TACA T--A TATA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * * * * *
289402 TACG TATA TGCA TACA TGCA TACA TGCA TACA TGCA AACA TGCA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * *
289450 TGCA TACA TGCA TACA TGCA TACA TAC
1 TACA TACA TACA TACA TACA TACA TAC
289477 TAGATCCAAT
Statistics
Matches: 637, Mismatches: 124, Indels: 40
0.80 0.15 0.05
Matches are distributed among these distances:
2 14 0.02
3 3 0.00
4 614 0.96
5 2 0.00
6 4 0.01
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (4 bp):
TACA
Found at i:289378 original size:8 final size:8
Alignment explanation
Indices: 288708--289401 Score: 424
Period size: 8 Copynumber: 86.8 Consensus size: 8
288698 CGTACCTACG
288708 TATATACA
1 TATATACA
*
288716 TACAT--A
1 TATATACA
*
288722 TACATACA
1 TATATACA
288730 TATATACA
1 TATATACA
* *
288738 TACATACC
1 TATATACA
*
288746 TACATAC-
1 TATATACA
288753 -ATATACA
1 TATATACA
*
288760 TACATACA
1 TATATACA
*
288768 TACATACA
1 TATATACA
*
288776 TACA-ACA
1 TATATACA
*
288783 TATGTACA
1 TATATACA
* *
288791 TACATATA
1 TATATACA
*
288799 TATATATA
1 TATATACA
*
288807 TACATACA
1 TATATACA
*
288815 TAAATACA
1 TATATACA
288823 TATAT--A
1 TATATACA
288829 -A-ATACA
1 TATATACA
*
288835 CATATACA
1 TATATACA
288843 TATATACA
1 TATATACA
* **
288851 TACATATT
1 TATATACA
288859 TATATACA
1 TATATACA
*
288867 TATATATA
1 TATATACA
*
288875 TACATACA
1 TATATACA
*
288883 TACATACA
1 TATATACA
*
288891 TACATACA
1 TATATACA
288899 TATATACATA
1 TATATAC--A
*
288909 TATATATA
1 TATATACA
288917 TATATACA
1 TATATACA
*
288925 TACATACA
1 TATATACA
*
288933 TACATACA
1 TATATACA
**
288941 TGCATACA
1 TATATACA
288949 TATATACA
1 TATATACA
*
288957 TACATACA
1 TATATACA
*
288965 TATATATA
1 TATATACA
**
288973 TGCATACA
1 TATATACA
* *
288981 TACATATA
1 TATATACA
288989 TATATACA
1 TATATACA
*
288997 TATATATA
1 TATATACA
*
289005 TACATACA
1 TATATACA
**
289013 TACGTATGTA
1 TA--TATACA
* *
289023 TGTATATA
1 TATATACA
*
289031 TATATACG
1 TATATACA
** *
289039 TACGTACG
1 TATATACA
289047 TATAT--A
1 TATATACA
*
289053 TATATATA
1 TATATACA
*
289061 TATATATA
1 TATATACA
*
289069 TATATATA
1 TATATACA
*
289077 TATATGCA
1 TATATACA
* *
289085 TACATATA
1 TATATACA
*
289093 TATATACG
1 TATATACA
289101 TATATACA
1 TATATACA
*
289109 TACATACA
1 TATATACA
*
289117 TGTATACA
1 TATATACA
*
289125 TACATACGTACG
1 T--ATA--TACA
289137 TATATACA
1 TATATACA
*
289145 TACATACA
1 TATATACA
*
289153 TATATATA
1 TATATACA
*
289161 TACATACA
1 TATATACA
289169 TATAT--A
1 TATATACA
289175 TATATACA
1 TATATACA
*
289183 TACATACA
1 TATATACA
*
289191 TACATACATA
1 TATATAC--A
289201 TATATACA
1 TATATACA
*
289209 TACATACA
1 TATATACA
*
289217 TACATACATA
1 TATATAC--A
*
289227 TATATATA
1 TATATACA
*
289235 TATATACG
1 TATATACA
*
289243 TATTATACG
1 TA-TATACA
* *
289252 TACATACG
1 TATATACA
*
289260 TATATATA
1 TATATACA
*
289268 TATATATA
1 TATATACA
*
289276 TATATATA
1 TATATACA
*
289284 TATATATA
1 TATATACA
*
289292 TATATATA
1 TATATACA
*
289300 TATATATA
1 TATATACA
*
289308 TATATATA
1 TATATACA
*
289316 TATATATA
1 TATATACA
*
289324 TATATATA
1 TATATACA
*
289332 TATATATA
1 TATATACA
* *
289340 TATGTACG
1 TATATACA
**
289348 TACGTACA
1 TATATACA
*
289356 TATATACT
1 TATATACA
*
289364 TACATACA
1 TATATACA
289372 TATATACA
1 TATATACA
**
289380 TGCATACA
1 TATATACA
*
289388 TATGTACA
1 TATATACA
289396 TATATA
1 TATATA
289402 TACGTATATG
Statistics
Matches: 552, Mismatches: 108, Indels: 52
0.78 0.15 0.07
Matches are distributed among these distances:
4 2 0.00
5 1 0.00
6 24 0.04
7 6 0.01
8 478 0.87
9 8 0.01
10 29 0.05
12 4 0.01
ACGTcount: A:0.47, C:0.14, G:0.03, T:0.37
Consensus pattern (8 bp):
TATATACA
Found at i:297934 original size:21 final size:21
Alignment explanation
Indices: 297910--297951 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
297900 CTCCCATACG
*
297910 GTTGTACAGTCAATTCTTTAC
1 GTTGTACAATCAATTCTTTAC
* *
297931 GTTGTATAATCGATTCTTTAC
1 GTTGTACAATCAATTCTTTAC
297952 AAAGTGCATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.45
Consensus pattern (21 bp):
GTTGTACAATCAATTCTTTAC
Found at i:303600 original size:23 final size:24
Alignment explanation
Indices: 303573--303628 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
303563 GTTTTTAAAT
303573 GTTTTGAAAATATATAATATAT-A
1 GTTTTGAAAATATATAATATATCA
*
303596 GTTTTTGAAAATATATATTATATCA
1 G-TTTTGAAAATATATAATATATCA
303621 -TTTTGAAA
1 GTTTTGAAA
303629 TTTTTTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 9 0.30
24 20 0.67
25 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (24 bp):
GTTTTGAAAATATATAATATATCA
Found at i:303696 original size:39 final size:38
Alignment explanation
Indices: 303653--303891 Score: 160
Period size: 36 Copynumber: 6.6 Consensus size: 38
303643 ATATATATAT
* * *
303653 ATATATAATATATAATTTTTAAAA-ACGTTTTTGAAAAAC
1 ATATATATTATATAGTTTTGAAAATA--TTTTTGAAAAAC
*
303692 ATATATATTATATAGTTTTGAAAATATTTTTGAAAAAT
1 ATATATATTATATAGTTTTGAAAATATTTTTGAAAAAC
*
303730 ATATATATTATATAGTTTTGAAAATTAATTTT----AA-
1 ATATATATTATATAGTTTTGAAAA-TATTTTTGAAAAAC
*
303764 ATATATA-TATATA-TTTTGAAAATTAGTTTTT--TAAA-
1 ATATATATTATATAGTTTTGAAAA-TA-TTTTTGAAAAAC
303799 A-ATATATTATATAGTTTTGAAAATTAGTTTTT--AAAA-
1 ATATATATTATATAGTTTTGAAAA-TA-TTTTTGAAAAAC
* * *
303835 ATATAT-TTAT-GA-TTTTAAAAATTATTTTT-TAAAAC
1 ATATATATTATATAGTTTTGAAAA-TATTTTTGAAAAAC
* *
303870 --ATATATTGTATAGTTTTAAAAA
1 ATATATATTATATAGTTTTGAAAA
303892 ATGTTTTTAA
Statistics
Matches: 176, Mismatches: 11, Indels: 29
0.81 0.05 0.13
Matches are distributed among these distances:
32 12 0.07
33 19 0.11
34 30 0.17
35 13 0.07
36 35 0.20
37 4 0.02
38 35 0.20
39 27 0.15
40 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.48
Consensus pattern (38 bp):
ATATATATTATATAGTTTTGAAAATATTTTTGAAAAAC
Found at i:303734 original size:38 final size:39
Alignment explanation
Indices: 303651--303840 Score: 201
Period size: 38 Copynumber: 5.2 Consensus size: 39
303641 ATATATATAT
* * *
303651 ATATATATAATATATAATTTTTAAAA--ACGTTTTTGAAAA
1 ATATATATATTATATAGTTTTGAAAATTA-GTTTTT-AAAA
*
303690 ACATATATATTATATAGTTTTGAAAA-TA-TTTTTGAAAA
1 ATATATATATTATATAGTTTTGAAAATTAGTTTTT-AAAA
*
303728 ATATATATATTATATAGTTTTGAAAATTA-ATTTT---A
1 ATATATATATTATATAGTTTTGAAAATTAGTTTTTAAAA
*
303763 A-ATATATA-TATATA-TTTTGAAAATTAGTTTTT-TAA
1 ATATATATATTATATAGTTTTGAAAATTAGTTTTTAAAA
303798 A-A-ATATATTATATAGTTTTGAAAATTAGTTTTTAAAA
1 ATATATATATTATATAGTTTTGAAAATTAGTTTTTAAAA
303835 ATATAT
1 ATATAT
303841 TTATGATTTT
Statistics
Matches: 133, Mismatches: 8, Indels: 20
0.83 0.05 0.12
Matches are distributed among these distances:
32 12 0.09
33 10 0.08
34 12 0.09
35 11 0.08
36 18 0.14
37 3 0.02
38 36 0.27
39 30 0.23
40 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.47
Consensus pattern (39 bp):
ATATATATATTATATAGTTTTGAAAATTAGTTTTTAAAA
Found at i:303766 original size:36 final size:36
Alignment explanation
Indices: 303692--303901 Score: 226
Period size: 35 Copynumber: 6.0 Consensus size: 36
303682 TTTGAAAAAC
303692 ATATATATTATATAGTTTTGAAAA-TA-TTTTTGAAAAA
1 ATATATATTATATAGTTTTGAAAATTAGTTTTT---AAA
*
303729 TATATATATTATATAGTTTTGAAAATTA-ATTTT-AA
1 -ATATATATTATATAGTTTTGAAAATTAGTTTTTAAA
303764 ATATATA-TATATA-TTTTGAAAATTAGTTTTTTAAA
1 ATATATATTATATAGTTTTGAAAATTAG-TTTTTAAA
303799 A-ATATATTATATAGTTTTGAAAATTAGTTTTTAAA
1 ATATATATTATATAGTTTTGAAAATTAGTTTTTAAA
* *
303834 A-ATATATT-TAT-GATTTTAAAAATTATTTTTTAAA
1 ATATATATTATATAG-TTTTGAAAATTAGTTTTTAAA
* * * *
303868 ACATATATTGTATAGTTTTAAAAAAT-GTTTTTAA
1 ATATATATTATATAGTTTTGAAAATTAGTTTTTAA
303902 TTTGTTTATT
