Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008964.1 Hibiscus syriacus cultivar Beakdansim tig00112305_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: 2156694
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 2 of 11
Found at i:139076 original size:2 final size:2
Alignment explanation
Indices: 139069--139103 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
139059 ACTAGGAAAC
139069 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
139104 AGTATAAGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:139652 original size:12 final size:14
Alignment explanation
Indices: 139635--139666 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
139625 GCATTCATTG
139635 TTATATTATA-G-T
1 TTATATTATATGTT
139647 TTATATTATATGTT
1 TTATATTATATGTT
139661 TTATAT
1 TTATAT
139667 GTCTCACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.56
13 1 0.06
14 7 0.39
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (14 bp):
TTATATTATATGTT
Found at i:143421 original size:18 final size:18
Alignment explanation
Indices: 143398--143449 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
143388 TATATGATAT
143398 GTGGTCATTCGGGACATA
1 GTGGTCATTCGGGACATA
*
143416 GTGGTCCTTCGGGACATA
1 GTGGTCATTCGGGACATA
143434 GTGGTCATTCGGGACA
1 GTGGTCATTCGGGACA
143450 AATTCTAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.19, C:0.19, G:0.35, T:0.27
Consensus pattern (18 bp):
GTGGTCATTCGGGACATA
Found at i:145502 original size:18 final size:19
Alignment explanation
Indices: 145479--145514 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
145469 CAAGTTGGTG
145479 AGTCTTATTTT-TAACTCC
1 AGTCTTATTTTATAACTCC
145497 AGTCTTATTTTATAACTC
1 AGTCTTATTTTATAACTC
145515 GAAGTTAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (19 bp):
AGTCTTATTTTATAACTCC
Found at i:151114 original size:30 final size:31
Alignment explanation
Indices: 151069--151151 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
151059 GTTTAATCCG
* *
151069 AATTTCTAAATATTTTGAGGGGATC-AAATTA-
1 AATTTTTAAA-ATTTTAAGGGG-TCTAAATTAT
151100 AATTTTTAAAATTTTTAA-GGGTCTAAATTAT
1 AATTTTTAAAA-TTTTAAGGGGTCTAAATTAT
*
151131 AACTTTTAAAATTTTAAGGGG
1 AATTTTTAAAATTTTAAGGGG
151152 CCATAACCCC
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
29 2 0.04
30 16 0.36
31 27 0.60
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.42
Consensus pattern (31 bp):
AATTTTTAAAATTTTAAGGGGTCTAAATTAT
Found at i:151563 original size:21 final size:21
Alignment explanation
Indices: 151529--151568 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
151519 TTATAATGAG
*
151529 TAGATTAAAATTTAGGATTAA
1 TAGATTAAAATTTAAGATTAA
* *
151550 TAGATTAGAGTTTAAGATT
1 TAGATTAAAATTTAAGATT
151569 TCTTATCAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.40
Consensus pattern (21 bp):
TAGATTAAAATTTAAGATTAA
Found at i:153732 original size:18 final size:17
Alignment explanation
Indices: 153678--153726 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 17
153668 TTGGACCCTT
*
153678 AGTGCATCGATGCACTAA
1 AGTGCATCGATGCA-TCA
153696 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
153714 AGTGCATTCGATG
1 AGTGCA-TCGATG
153727 TTTCAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 6 0.21
18 8 0.29
19 14 0.50
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:153831 original size:65 final size:65
Alignment explanation
Indices: 153678--153857 Score: 215
Period size: 65 Copynumber: 2.8 Consensus size: 65
153668 TTGGACCCTT
** *
153678 AGTGCATCGATGCACT-AAGAGTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCA
1 AGTGCATCGATGCA-TGACTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCA
*
153741 G
65 C
* *
153742 AGTGCATCGATGCATGACTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCT
1 AGTGCATCGATGCATGACTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCA
153806 C
65 C
* * * *
153807 AGTGCATCGGTGCATG-GTATGTGCATCAATGCATGAAATGCATTCGATGTT
1 AGTGCATCGATGCATGACTA-GTGCATCGATGCATCAAATGCATTCGATGTT
153858 CAATTTAATT
Statistics
Matches: 102, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
63 1 0.01
64 46 0.45
65 52 0.51
66 3 0.03
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (65 bp):
AGTGCATCGATGCATGACTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCAC
Found at i:153896 original size:65 final size:63
Alignment explanation
Indices: 153698--153907 Score: 180