Statistics
Matches: 156, Mismatches: 6, Indels: 23
0.84 0.03 0.12
Matches are distributed among these distances:
32 12 0.08
33 7 0.04
34 39 0.25
35 41 0.26
36 26 0.17
37 1 0.01
38 24 0.15
39 6 0.04
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (36 bp):
ATATATATTATATAGTTTTGAAAATTAGTTTTTAAA
Found at i:303900 original size:35 final size:33
Alignment explanation
Indices: 303732--303901 Score: 139
Period size: 34 Copynumber: 4.9 Consensus size: 33
303722 TGAAAAATAT
* * ** *
303732 ATATATTATATAGTTTTGAAAATTAATTTTAAAT
1 ATATATT-TATAGTTTTAAAAAATGTTTTTAAAA
* * *
303766 ATATATATATA-TTTTGAAAATTAGTTTTTTAAAA
1 ATATATTTATAGTTTTAAAAAAT-G-TTTTTAAAA
* *
303800 ATATATTATATAGTTTTGAAAATTAGTTTTTAAAA
1 ATATATT-TATAGTTTTAAAAAAT-GTTTTTAAAA
303835 ATATATTTAT-GATTTTAAAAATTAT-TTTTTAAAA
1 ATATATTTATAG-TTTTAAAAA--ATGTTTTTAAAA
303869 CATATATTGTATAGTTTTAAAAAATGTTTTTAA
1 -ATATATT-TATAGTTTTAAAAAATGTTTTTAA
303902 TTTGTTTATT
Statistics
Matches: 118, Mismatches: 7, Indels: 21
0.81 0.05 0.14
Matches are distributed among these distances:
32 11 0.09
33 5 0.04
34 41 0.35
35 34 0.29
36 26 0.22
37 1 0.01
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (33 bp):
ATATATTTATAGTTTTAAAAAATGTTTTTAAAA
Found at i:303914 original size:70 final size:70
Alignment explanation
Indices: 303732--303901 Score: 222
Period size: 69 Copynumber: 2.5 Consensus size: 70
303722 TGAAAAATAT
* * * * * *
303732 ATATATTATATAGTTTTGAAAATTA-ATTTTAAATATATATATAT-ATTTTGAAAATTAGTTTTT
1 ATATATTATATAGTTTTAAAAAATAGTTTTTAAAAATATATTTATGATTTTAAAAATTAGTTTTT
303795 TAAAA
66 TAAAA
* *
303800 ATATATTATATAGTTTTGAAAATTAGTTTTTAAAAATATATTTATGATTTTAAAAATTA-TTTTT
1 ATATATTATATAGTTTTAAAAAATAGTTTTTAAAAATATATTTATGATTTTAAAAATTAGTTTTT
303864 TAAAA
66 TAAAA
*
303869 CATATATTGTATAGTTTTAAAAAAT-GTTTTTAA
1 -ATATATTATATAGTTTTAAAAAATAGTTTTTAA
303902 TTTGTTTATT
Statistics
Matches: 92, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
68 25 0.27
69 34 0.37
70 33 0.36
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (70 bp):
ATATATTATATAGTTTTAAAAAATAGTTTTTAAAAATATATTTATGATTTTAAAAATTAGTTTTT
TAAAA
Found at i:306033 original size:17 final size:17
Alignment explanation
Indices: 306011--306048 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
306001 AAGTTTAAGA
306011 ATCAAATTAAAATGAAG
1 ATCAAATTAAAATGAAG
306028 ATCAAATTAAAATGAAG
1 ATCAAATTAAAATGAAG
306045 ATCA
1 ATCA
306049 TAGTTTGAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.58, C:0.08, G:0.11, T:0.24
Consensus pattern (17 bp):
ATCAAATTAAAATGAAG
Found at i:309171 original size:32 final size:31
Alignment explanation
Indices: 309135--309272 Score: 156
Period size: 31 Copynumber: 4.4 Consensus size: 31
309125 TTGGGCATAG
* *
309135 GAGCCAACCTAAGGGAATGCCTTGGGGCC-CTA
1 GAGCCTACCCAAGGGAAT-CCTTGGGGCCTC-A
309167 GAGCCTACCCAA-GGAATACCTTGGGGCCTCA
1 GAGCCTACCCAAGGGAAT-CCTTGGGGCCTCA
* *
309198 GAGCCTACCCAAGGGAGTACTTGGGGCCTCA
1 GAGCCTACCCAAGGGAATCCTTGGGGCCTCA
* *
309229 GAGCCTACCCAAGGGAA-CATCTTAGGGCCTAA
1 GAGCCTACCCAAGGGAATC--CTTGGGGCCTCA
309261 GAGCCTACCCAA
1 GAGCCTACCCAA
309273 AGGTTACCTT
Statistics
Matches: 93, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
31 56 0.60
32 37 0.40
ACGTcount: A:0.27, C:0.30, G:0.28, T:0.15
Consensus pattern (31 bp):
GAGCCTACCCAAGGGAATCCTTGGGGCCTCA
Found at i:309264 original size:63 final size:62
Alignment explanation
Indices: 309155--309272 Score: 175
Period size: 63 Copynumber: 1.9 Consensus size: 62
309145 AAGGGAATGC
* * *
309155 CTTGGGGCCCTAGAGCCTACCCAAGGAATACCTTGGGGCCTCAGAGCCTACCCAAGGGAGTA
1 CTTGGGGCCCTAGAGCCTACCCAAGGAACACCTTAGGGCCTAAGAGCCTACCCAAGGGAGTA
*
309217 CTTGGGG-CCTCAGAGCCTACCCAAGGGAACATCTTAGGGCCTAAGAGCCTACCCAA
1 CTTGGGGCCCT-AGAGCCTACCCAA-GGAACACCTTAGGGCCTAAGAGCCTACCCAA
309273 AGGTTACCTT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
61 3 0.06
62 20 0.40
63 27 0.54
ACGTcount: A:0.25, C:0.31, G:0.27, T:0.16
Consensus pattern (62 bp):
CTTGGGGCCCTAGAGCCTACCCAAGGAACACCTTAGGGCCTAAGAGCCTACCCAAGGGAGTA
Found at i:309609 original size:32 final size:32
Alignment explanation
Indices: 309566--309638 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
309556 CGTTAGAACA
** *
309566 TACCCAA-GGAATACCTTGGGGCCTTAA-AGCC
1 TACCCAAGGGAATACCTCAGAGCC-TAAGAGCC
*
309597 TACCCAAGGGAATATCTCAGAGCCTAAGAGCC
1 TACCCAAGGGAATACCTCAGAGCCTAAGAGCC
309629 TACCCAAGGG
1 TACCCAAGGG
309639 TCACCTTAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 10 0.28
32 26 0.72
ACGTcount: A:0.32, C:0.29, G:0.23, T:0.16
Consensus pattern (32 bp):
TACCCAAGGGAATACCTCAGAGCCTAAGAGCC
Found at i:313951 original size:20 final size:20
Alignment explanation
Indices: 313910--313952 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
313900 AATGGGTGAT
*
313910 TAGTATCAATACTACTAGAC
1 TAGTATCAATACTACGAGAC
313930 TAGTATCAATACTCACGA-AC
1 TAGTATCAATACT-ACGAGAC
313950 TAG
1 TAG
313953 GGTATCCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.28
Consensus pattern (20 bp):
TAGTATCAATACTACGAGAC
Found at i:318835 original size:19 final size:19
Alignment explanation
Indices: 318802--318851 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
318792 GGTAGCCAAC
*
318802 GATCT-CCTACACTGATCA
1 GATCTACCTCCACTGATCA
318820 GATCTACCTCCACTGATCA
1 GATCTACCTCCACTGATCA
*
318839 GATTTACCTCCAC
1 GATCTACCTCCAC
318852 CTCTACTCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 5 0.17
19 24 0.83
ACGTcount: A:0.26, C:0.36, G:0.10, T:0.28
Consensus pattern (19 bp):
GATCTACCTCCACTGATCA
Found at i:326607 original size:20 final size:21
Alignment explanation
Indices: 326582--326621 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
326572 AATTGAAATA
326582 ATTAAAAAGATAATA-AAAAC
1 ATTAAAAAGATAATATAAAAC
*
326602 ATTAAAAATATAATATAAAA
1 ATTAAAAAGATAATATAAAA
326622 TAAACATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (21 bp):
ATTAAAAAGATAATATAAAAC
Found at i:328002 original size:41 final size:40
Alignment explanation
Indices: 327941--328069 Score: 116
Period size: 42 Copynumber: 3.1 Consensus size: 40
327931 ATATTGAAAA
* * *
327941 CATCTTGCCCGAAGGTCTTATGGATGGCCCGAAGGTCTTAT
1 CATCTTGCTCGAAAGACTTAT-GATGGCCCGAAGGTCTTAT
* *
327982 CATCTTGCTCGAAAGACTTATAGATGACCCGAAGGAT-TTAAG
1 CATCTTGCTCGAAAGACTTAT-GATGGCCCGAAGG-TCTT-AT
* * * *
328024 CATCATACTCGAAAGACTTACTGATGGCCGGAAGGACTTACT
1 CATCTTGCTCGAAAGACTTA-TGATGGCCCGAAGGTCTTA-T
328066 CATC
1 CATC
328070 GAGAAACCCT
Statistics
Matches: 71, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
41 33 0.46
42 37 0.52
43 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.26
Consensus pattern (40 bp):
CATCTTGCTCGAAAGACTTATGATGGCCCGAAGGTCTTAT
Found at i:328161 original size:39 final size:39
Alignment explanation
Indices: 328103--328458 Score: 500
Period size: 39 Copynumber: 9.2 Consensus size: 39
328093 TAGATTCTTT
328103 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
1 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* * * *
328142 AAATCTTTTGTTTCAAGGGAAACTATCTCAAGAGATACA
1 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* * * *
328181 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGTGACAAA
1 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* *
328220 AAATCTTTTATTTCGAGGGAAACTATCACAAGCGAGATA
1 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* * *
328259 ATATCTTCTGTTTCGAGGGAAACTATCTCAAGTGAGATA
1 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* *
328298 AAATCTTCTGTTTCGAGGGAAACTATC-CAAGCAAGATA
1 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* *
328336 AAATCTTTTGTTTCGA-GGAAACTATCTCAAGCAAGACA
1 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* * * *
328374 AAATCTTTTATTTCAAGGGAAACTATCTTAAGCGAGACA
1 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
*
328413 AAATCTTATGTTTCGAGGGAAACTATCTCAAGCGAGATA
1 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
328452 AAATCTT
1 AAATCTT
328459 CTTTAAAATC
Statistics
Matches: 281, Mismatches: 34, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
37 10 0.04
38 48 0.17
39 223 0.79
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (39 bp):
AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
Found at i:328557 original size:76 final size:76
Alignment explanation
Indices: 328463--328676 Score: 288
Period size: 76 Copynumber: 2.8 Consensus size: 76
328453 AATCTTCTTT
* * *
328463 AAAATCAATCTTGAGTGAAATGAAAT-GTCTTCG-TTCGAGTAAAAATCATCTCAAGTGAGACAA
1 AAAAT-AATCTTGAGTGAAAT-AAATCTTCTT-GTTTCGAGTAAAAACCATCTCAAGCGAGACAA
328526 ATATTGTTTTAAGA
63 ATATTGTTTTAAGA
* * *
328540 AAAATAATCTTGAGTGAAATAAATCTTCTTGTTTCAAGTAAAAACCGTCTCAAGCGAGACAAATC
1 AAAATAATCTTGAGTGAAATAAATCTTCTTGTTTCGAGTAAAAACCATCTCAAGCGAGACAAATA
328605 TTGTTTTAAGA
66 TTGTTTTAAGA
* * ***
328616 AAAACAATCTTTAGTGAAATAAATCTTCTTGTTTCGAGTAAAAACTGCCTCAAGCGAGACA
1 AAAATAATCTTGAGTGAAATAAATCTTCTTGTTTCGAGTAAAAACCATCTCAAGCGAGACA
328677 TATCTTCTGT
Statistics
Matches: 124, Mismatches: 11, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
75 5 0.04
76 114 0.92
77 5 0.04
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.30
Consensus pattern (76 bp):
AAAATAATCTTGAGTGAAATAAATCTTCTTGTTTCGAGTAAAAACCATCTCAAGCGAGACAAATA
TTGTTTTAAGA
Found at i:328640 original size:36 final size:36
Alignment explanation
Indices: 328510--328642 Score: 104
Period size: 36 Copynumber: 3.6 Consensus size: 36
328500 AGTAAAAATC
* * * * *
328510 ATCTCAAGTGAGACAAATATTGTTTTAAGAAAAATA
1 ATCTTAAGTGAAATAAATCTTGTTTTAAGAAAAACA
* * *
328546 ATCTTGAGTGAAATAAATCTTCTTGTTTCAAGTAAAAACC
1 ATCTTAAGTGAAATAAA---TCTTGTTTTAAG-AAAAACA
* * * * *
328586 GTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACA
1 ATCTTAAGTGAAATAAATCTTGTTTTAAGAAAAACA
*
328622 ATCTTTAGTGAAATAAATCTT
1 ATCTTAAGTGAAATAAATCTT
328643 CTTGTTTCGA
Statistics
Matches: 71, Mismatches: 22, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
36 34 0.48
37 11 0.15
39 10 0.14
40 16 0.23
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (36 bp):
ATCTTAAGTGAAATAAATCTTGTTTTAAGAAAAACA
Found at i:328706 original size:38 final size:39
Alignment explanation
Indices: 328560--328727 Score: 128
Period size: 38 Copynumber: 4.4 Consensus size: 39
328550 TGAGTGAAAT
* * *
328560 AAATCTTCTTGTTTCAAGTAAAAACCGTCTCAAGCGAGAC
1 AAATCTTC-TGTTTCGAGTAAAAACTGCCTCAAGCGAGAC
** *** ** * * *
328600 AAATC-T-TGTTTTAAG-AAAAACAATCTTTAGTGAAAT
1 AAATCTTCTGTTTCGAGTAAAAACTGCCTCAAGCGAGAC
328636 AAATCTTCTTGTTTCGAGTAAAAACTGCCTCAAGCGAGAC
1 AAATCTTC-TGTTTCGAGTAAAAACTGCCTCAAGCGAGAC
* * * *
328676 ATATCTTCTGTTT-GAGTAAAATCTGTCTCAAGCGAGGC
1 AAATCTTCTGTTTCGAGTAAAAACTGCCTCAAGCGAGAC
*
328714 AAATCTTCTTTTTC
1 AAATCTTCTGTTTC
328728 AGTTCTCTGA
Statistics
Matches: 99, Mismatches: 24, Indels: 11
0.74 0.18 0.08
Matches are distributed among these distances:
36 19 0.19
37 9 0.09
38 33 0.33
39 13 0.13
40 25 0.25
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (39 bp):
AAATCTTCTGTTTCGAGTAAAAACTGCCTCAAGCGAGAC
Found at i:347490 original size:11 final size:11
Alignment explanation
Indices: 347474--347501 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
347464 AATAGTAAGT
347474 AAAATATATAA
1 AAAATATATAA
347485 AAAATATATAA
1 AAAATATATAA
347496 AAAATA
1 AAAATA
347502 AAGAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
AAAATATATAA
Found at i:347540 original size:38 final size:36
Alignment explanation
Indices: 347483--347580 Score: 96
Period size: 36 Copynumber: 2.8 Consensus size: 36
347473 TAAAATATAT
* *
347483 AAAAAATATATAAA-A-AATAAAGAAAAAGAAG-AA
1 AAAAAATATATAAATATAATAAATAAAAAAAAGAAA
* * *
347516 GAAAAATATATAAATA-AATTAATAATAAAAAAGTAA
1 AAAAAATATATAAATATAATAAATAA-AAAAAAGAAA
* *
347552 AAATAATATATATATATAATAAATAAAAA
1 AAAAAATATATAAATATAATAAATAAAAA
347581 CATAAAAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
33 13 0.25
34 8 0.15
35 6 0.11
36 18 0.34
37 8 0.15
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.22
Consensus pattern (36 bp):
AAAAAATATATAAATATAATAAATAAAAAAAAGAAA
Found at i:347554 original size:33 final size:33
Alignment explanation
Indices: 347484--347588 Score: 92
Period size: 33 Copynumber: 3.2 Consensus size: 33
347474 AAAATATATA
* * *
347484 AAAAATATATAAA-AAATAAAGAAAAAGAAGAAG-
1 AAAAATATATAAATAAATTAATAATAA-AA-AAGT
347517 AAAAATATATAAATAAATTAATAATAAAAAAGT
1 AAAAATATATAAATAAATTAATAATAAAAAAGT
* *
347550 AAAAATA-ATATATATATATAATAAATAAAAACA-T
1 AAAAATATATAAATAAAT-TAAT-AATAAAAA-AGT
347584 AAAAA
1 AAAAA
347589 AAATAGTAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
32 11 0.18
33 26 0.42
34 24 0.39
35 1 0.02
ACGTcount: A:0.72, C:0.01, G:0.05, T:0.22
Consensus pattern (33 bp):
AAAAATATATAAATAAATTAATAATAAAAAAGT
Found at i:347577 original size:34 final size:34
Alignment explanation
Indices: 347517--347599 Score: 91
Period size: 34 Copynumber: 2.4 Consensus size: 34
347507 AAAGAAGAAG
347517 AAAAAT-ATATAAATAAATTAATAATAAAAA-AGT
1 AAAAATAATATAAATAAATTAATAATAAAAACA-T
* *
347550 AAAAATAATATATATATA-TAATAAATAAAAACAT
1 AAAAATAATATAAATAAATTAAT-AATAAAAACAT
*
347584 AAAAAAAATAGTAAAT
1 AAAAATAATA-TAAAT
347600 GTGTATATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
33 10 0.24
34 27 0.64
35 5 0.12
ACGTcount: A:0.70, C:0.01, G:0.02, T:0.27
Consensus pattern (34 bp):
AAAAATAATATAAATAAATTAATAATAAAAACAT
Found at i:348251 original size:37 final size:36
Alignment explanation
Indices: 348201--348308 Score: 162
Period size: 37 Copynumber: 2.9 Consensus size: 36
348191 TTCTGGATCC
*
348201 TATTTTTAGGAGTTTGAATCATAGTAGAACTCTATCA
1 TATTTTTAGGAGTTTGAATC-TAGTAAAACTCTATCA
* *
348238 TATTTTTAGGAGTTTGAATCCTAATAAAACTCTATCC
1 TATTTTTAGGAGTTTGAAT-CTAGTAAAACTCTATCA
348275 TATTTTTAGGAGTTTGAATTCTAGTAAAACTCTA
1 TATTTTTAGGAGTTTGAA-TCTAGTAAAACTCTA
348309 ACACTATGTT
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
37 63 0.97
38 2 0.03
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (36 bp):
TATTTTTAGGAGTTTGAATCTAGTAAAACTCTATCA
Found at i:348977 original size:83 final size:85
Alignment explanation
Indices: 348880--349067 Score: 240
Period size: 83 Copynumber: 2.3 Consensus size: 85
348870 GAGTTGAATA
* * * *
348880 TAATCAAACACGAAGGTCTTTGA-TGACTGATAACCCTTCTTGCCTTGAGTTATATTACAAATGA
1 TAATCAAACTCGAAGGTCTTTGATTGACAGATAACCCTTCTAGCCTTGAGTTATACTACAAATGA
* *
348944 TGTG-CCTTGGAGCTGAGCG
66 TGTGCCCTCGAAGCTGAGCG
* * *
348963 TAGTCAAACTCGAAGGTCTTT-ATTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGA
1 TAATCAAACTCGAAGGTCTTTGATTGACAGATAACCCTTCTAGCCTTGAGTTATACTACAAATGA
* *
349027 TGTGCCCTCGAAGTTGAGTG
66 TGTGCCCTCGAAGCTGAGCG
*
349047 TAATCGAACTCGAAGG-CTTTG
1 TAATCAAACTCGAAGGTCTTTG
349068 TGTTTCAAGA
Statistics
Matches: 89, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
82 1 0.01
83 63 0.71
84 25 0.28
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (85 bp):
TAATCAAACTCGAAGGTCTTTGATTGACAGATAACCCTTCTAGCCTTGAGTTATACTACAAATGA
TGTGCCCTCGAAGCTGAGCG
Found at i:349183 original size:36 final size:36
Alignment explanation
Indices: 349134--349370 Score: 147
Period size: 36 Copynumber: 6.7 Consensus size: 36