Period size: 65 Copynumber: 3.3 Consensus size: 63
153688 TGCACTAAGA
* * *
153698 GTGCATCGATGCATCAAGTGCATTCGATGTTTCA-AAATAGC-CAGAGTGCATCGATGCAT-GAC
1 GTGCATCAATGCATCAAATGCATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGA-
*
153760 TA
62 TT
* *
153762 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGG-TA
1 GTGCATCAATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGAT-
153826 T
63 T
* **
153827 GTGCATCAATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCATCAATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGGAT
153890 T
63 T
**
153891 GGTGCATCGGTGCATCA
1 -GTGCATCAATGCATCA
153908 CTCTGAAAAA
Statistics
Matches: 123, Mismatches: 12, Indels: 21
0.79 0.08 0.13
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 50 0.41
65 61 0.50
66 5 0.04
67 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.30
Consensus pattern (63 bp):
GTGCATCAATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGATT
Found at i:155162 original size:30 final size:30
Alignment explanation
Indices: 155100--155192 Score: 91
Period size: 30 Copynumber: 3.1 Consensus size: 30
155090 TTATAATTAC
* * *
155100 AAGGACCAAAAT-GGAAAAACCACAA-CTTA
1 AAGGACCAAAATAGCAAAAA-TAGAATCTTA
* * * *
155129 AAGGACCAAAATAGTATAAATAGGATTTTA
1 AAGGACCAAAATAGCAAAAATAGAATCTTA
*
155159 AAGGACTAAAATAGCAAAAATAGAATCTTA
1 AAGGACCAAAATAGCAAAAATAGAATCTTA
155189 AAGG
1 AAGG
155193 GCTAAATAGT
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
29 14 0.27
30 37 0.73
ACGTcount: A:0.54, C:0.12, G:0.16, T:0.18
Consensus pattern (30 bp):
AAGGACCAAAATAGCAAAAATAGAATCTTA
Found at i:155198 original size:30 final size:30
Alignment explanation
Indices: 155125--155198 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 30
155115 AAAACCACAA
* * * *
155125 CTTAAAGGACCAAAATAGTATAAATAGGAT
1 CTTAAAGGACTAAAATAGCAAAAATAGAAT
*
155155 TTTAAAGGACTAAAATAGCAAAAATAGAAT
1 CTTAAAGGACTAAAATAGCAAAAATAGAAT
*
155185 CTTAAAGGGCTAAA
1 CTTAAAGGACTAAA
155199 TAGTTAAAAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.51, C:0.09, G:0.16, T:0.23
Consensus pattern (30 bp):
CTTAAAGGACTAAAATAGCAAAAATAGAAT
Found at i:156530 original size:3 final size:3
Alignment explanation
Indices: 156522--156568 Score: 85
Period size: 3 Copynumber: 15.3 Consensus size: 3
156512 AATGTAACAC
156522 ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
156568 A
1 A
156569 AAAACTCGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:156840 original size:21 final size:22
Alignment explanation
Indices: 156781--156843 Score: 78
Period size: 21 Copynumber: 2.9 Consensus size: 22
156771 AAATTAATCA
156781 ATTA-ATAAATTATATATTAGTG
1 ATTATATAAA-TATATATTAGTG
156803 ATTATATCAAATATATATT-GT-
1 ATTATAT-AAATATATATTAGTG
156824 ATGTATATAAATATATATTA
1 AT-TATATAAATATATATTA
156844 TTATTATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
21 13 0.35
22 11 0.30
23 10 0.27
24 3 0.08
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (22 bp):
ATTATATAAATATATATTAGTG
Found at i:159888 original size:9 final size:9
Alignment explanation
Indices: 159874--159898 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
159864 ACAGTTACCT
159874 CTGGTGGAG
1 CTGGTGGAG
159883 CTGGTGGAG
1 CTGGTGGAG
159892 CTGGTGG
1 CTGGTGG
159899 CGCTTCTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.12, G:0.56, T:0.24
Consensus pattern (9 bp):
CTGGTGGAG
Found at i:160682 original size:14 final size:15
Alignment explanation
Indices: 160641--160689 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
160631 TTTTCAAGAG
160641 TTTA-AAAAAATAT-
1 TTTATAAAAAATATA
160654 TTATATAAAATAATATA
1 TT-TATAAAA-AATATA
*
160671 TTT-TAAAAAATAAA
1 TTTATAAAAAATATA
160685 TTTAT
1 TTTAT
160690 TTAGTATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
13 2 0.07
14 10 0.33
15 10 0.33
16 6 0.20
17 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTTATAAAAAATATA
Found at i:160682 original size:17 final size:18
Alignment explanation
Indices: 160650--160683 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
160640 GTTTAAAAAA
*
160650 ATATTTATATAAAATAAT
1 ATATTTATAAAAAATAAT
160668 ATATTT-TAAAAAATAA
1 ATATTTATAAAAAATAA
160684 ATTTATTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATTTATAAAAAATAAT
Found at i:160871 original size:27 final size:28
Alignment explanation
Indices: 160841--160899 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
160831 ATGCCTCCAT
* *