349124 TTTTTTTTTG
* *
349134 TGTTTCAAGAGAAACTGTCTCAAGAGGGATAAAATT
1 TGTTTCAAAAGAAACTGTCTCAAGAGGGACAAAATT
* *
349170 TGTTTCAAAAGAAACTGTCTCAAAAGAGACAAAACTT
1 TGTTTCAAAAGAAACTGTCTCAAGAGGGACAAAA-TT
* *
349207 AG-TTCTAAAAGAAACTGTCTCAAG-GGAGACGAAATT
1 TGTTTC-AAAAGAAACTGTCTCAAGAGG-GACAAAATT
* *
349243 TGTTTCAAGGAA-AAGA-TAT-TCAA-A--G----ATTT
1 TGTTTCAA--AAGAA-ACTGTCTCAAGAGGGACAAAATT
** * * *
349272 TGTTTCAAGGGAAACTATCCCAAGAGAGACAAAATT
1 TGTTTCAAAAGAAACTGTCTCAAGAGGGACAAAATT
* ** * *
349308 TATTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAAAGAAACTGTCTCAAGAGGGACAA-AATT
**
349345 TGTTTCAAGGGAAACTGTCTCAAGAG
1 TGTTTCAAAAGAAACTGTCTCAAGAG
349371 AGAAAAAACT
Statistics
Matches: 162, Mismatches: 20, Indels: 37
0.74 0.09 0.17
Matches are distributed among these distances:
27 1 0.01
28 5 0.03
29 14 0.09
30 1 0.01
32 1 0.01
33 1 0.01
36 75 0.46
37 61 0.38
38 3 0.02
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (36 bp):
TGTTTCAAAAGAAACTGTCTCAAGAGGGACAAAATT
Found at i:349347 original size:102 final size:102
Alignment explanation
Indices: 349168--349354 Score: 252
Period size: 102 Copynumber: 1.8 Consensus size: 102
349158 AGGGATAAAA
* * *
349168 TTTGTTTCAAAAGAAACTGTCTCAAAAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGGG
1 TTTGTTTCAAAAGAAACTATCCCAAAAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGAG
349233 AGACGAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
66 AGACGAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
** * * * **
349270 TTTGTTTCAAGGGAAACTATCCCAAGAGAGACAAAATTTATTTC-AAGGGAAACTGTCTCAAGAG
1 TTTGTTTCAAAAGAAACTATCCCAAAAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGAG
349334 AGAC-AAGATTTTGTTTCAAGG
66 AGACGAA-A-TTTGTTTCAAGG
349355 GAAACTGTCT
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
100 2 0.03
101 22 0.30
102 49 0.67
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.27
Consensus pattern (102 bp):
TTTGTTTCAAAAGAAACTATCCCAAAAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGAG
AGACGAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
Found at i:349359 original size:37 final size:37
Alignment explanation
Indices: 349265--349373 Score: 175
Period size: 37 Copynumber: 3.0 Consensus size: 37
349255 AAGATATTCA
* *
349265 AAGATTTTGTTTCAAGGGAAACTATCCCAAGAGAGAC
1 AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
* *
349302 AA-AATTTATTTCAAGGGAAACTGTCTCAAGAGAGAC
1 AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
349338 AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
349374 AAAAACTTGG
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
36 32 0.49
37 33 0.51
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.26
Consensus pattern (37 bp):
AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
Found at i:350690 original size:32 final size:30
Alignment explanation
Indices: 350577--350690 Score: 93
Period size: 32 Copynumber: 3.6 Consensus size: 30
350567 CATCAGGATA
* * *
350577 TTGAATTCCCAAAGATGCCCCAATATTCGATG
1 TTGAA-TCTCAAAAATGCCCCAACATT-GATG
* * * *
350609 CTGAATCTCAAAAATACCCTAACATTTTATG
1 TTGAATCTCAAAAATGCCCCAACA-TTGATG
*
350640 TTAAATCTCAAAAAATGCCCCAACATCTGATG
1 TTGAATCTC-AAAAATGCCCCAACAT-TGATG
*
350672 TTGAATCTTCAAAGATGCC
1 TTGAATC-TCAAAAATGCC
350691 TTCATTGTTC
Statistics
Matches: 64, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
31 25 0.39
32 37 0.58
33 2 0.03
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.29
Consensus pattern (30 bp):
TTGAATCTCAAAAATGCCCCAACATTGATG
Found at i:351732 original size:69 final size:69
Alignment explanation
Indices: 351620--351754 Score: 225
Period size: 69 Copynumber: 2.0 Consensus size: 69
351610 CTCTCTCTTG
* * *
351620 ATGCTCTATGATCTTCGAGTGGAGTGATTCATTGATTCAGAAATGATTGTGCTTGATCAATCTCA
1 ATGCTCTATGATCTTCGAGTGAAATGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATCTCA
351685 TTTA
66 TTTA
* *
351689 ATGCTCTATGATCTTCGAGTGAAATGGTTCAGTGATTCGGAAATGATTGTGCTTGATCAATCTCA
1 ATGCTCTATGATCTTCGAGTGAAATGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATCTCA
351754 T
66 T
351755 AGTTTGAATC
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 61 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (69 bp):
ATGCTCTATGATCTTCGAGTGAAATGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATCTCA
TTTA
Found at i:351856 original size:13 final size:13
Alignment explanation
Indices: 351826--351886 Score: 85
Period size: 13 Copynumber: 5.0 Consensus size: 13
351816 TTTTTCTTCA
*
351826 ATTTTC-CTTTGT
1 ATTTTCTCTTTTT
351838 -TTTTCTCTTTTT
1 ATTTTCTCTTTTT
351850 ATTTTCTCTTTTT
1 ATTTTCTCTTTTT
351863 ATTTTCT-TTTTT
1 ATTTTCTCTTTTT
351875 -TTTTCTCTTTTT
1 ATTTTCTCTTTTT
351887 GTTCTGATTG
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
11 11 0.24
12 15 0.33
13 19 0.42
ACGTcount: A:0.05, C:0.15, G:0.02, T:0.79
Consensus pattern (13 bp):
ATTTTCTCTTTTT
Found at i:351870 original size:24 final size:24
Alignment explanation
Indices: 351826--351891 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
351816 TTTTTCTTCA
351826 ATTTTC-CTTTGTTTTTCTCTTTTT
1 ATTTTCTCTTT-TTTTTCTCTTTTT
351850 ATTTTCTCTTTTTATTT-TCTTTTT
1 ATTTTCTCTTTTT-TTTCTCTTTTT
* *
351874 TTTTTCTCTTTTTGTTCT
1 ATTTTCTCTTTTTTTTCT
351892 GATTGAATCT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
23 2 0.05
24 28 0.76
25 7 0.19
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.77
Consensus pattern (24 bp):
ATTTTCTCTTTTTTTTCTCTTTTT
Found at i:355118 original size:32 final size:35
Alignment explanation
Indices: 355082--355191 Score: 102
Period size: 39 Copynumber: 3.1 Consensus size: 35
355072 AAAAAGAAGA
*
355082 AAAAATATATAAATA-AAATAAT-AATAAAAA-GT
1 AAAAATATATAAATATAAATAATAAATAAAAACAT
* *
355114 AAAAATA-ATATATATATATAATAAATAAAAACAT
1 AAAAATATATAAATATAAATAATAAATAAAAACAT
* * *
355148 AAAAAAATAGTAAATATATATAAAAATTAATAAAAACAT
1 AAAAATATA-T-AA-ATATA-AATAATAAATAAAAACAT
355187 AAAAA
1 AAAAA
355192 AAATAACATA
Statistics
Matches: 62, Mismatches: 8, Indels: 9
0.78 0.10 0.11
Matches are distributed among these distances:
31 6 0.10
32 13 0.21
33 8 0.13
34 7 0.11
35 1 0.02
36 1 0.02
37 1 0.02
38 5 0.08
39 20 0.32
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (35 bp):
AAAAATATATAAATATAAATAATAAATAAAAACAT
Found at i:355118 original size:33 final size:32
Alignment explanation
Indices: 355049--355163 Score: 94
Period size: 33 Copynumber: 3.5 Consensus size: 32
355039 GTAAAATAAA
* *
355049 TAAAAAAATATAAA-GAAATAA-AGAAAAAGAAG
1 TAAAAAAATATAAATAAAATAATA-ATAAA-AAG
355081 -AAAAAATATATAAATAAAATAATAATAAAAAG
1 TAAAAAA-ATATAAATAAAATAATAATAAAAAG
* * *
355113 TAAAAATAATATATAT-ATATAATAAATAAAAACA
1 TAAAAA-AATATAAATAAAATAAT-AATAAAAA-G
355147 TAAAAAAATAGTAAATA
1 TAAAAAAATA-TAAATA
355164 TATATAAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
31 6 0.09
32 16 0.24
33 34 0.50
34 12 0.18
ACGTcount: A:0.72, C:0.01, G:0.05, T:0.22
Consensus pattern (32 bp):
TAAAAAAATATAAATAAAATAATAATAAAAAG
Found at i:355124 original size:35 final size:33
Alignment explanation
Indices: 355050--355144 Score: 97
Period size: 35 Copynumber: 2.9 Consensus size: 33
355040 TAAAATAAAT
* *
355050 AAAAAA-ATATAAA-GAAATAAAGAAAAAGAAG
1 AAAAAATATATAAATAAAATAAATAAAAAGAAG
355081 AAAAAATATATAAATAAAATAATAATAAAAAGTAA-
1 AAAAAATATATAAATAAAAT-A-AATAAAAAG-AAG
* * *
355116 AAATAATATATATATATAATAAATAAAAA
1 AAAAAATATATAAATAAAATAAATAAAAA
355145 CATAAAAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
31 6 0.11
32 7 0.13
33 12 0.22
34 2 0.04
35 25 0.46
36 2 0.04
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (33 bp):
AAAAAATATATAAATAAAATAAATAAAAAGAAG
Found at i:355140 original size:39 final size:36
Alignment explanation
Indices: 355072--355209 Score: 104
Period size: 36 Copynumber: 3.8 Consensus size: 36
355062 AGAAATAAAG
* * *
355072 AAAAAGAAGAAAA-AATATATAAATAAAAT-AATAAT
1 AAAAA-AAAAAAATAATATATATATATAATAAATAAT
**
355107 AAAAAGTAAAAATAATATATATATATAATAAATAA-
1 AAAAAAAAAAAATAATATATATATATAATAAATAAT
* * *
355142 AAACATAAAAAAATAGTAAATATATATAA-AAATTAAT
1 AAA-AAAAAAAAATAATATATATATATAATAAA-TAAT
*
355179 AAAAACATAAAAAAAATAACATATATATATA
1 --AAA-A-AAAAAAAATAATATATATATATA
355210 TGTAATCTAA
Statistics
Matches: 81, Mismatches: 14, Indels: 11
0.76 0.13 0.10
Matches are distributed among these distances:
34 4 0.05
35 25 0.31
36 28 0.35
39 5 0.06
40 19 0.23
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (36 bp):
AAAAAAAAAAAATAATATATATATATAATAAATAAT
Found at i:355164 original size:40 final size:38
Alignment explanation
Indices: 355114--355210 Score: 135
Period size: 39 Copynumber: 2.5 Consensus size: 38
355104 AATAAAAAGT
355114 AAAAAT-AATATATATATATAATAAATAAAAACATAAA
1 AAAAATAAATATATATATATAATAAATAAAAACATAAA
* *
355151 AAAATAGTAAATATATATA-AAAATTAATAAAAACATAAA
1 AAAA-A-TAAATATATATATATAATAAATAAAAACATAAA
355190 AAAAATAACATATATATATAT
1 AAAAATAA-ATATATATATAT
355211 GTAATCTAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
37 7 0.13
38 11 0.21
39 24 0.46
40 10 0.19
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (38 bp):
AAAAATAAATATATATATATAATAAATAAAAACATAAA
Found at i:355191 original size:38 final size:39
Alignment explanation
Indices: 355084--355209 Score: 129
Period size: 38 Copynumber: 3.3 Consensus size: 39
355074 AAAGAAGAAA
* * **
355084 AAATATATAAATAAAAT-AATAATAA-A-AAGTAAAAAT
1 AAATATATATATAAAATAAATAAAAACATAAAAAAAAAT
* *
355120 -AATATATATATATAATAAATAAAAACATAAAAAAATAGT
1 AAATATATATATAAAATAAATAAAAACATAAAAAAA-AAT
*
355159 AAATATATATA-AAAATTAATAAAAACAT-AAAAAAAAT
1 AAATATATATATAAAATAAATAAAAACATAAAAAAAAAT
355196 AACATATATATATA
1 AA-ATATATATATA
355210 TGTAATCTAA
Statistics
Matches: 74, Mismatches: 9, Indels: 11
0.79 0.10 0.12
Matches are distributed among these distances:
35 14 0.19
36 7 0.09
37 5 0.07
38 20 0.27
39 18 0.24
40 10 0.14
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (39 bp):
AAATATATATATAAAATAAATAAAAACATAAAAAAAAAT
Found at i:355223 original size:40 final size:36
Alignment explanation
Indices: 355114--355231 Score: 107
Period size: 39 Copynumber: 3.1 Consensus size: 36
355104 AATAAAAAGT
*
355114 AAAAAT-AATATATATATATAATAAATAAAAACATAAA
1 AAAAATAAATATATATATATAAT-TA-AAAAACATAAA
*
355151 AAAATAGTAAATATATATA-AAAATTAATAAAAACATAAA
1 AAAA-A-TAAATATATATATATAATT-A-AAAAACATAAA
355190 AAAAATAACATATATATATATGTAATCTAAAAAA-ATAAA
1 AAAAATAA-ATATATATATA--TAAT-TAAAAAACATAAA
355229 AAA
1 AAA
355232 TATATACTAA
Statistics
Matches: 69, Mismatches: 3, Indels: 16
0.78 0.03 0.18
Matches are distributed among these distances:
37 7 0.10
38 11 0.16
39 31 0.45
40 15 0.22
41 4 0.06
42 1 0.01
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (36 bp):
AAAAATAAATATATATATATAATTAAAAAACATAAA
Found at i:355801 original size:37 final size:37
Alignment explanation
Indices: 355760--355871 Score: 179
Period size: 37 Copynumber: 3.0 Consensus size: 37
355750 ATGCTTCTGG
** *
355760 ATCCTATTTTTAGGAGTTTGAATTATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
*
355797 ATCCTATTTTTAGAAGTTTGAATCCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
*
355834 ATCTTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
355871 A
1 A
355872 ACGCTATGTT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
Found at i:358367 original size:37 final size:37
Alignment explanation
Indices: 358265--358373 Score: 123
Period size: 37 Copynumber: 2.9 Consensus size: 37
358255 TTTATTATTT
* *
358265 CAATAGATGAATTGTAATCATTCTTT-CAAAAAAAACA
1 CAATAAATGAATTGTAATCATT-TTTCCTAAAAAAACA
* * **
358302 CAATAAATAAATTTTAAT-ATTTTCTTCCTAAAAACCCA
1 CAATAAATGAATTGTAATCA-TTT-TTCCTAAAAAAACA
358340 CAATAAATGAATTGTAATCATTTTTCCTAAAAAA
1 CAATAAATGAATTGTAATCATTTTTCCTAAAAAA
358374 TCCATTAAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
36 2 0.03
37 29 0.49
38 27 0.46
39 1 0.02
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.34
Consensus pattern (37 bp):
CAATAAATGAATTGTAATCATTTTTCCTAAAAAAACA
Found at i:358373 original size:38 final size:38
Alignment explanation
Indices: 358265--358373 Score: 118
Period size: 38 Copynumber: 2.9 Consensus size: 38
358255 TTTATTATTT
*
358265 CAATAGATGAATTGTAATCATTCTTT-C-AAAAAAAACA
1 CAATAAATGAATTGTAATCATT-TTTCCTAAAAAAAACA
* * **
358302 CAATAAATAAATTTTAAT-ATTTTCTTCCT-AAAAACCCA
1 CAATAAATGAATTGTAATCA-TTT-TTCCTAAAAAAAACA
358340 CAATAAATGAATTGTAATCATTTTTCCTAAAAAA
1 CAATAAATGAATTGTAATCATTTTTCCTAAAAAA
358374 TCCATTAAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
36 2 0.03
37 24 0.41
38 32 0.54
39 1 0.02
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.34
Consensus pattern (38 bp):
CAATAAATGAATTGTAATCATTTTTCCTAAAAAAAACA
Found at i:360932 original size:6 final size:6
Alignment explanation
Indices: 359928--360932 Score: 1495
Period size: 6 Copynumber: 168.0 Consensus size: 6
359918 TACGCATATG
* * * * * * * * *
359928 CATACG CATACG CATACG CATACG CATACC CATACC CATACG CAGACC
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
* * * * * * *
359976 CATACC CATACG CATACC CATACG CATACC CATACC CATACG CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
* * * * * *
360024 CATACG CATACA CATACG CATACG CATACG CATACG CATACG CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
*
360072 CATATC- CATACA CATACA CATACA AATACA CATACA CATACA CATACA
1 CATA-CA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
360120 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
360168 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
360216 CAT--A CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
360262 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
360310 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
360358 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
360406 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
360454 CATACA CATACACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CAT--ACA CATACA CATACA CATACA CATACA CATACA CATACA
360504 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
360552 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
360600 CATACA C--ACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
360646 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
360694 CATACA CATACA CATACA CATACA CATACA CATACA CATATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA C--ATACA CATACA
* * *
360744 CATACA CATACA CATACA CATACA CATAC- CATACC CATACC CATACC
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
* * * * * * *
360791 CATACC CATACC CATACC CATACC CATAC- CATACC CATACC CATACC
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
* * * * * * *
360838 CATAC- CATACC CATACG CATACG CATACG CATACG CATACG CATACG
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
* * * * * *
360885 CATACG CATACG CATACG CATACG CATACG CATACG CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
360933 GAATACTTGA
Statistics
Matches: 967, Mismatches: 19, Indels: 26
0.96 0.02 0.03
Matches are distributed among these distances:
4 8 0.01
5 16 0.02
6 930 0.96
7 1 0.00
8 12 0.01
ACGTcount: A:0.45, C:0.35, G:0.03, T:0.17
Consensus pattern (6 bp):
CATACA
Found at i:362692 original size:32 final size:32
Alignment explanation
Indices: 362676--362823 Score: 143
Period size: 32 Copynumber: 4.6 Consensus size: 32
362666 GTAGAGTTAG
* * *
362676 TATTGCATTCATATAATGCATAATAGAGTCAA
1 TATTGCATTCAGATAATGCATAACAGAGACAA
* * * *
362708 TATTACATTCGGATACTGCATAACAAAGACAA
1 TATTGCATTCAGATAATGCATAACAGAGACAA
* *
362740 TATTGCATTCAGATAATGCATAACAGAGATAG
1 TATTGCATTCAGATAATGCATAACAGAGACAA
* * * * *
362772 TATTGCATTCATATAATGCACAAGAGCGTCAA
1 TATTGCATTCAGATAATGCATAACAGAGACAA
* * *
362804 TATCGCATTTAGACAATGCA
1 TATTGCATTCAGATAATGCA
362824 CATCAGATAC
Statistics
Matches: 92, Mismatches: 24, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
32 92 1.00
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (32 bp):
TATTGCATTCAGATAATGCATAACAGAGACAA
Found at i:362722 original size:64 final size:64
Alignment explanation
Indices: 362598--362767 Score: 162
Period size: 64 Copynumber: 2.7 Consensus size: 64
362588 TTGTGTGTTG
* * * * * ** *
362598 CATAGTAGTA-TTAGCATTGCATTCAGACAATGCTTAGCAGAGTTAATATTTTATTTGGATAATA
1 CATAGTAG-AGTTAGTATTGCATTCAGATAATGCATAACAGAGTCAATATTACATTCGGATAATA
* * * *
362662 CATAGTAGAGTTAGTATTGCATTCATATAATGCATAATAGAGTCAATATTACATTCGGATACTG
1 CATAGTAGAGTTAGTATTGCATTCAGATAATGCATAACAGAGTCAATATTACATTCGGATAATA
** * ** *
362726 CATAACAAAGACAATATTGCATTCAGATAATGCATAACAGAG
1 CATAGTAGAGTTAGTATTGCATTCAGATAATGCATAACAGAG
362768 ATAGTATTGC
Statistics
Matches: 85, Mismatches: 20, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
63 1 0.01
64 84 0.99
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.32
Consensus pattern (64 bp):
CATAGTAGAGTTAGTATTGCATTCAGATAATGCATAACAGAGTCAATATTACATTCGGATAATA
Found at i:363017 original size:42 final size:42
Alignment explanation
Indices: 362954--363040 Score: 129
Period size: 42 Copynumber: 2.1 Consensus size: 42
362944 GTAGGTAGCA
* * * *
362954 CTTGATCTATATCATGTATGTACCTACTGGTTAGTACCATGT
1 CTTGATCTATATCATGCATGTACCTACTGCTAAGTACCACGT
*
362996 CTTGATCTATATCATGCATGTATCTACTGCTAAGTACCACGT
1 CTTGATCTATATCATGCATGTACCTACTGCTAAGTACCACGT
363038 CTT
1 CTT
363041 TAGCATGCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (42 bp):
CTTGATCTATATCATGCATGTACCTACTGCTAAGTACCACGT
Found at i:363575 original size:30 final size:30
Alignment explanation
Indices: 363539--363623 Score: 107
Period size: 32 Copynumber: 2.8 Consensus size: 30
363529 TAACACGTTT
* *
363539 ACTTTTTGTTTCATTTTAGTACTGTTGTTA
1 ACTTTTTGTTTCATTTTAGTACCGCTGTTA
* * *
363569 ATTTTTTGTATCATTTTAGTGTCCCGCTGTTA
1 ACTTTTTGTTTCATTTTA--GTACCGCTGTTA
363601 ACTTTTTGTTTCATTTTAGTACC
1 ACTTTTTGTTTCATTTTAGTACC
363624 TAAAGTTTTA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
30 20 0.44
32 25 0.56
ACGTcount: A:0.16, C:0.14, G:0.13, T:0.56
Consensus pattern (30 bp):
ACTTTTTGTTTCATTTTAGTACCGCTGTTA
Found at i:363773 original size:29 final size:29
Alignment explanation
Indices: 363727--363810 Score: 132
Period size: 29 Copynumber: 2.9 Consensus size: 29
363717 ATGCCTTTGG
*
363727 TTCCAGTTTAGTGCCTAACTTTTATATCT
1 TTCCAGTTTGGTGCCTAACTTTTATATCT
* *
363756 TTCTAGTTTGGTGCCTAACGTTTATATCT
1 TTCCAGTTTGGTGCCTAACTTTTATATCT
363785 TTCCAGTTTGGTGCCTAACGTTTTAT
1 TTCCAGTTTGGTGCCTAAC-TTTTAT
363811 TCCGTTACTC
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.18, C:0.19, G:0.15, T:0.48
Consensus pattern (29 bp):
TTCCAGTTTGGTGCCTAACTTTTATATCT
Found at i:364446 original size:16 final size:17
Alignment explanation
Indices: 364415--364447 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
364405 ATGATTTATG
364415 AAAATAAAAAATTAATT
1 AAAATAAAAAATTAATT
364432 AAAATAAAAAA-TAATT
1 AAAATAAAAAATTAATT
364448 TATTTCTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAATAAAAAATTAATT
Found at i:370390 original size:17 final size:19
Alignment explanation
Indices: 370362--370398 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
370352 ATTTTATATC
370362 AATTTATAAATATT-TTTT
1 AATTTATAAATATTATTTT
370380 AATTT-TAAATATTATTTT
1 AATTTATAAATATTATTTT
370398 A
1 A
370399 TAAAAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
AATTTATAAATATTATTTT
Found at i:371654 original size:22 final size:22
Alignment explanation
Indices: 371597--371655 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
371587 ACGCGATTCT
*
371597 GACTATCGCATTACGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * *
371619 AAAT-TCGCGTTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
*
371640 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
371656 ATATGTAAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:371717 original size:20 final size:20
Alignment explanation
Indices: 371640--371790 Score: 144
Period size: 20 Copynumber: 7.5 Consensus size: 20
371630 GCGATTTTCC
* *
371640 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGATTCT
* * *
371660 GTA-AATCGCAATGCGAATAT
1 G-ACTATCGCAATGCGATTCT
* * *
371680 GTA-AATCGCAATGTGATTAT
1 G-ACTATCGCAATGCGATTCT
371700 GACTATCGCAATGCGATTCT
1 GACTATCGCAATGCGATTCT
*
371720 GACTATCGCAACGCGATTCT
1 GACTATCGCAATGCGATTCT
* *
371740 GACTATCGCAACGAGATTCT
1 GACTATCGCAATGCGATTCT
* *
371760 GACTATCGCAACGAGATTCT
1 GACTATCGCAATGCGATTCT
*
371780 GACTGTCGCAA
1 GACTATCGCAA
371791 CACTGAATTT
Statistics
Matches: 120, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
19 1 0.01
20 118 0.98
21 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (20 bp):
GACTATCGCAATGCGATTCT
Found at i:371791 original size:20 final size:20
Alignment explanation
Indices: 371684--371791 Score: 153
Period size: 20 Copynumber: 5.4 Consensus size: 20
371674 GAATATGTAA
* * *
371684 ATCGCAATGTGATTATGACT
1 ATCGCAACGAGATTCTGACT
* *
371704 ATCGCAATGCGATTCTGACT
1 ATCGCAACGAGATTCTGACT
*
371724 ATCGCAACGCGATTCTGACT
1 ATCGCAACGAGATTCTGACT
371744 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
371764 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
*
371784 GTCGCAAC
1 ATCGCAAC
371792 ACTGAATTTC
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 83 1.00
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:372643 original size:24 final size:24
Alignment explanation
Indices: 372611--372664 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
372601 GTATTCGAAA
* *
372611 TTTGATCTTTGTCAGTACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
372635 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
372659 TTTGAT
1 TTTGAT
372665 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:374939 original size:6 final size:6
Alignment explanation
Indices: 374918--374952 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
374908 AGAAAAAGGC
**
374918 AATCAA AATCGC AATCAA AATCAA AATCAA AATCA
1 AATCAA AATCAA AATCAA AATCAA AATCAA AATCA
374953 CATTTTGGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (6 bp):
AATCAA
Found at i:375252 original size:140 final size:140
Alignment explanation
Indices: 375000--375269 Score: 513
Period size: 140 Copynumber: 1.9 Consensus size: 140
374990 AAACGTTGTA
*
375000 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAATATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
* *
375065 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTATTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
375130 TATGTGTATT
131 TATGTGTATT
375140 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
375205 TGATATGTTCAGTTATTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTATTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
375270 CGCAACGCGA
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 127 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTATTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:375265 original size:20 final size:20
Alignment explanation
Indices: 375240--375399 Score: 139
Period size: 20 Copynumber: 8.7 Consensus size: 20
375230 TTACACATTC
*
375240 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
375260 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
375280 ATTTGATTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
375299 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
375314 ATTTTACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
375334 ATATGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
*
375353 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
375368 ATTTGACTATCGCAACTCGA
1 ATTTGACTATCGCAACGCGA
*
375388 A-TTGACTTTCGC
1 ATTTGACTATCGC
375400 GTTGCGATTT
Statistics
Matches: 114, Mismatches: 14, Indels: 25
0.75 0.09 0.16
Matches are distributed among these distances:
14 19 0.17
15 6 0.05
19 16 0.14
20 73 0.64
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:375335 original size:54 final size:54
Alignment explanation
Indices: 375248--375399 Score: 234
Period size: 54 Copynumber: 2.8 Consensus size: 54
375238 TCATTTGAAT
* * *
375248 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACTCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACACGAATTTGACTATCGCAACGCAAAA
* *
375302 ATCGCAACGCGAATTTTACTATCGCAACACGAATATGACTATCGCAACGCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACACGAATTTGACTATCGCAACGCAAAA
* *
375356 ATCGCAACGCGAATTTGACTATCGCAACTCGAA-TTGACTTTCGC
1 ATCGCAACGCGAATTTGACTATCGCAACACGAATTTGACTATCGC
375400 GTTGCGATTT
Statistics
Matches: 89, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
53 9 0.10
54 80 0.90
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (54 bp):
ATCGCAACGCGAATTTGACTATCGCAACACGAATTTGACTATCGCAACGCAAAA
Found at i:375418 original size:20 final size:21
Alignment explanation
Indices: 375389--375446 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
375379 GCAACTCGAA
375389 TTGA-CTTTCGCGTTGCGATT
1 TTGAGCTTTCGCGTTGCGATT
* *
375409 TTG-GCTTTCGCATTGTGATT
1 TTGAGCTTTCGCGTTGCGATT
*
375429 TTGAG-TTTAGCGTTGCGA
1 TTGAGCTTTCGCGTTGCGA
375447 AAGTGTACCT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.12, C:0.16, G:0.28, T:0.45
Consensus pattern (21 bp):
TTGAGCTTTCGCGTTGCGATT
Found at i:375623 original size:7 final size:7
Alignment explanation
Indices: 375611--375654 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
375601 CTTTGCAATG
375611 AACCTTA
1 AACCTTA
375618 AACCTTA
1 AACCTTA
*
375625 AACCCTA
1 AACCTTA
375632 AACCTTA
1 AACCTTA
375639 AA-CTCTA
1 AACCT-TA
375646 AACCATTA
1 AACC-TTA
375654 A
1 A
375655 TCTGATTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 2 0.06
7 25 0.78
8 4 0.12
9 1 0.03
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (7 bp):
AACCTTA
Found at i:375633 original size:14 final size:14
Alignment explanation
Indices: 375611--375654 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
375601 CTTTGCAATG
*
375611 AACCTTAAACCTTA
1 AACCCTAAACCTTA
375625 AACCCTAAACCTTA
1 AACCCTAAACCTTA
*
375639 AACTCTAAACCATTA
1 AACCCTAAACC-TTA
375654 A
1 A
375655 TCTGATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 23 0.85
15 4 0.15
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (14 bp):
AACCCTAAACCTTA
Found at i:377283 original size:24 final size:23
Alignment explanation
Indices: 377224--377283 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
377214 TGGCTAAGAT
*
377224 TCGAGTTTGAATCGAGCTCAAAA
1 TCGAGTTTGAATTGAGCTCAAAA
* **
377247 TCGAGTTTTAATTGAGCTCGAGGA
1 TCGAGTTTGAATTGAGCTC-AAAA
*
377271 TCGAGTTCGAATT
1 TCGAGTTTGAATT
377284 TTGAGCTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 17 0.57
24 13 0.43
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (23 bp):
TCGAGTTTGAATTGAGCTCAAAA
Found at i:380757 original size:70 final size:70
Alignment explanation
Indices: 380673--380925 Score: 470
Period size: 70 Copynumber: 3.6 Consensus size: 70
380663 ATTTTTTTTA
* *
380673 AAAACAATCACACATGGCTAAGAAACATAGAAGAACATCCCAAAAGTCTAAAGAGTAAAAATATG
1 AAAACAATCTCACATGGCTAAGAAACATAGAAGAGCATCCCAAAAGTCTAAAGAGTAAAAATATG
380738 AGAAC
66 AGAAC
380743 AAAACAATCTCACATGGCTAAGAAACATAGAAGAGCATCCCAAAAGTCTAAAGAGTAAAAATATG
1 AAAACAATCTCACATGGCTAAGAAACATAGAAGAGCATCCCAAAAGTCTAAAGAGTAAAAATATG
380808 AGAAC
66 AGAAC
380813 AAAACAATCTCACATGGCTAAGAAACATAGAAGAGCATCCCAAAAGTCTAAAGAGTAAAAATATG
1 AAAACAATCTCACATGGCTAAGAAACATAGAAGAGCATCCCAAAAGTCTAAAGAGTAAAAATATG
380878 AGAAC
66 AGAAC
* *
380883 AAAACAATCCCACATGGTTAAGAAACATAGAAGAGCATCCCAA
1 AAAACAATCTCACATGGCTAAGAAACATAGAAGAGCATCCCAA
380926 CTAACTTCTA
Statistics
Matches: 179, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
70 179 1.00
ACGTcount: A:0.52, C:0.18, G:0.15, T:0.15
Consensus pattern (70 bp):
AAAACAATCTCACATGGCTAAGAAACATAGAAGAGCATCCCAAAAGTCTAAAGAGTAAAAATATG
AGAAC
Found at i:388372 original size:23 final size:25
Alignment explanation
Indices: 388346--388392 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
388336 TTGATATGAG
388346 TAAAATG-A-GAAAAGTAGTATACT
1 TAAAATGAATGAAAAGTAGTATACT
*
388369 TAAAATGAATGAGAAGTAGTATAC
1 TAAAATGAATGAAAAGTAGTATAC
388393 AACCAAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 1 0.05
25 13 0.62
ACGTcount: A:0.51, C:0.04, G:0.19, T:0.26
Consensus pattern (25 bp):
TAAAATGAATGAAAAGTAGTATACT
Found at i:394524 original size:26 final size:26
Alignment explanation
Indices: 394495--394573 Score: 158
Period size: 26 Copynumber: 3.0 Consensus size: 26
394485 ATGGGTTAAT
394495 AGACTTGTGTTAGAATTGAAGATGCA
1 AGACTTGTGTTAGAATTGAAGATGCA
394521 AGACTTGTGTTAGAATTGAAGATGCA
1 AGACTTGTGTTAGAATTGAAGATGCA
394547 AGACTTGTGTTAGAATTGAAGATGCA
1 AGACTTGTGTTAGAATTGAAGATGCA
394573 A
1 A
394574 TGTATGTAAC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.30
Consensus pattern (26 bp):
AGACTTGTGTTAGAATTGAAGATGCA
Found at i:395303 original size:16 final size:16
Alignment explanation
Indices: 395284--395332 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
395274 AATCAATAAA
*
395284 AAATTTAATCTAAAAC
1 AAATTCAATCTAAAAC
* *
395300 AAATGCAAGCTAAAAC
1 AAATTCAATCTAAAAC
*
395316 AAAGTCAATCTAAAAC
1 AAATTCAATCTAAAAC
395332 A
1 A
395333 TACTGCAGTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.57, C:0.16, G:0.06, T:0.20
Consensus pattern (16 bp):
AAATTCAATCTAAAAC
Found at i:396114 original size:34 final size:32
Alignment explanation
Indices: 396047--396116 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
396037 ACCTTACAAC
* * *
396047 TCCCTAGTTTTTCCGGGCTAAACTAGAATCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
396079 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
396113 TCCC
1 TCCC
396117 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:396508 original size:20 final size:20
Alignment explanation
Indices: 396483--396576 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
396473 GCAGCCTTCG
*
396483 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
* *
396503 TGCATGGATGCACAGCAAGA
1 TGCATCGATGCACAGCAGGA
**
396523 TGCATCGATGCACAGCCTTGA
1 TGCATCGATGCACAG-CAGGA
*
396544 TGCATCGATGCACAGAAGGA
1 TGCATCGATGCACAGCAGGA
396564 TGCATCGATGCAC
1 TGCATCGATGCAC
396577 TAATTGCATT
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 48 0.73
21 18 0.27
ACGTcount: A:0.30, C:0.23, G:0.29, T:0.18
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:396557 original size:41 final size:40
Alignment explanation
Indices: 396483--396576 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 40
396473 GCAGCCTTCG
* *
396483 TGCATGGATGCACAGCAGGATGCATGGATGCACAGCAA-GA
1 TGCATCGATGCACAGCAGGATGCATCGATGCACAG-AAGGA
**
396523 TGCATCGATGCACAGCCTTGATGCATCGATGCACAGAAGGA
1 TGCATCGATGCACAG-CAGGATGCATCGATGCACAGAAGGA
396564 TGCATCGATGCAC
1 TGCATCGATGCAC
396577 TAATTGCATT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
40 16 0.33
41 32 0.67
ACGTcount: A:0.30, C:0.23, G:0.29, T:0.18
Consensus pattern (40 bp):
TGCATCGATGCACAGCAGGATGCATCGATGCACAGAAGGA
Found at i:396679 original size:25 final size:21
Alignment explanation
Indices: 396620--396671 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
396610 CTAGTGCAGG
396620 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCAGGGA
*
396641 TGCATGGATGCACTGCAGGGG
1 TGCATGGATGCACTGCAGGGA
396662 TGCATGGATG
1 TGCATGGATG
396672 GATGCACTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.21, C:0.17, G:0.40, T:0.21
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGGA
Found at i:404323 original size:21 final size:21
Alignment explanation
Indices: 404286--404349 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
404276 TTTTGGTGCA
*
404286 GAGGGAA-TCGATCCCCCCCAT
1 GAGGGAACT-GATTCCCCCCAT
**
404307 GAGGGAACTGATTCCCCCTTT
1 GAGGGAACTGATTCCCCCCAT
*
404328 GAATGGGAACCGATTCCCCCCA
1 G-A-GGGAACTGATTCCCCCCA
404350 CAGGGGAATC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 17 0.50
22 2 0.06
23 15 0.44
ACGTcount: A:0.23, C:0.34, G:0.23, T:0.19
Consensus pattern (21 bp):
GAGGGAACTGATTCCCCCCAT
Found at i:408334 original size:31 final size:30
Alignment explanation
Indices: 408279--408384 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 30
408269 ATGTTCTACG
408279 GAACATATGGAC-ATAATTACCTATGTCTTTC
1 GAACATATGGACAAT-A-TACCTATGTCTTTC
***
408310 GAGACATATGGACAATATACCTATGTTCTAAG
1 GA-ACATATGGACAATATACCTATG-TCTTTC
* * * *
408342 GAACATATGGACAGTTTACCTAGGTCCTTC
1 GAACATATGGACAATATACCTATGTCTTTC
*
408372 GAACCTATGGACA
1 GAACATATGGACA
408385 GTTGCCGAGG
Statistics
Matches: 61, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
30 14 0.23
31 29 0.48
32 16 0.26
33 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (30 bp):
GAACATATGGACAATATACCTATGTCTTTC
Found at i:408337 original size:63 final size:61
Alignment explanation
Indices: 408264--408384 Score: 172
Period size: 63 Copynumber: 2.0 Consensus size: 61
408254 GAGTCGAGGG
* * *
408264 TACCTATGTTCTACGGAACATATGGACA-TAATTACCTATGTCTTTCGAGACATATGGACAATA
1 TACCTATGTTCTAAGGAACATATGGACAGT--TTACCTAGGTCCTTCGA-ACATATGGACAATA
*
408327 TACCTATGTTCTAAGGAACATATGGACAGTTTACCTAGGTCCTTCGAACCTATGGACA
1 TACCTATGTTCTAAGGAACATATGGACAGTTTACCTAGGTCCTTCGAACATATGGACA
408385 GTTGCCGAGG
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
61 10 0.19
62 15 0.28
63 27 0.51
64 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (61 bp):
TACCTATGTTCTAAGGAACATATGGACAGTTTACCTAGGTCCTTCGAACATATGGACAATA
Found at i:409623 original size:45 final size:45
Alignment explanation
Indices: 409553--409679 Score: 155
Period size: 45 Copynumber: 2.8 Consensus size: 45
409543 CTATCCTAAC
* *
409553 CTCAGCAGGTTCTGGTTCATCAATTTCAGGTTCATTAATTTAGGG
1 CTCAACAGGTTCTGGTTCATCAATTTCAGGTTCATTAATTTAGAG
* * * **
409598 CTCAACAGGTTCTGGTTCATTAATTTCGGGTTCACTAATTTCTAG
1 CTCAACAGGTTCTGGTTCATCAATTTCAGGTTCATTAATTTAGAG
* * * *
409643 TTCAACTGGTTATGCTTCATCAATTTCAGGTTCATTA
1 CTCAACAGGTTCTGGTTCATCAATTTCAGGTTCATTA
409680 TGTTCAGACC
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 68 1.00
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (45 bp):
CTCAACAGGTTCTGGTTCATCAATTTCAGGTTCATTAATTTAGAG
Found at i:409631 original size:15 final size:15
Alignment explanation
Indices: 409566--409639 Score: 58
Period size: 15 Copynumber: 4.9 Consensus size: 15
409556 AGCAGGTTCT
* *
409566 GGTTCATCAATTTCA
1 GGTTCATTAATTTCG
*
409581 GGTTCATTAATTTAG
1 GGTTCATTAATTTCG
* ** ** *
409596 GGCTCAACAGGTTCT
1 GGTTCATTAATTTCG
409611 GGTTCATTAATTTCG
1 GGTTCATTAATTTCG
*
409626 GGTTCACTAATTTC
1 GGTTCATTAATTTC
409640 TAGTTCAACT
Statistics
Matches: 42, Mismatches: 17, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.41
Consensus pattern (15 bp):
GGTTCATTAATTTCG
Found at i:409645 original size:15 final size:15
Alignment explanation
Indices: 409607--409646 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
409597 GCTCAACAGG
*
409607 TTCTGGTTCATTAAT
1 TTCTGGTTCACTAAT
*
409622 TTCGGGTTCACTAAT
1 TTCTGGTTCACTAAT
*
409637 TTCTAGTTCA
1 TTCTGGTTCA
409647 ACTGGTTATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (15 bp):
TTCTGGTTCACTAAT
Found at i:410949 original size:129 final size:128
Alignment explanation
Indices: 410712--410949 Score: 408
Period size: 129 Copynumber: 1.9 Consensus size: 128
410702 GCATAAGAAA
* *
410712 AAACCATATAATCTCATATATACTATTCTCATTCGTGTAATCAGTAAGCAGTAAAACCATTTATA
1 AAACCATATAATCTCATATATACTATTCTCATTCGTGCAATCAGTAACCAGTAAAACCATTTATA
*
410777 CTAACAGTAAACCAACTAAACTCATATAAACTCCCTAACATATATACTAACAGTAACCCCACT
66 CTAACAGTAAACCAACTAAACCCATATAAACTCCCTAACATATATACTAACAGTAACCCCACT
410840 AAACTCATATAATCTCATATATACTATTCTCATTCGTGCAATCAGTAACCAGTAAAACCATTTAT
1 AAAC-CATATAATCTCATATATACTATTCTCATTCGTGCAATCAGTAACCAGTAAAACCATTTAT
* *
410905 ACTAACAGT-AAGC-AGTAAACCCATATAAACTCCCTAACATATATA
65 ACTAACAGTAAACCAACTAAACCCATATAAACTCCCTAACATATATA
410950 GCATTTTAAT
Statistics
Matches: 104, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
127 30 0.29
128 7 0.07
129 67 0.64
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.29
Consensus pattern (128 bp):
AAACCATATAATCTCATATATACTATTCTCATTCGTGCAATCAGTAACCAGTAAAACCATTTATA
CTAACAGTAAACCAACTAAACCCATATAAACTCCCTAACATATATACTAACAGTAACCCCACT
Found at i:412482 original size:23 final size:23
Alignment explanation
Indices: 412456--412514 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
412446 TATATTTTTT
*
412456 AAATA-AAAACAATTTAATTTTAC
1 AAATATAAAA-AATTTAATTTTAA
* *
412479 AAATATTAAAATTTTAATTTTAA
1 AAATATAAAAAATTTAATTTTAA
*
412502 AAATATATAAAAT
1 AAATATAAAAAAT
412515 CAGAAATAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
23 26 0.90
24 3 0.10
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (23 bp):
AAATATAAAAAATTTAATTTTAA
Found at i:424781 original size:17 final size:17
Alignment explanation
Indices: 424744--424787 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
424734 AGATTTTATT
*
424744 ATTTATTTTA-TTAGAA
1 ATTTATTTTACATAGAA
424760 ATTTATTTTACATAGAA
1 ATTTATTTTACATAGAA
* *
424777 TTTTAGTTTAC
1 ATTTATTTTAC
424788 CATTGCTAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.55
Consensus pattern (17 bp):
ATTTATTTTACATAGAA
Found at i:426677 original size:21 final size:21
Alignment explanation
Indices: 426635--426677 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
426625 TTTCTGGGCT
*
426635 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
426656 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
426677 A
1 A
426678 ACGAACATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:427575 original size:2 final size:2
Alignment explanation
Indices: 427568--427592 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
427558 AATAATAGAG
427568 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 T
427593 CAGTATAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.