160841 CAAACGC-CACCCTCCTATATTTCAACA
1 CAAACGCTCACCATCCCATATTTCAACA
*
160868 CAAACGCTCATCATCCCATATTTCAACA
1 CAAACGCTCACCATCCCATATTTCAACA
160896 CAAA
1 CAAA
160900 ATACCCCCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.37, C:0.37, G:0.03, T:0.22
Consensus pattern (28 bp):
CAAACGCTCACCATCCCATATTTCAACA
Found at i:162181 original size:22 final size:22
Alignment explanation
Indices: 162120--162184 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
162110 TTTAATTTCC
* *
162120 TTTATTATTTTAATTTTATTTTA
1 TTTATT-TTGTAATTTTATTTAA
*
162143 TTCAGTTTTAGT-A-TTTATTTAA
1 TTTA-TTTT-GTAATTTTATTTAA
162165 TTTATTTTGTAATTTTATTT
1 TTTATTTTGTAATTTTATTT
162185 CTTAATTAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
20 2 0.06
21 5 0.15
22 18 0.53
23 6 0.18
24 3 0.09
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.69
Consensus pattern (22 bp):
TTTATTTTGTAATTTTATTTAA
Found at i:166424 original size:76 final size:76
Alignment explanation
Indices: 166303--166547 Score: 354
Period size: 76 Copynumber: 3.2 Consensus size: 76
166293 AGGATTTGTC
* * *
166303 TCACTTGAGATTGTTTTT-TTAAAA-TAGACTTTGTCTCACTTGAGACAGTTTTTACTCGAAACA
1 TCACTTAAGATTGTTTTTCTTAAAACAAGA-TTTGTCTCGCTTGAGACAGTTTTTACTCGAAACA
166366 AGAAGATTTATT
65 AGAAGATTTATT
*
166378 TCACTTAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAGTTTTTACGCGAAACAA
1 TCACTTAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAGTTTTTACTCGAAACAA
166443 GAAGATTTATT
66 GAAGATTTATT
* * *
166454 TCACTCT-AGATTGTTTTTCTTAAAACAAGATTTGTCACGCTTGAGACGGTTTTTACTCGAAAGA
1 TCACT-TAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAGTTTTTACTCGAAACA
*
166518 AG-ACATTTCATT
65 AGAAGATTT-ATT
*
166530 TCACTCAAGATTGTTTTT
1 TCACTTAAGATTGTTTTT
166548 AAAGAAGATT
Statistics
Matches: 155, Mismatches: 10, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
75 22 0.14
76 129 0.83
77 4 0.03
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (76 bp):
TCACTTAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAGTTTTTACTCGAAACAA
GAAGATTTATT
Found at i:166430 original size:36 final size:36
Alignment explanation
Indices: 166295--166507 Score: 135
Period size: 36 Copynumber: 5.7 Consensus size: 36
166285 TAATACTGAG
* *
166295 GATTTGTCTCACTTGAGATTGTTTTT-TTAAAA-TA
1 GATTTGTCTCACTTGAGACTGTTTTTCTTAAAACAA
* * *
166329 GACTTTGTCTCACTTGAGACAGTTTTTACTCGAAACAAGAA
1 GA-TTTGTCTCACTTGAGACTGTTTTT-CT--TAA-AACAA
* * * *
166370 GATTTATTTCACTTAAGATTGTTTTTCTTAAAACAA
1 GATTTGTCTCACTTGAGACTGTTTTTCTTAAAACAA
* * ** *
166406 GATTTGTCTCGCTTGAGACAGTTTTTACGCGAAACAAGAA
1 GATTTGTCTCACTTGAGACTGTTTTT---CTTAA-AACAA
* * *
166446 GATTTATTTCACTCT-AGATTGTTTTTCTTAAAACAA
1 GATTTGTCTCACT-TGAGACTGTTTTTCTTAAAACAA
* * *
166482 GATTTGTCACGCTTGAGACGGTTTTT
1 GATTTGTCTCACTTGAGACTGTTTTT
166508 ACTCGAAAGA
Statistics
Matches: 132, Mismatches: 34, Indels: 24
0.69 0.18 0.13
Matches are distributed among these distances:
34 2 0.02
35 23 0.17
36 46 0.35
37 6 0.05
39 7 0.05
40 44 0.33
41 4 0.03
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.41
Consensus pattern (36 bp):
GATTTGTCTCACTTGAGACTGTTTTTCTTAAAACAA
Found at i:166614 original size:39 final size:39
Alignment explanation
Indices: 166550--166870 Score: 464
Period size: 39 Copynumber: 8.2 Consensus size: 39
166540 TTGTTTTTAA
*
166550 AGAAGATTTTATCT-GCTTGAGATAGTTTTCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
166588 ATAAGATTTTATCTCGCTTGAGATAGTTTCCCTCAAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
166627 ATAAGATTTTATCTCGCTTGAGATAGTTTTCCTGGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * * *
166666 ATAATATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAT
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
166705 AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
166744 AGAATATTTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGA-TTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
166784 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * *
166823 AGAATATTTTGTCTCGCTTGCGATAGTTTCGCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
166862 AAAAGATTT
1 AGAAGATTT
166871 AAAGAAACTA
Statistics
Matches: 255, Mismatches: 26, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
38 13 0.05
39 205 0.80
40 37 0.15
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (39 bp):
AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
Found at i:166778 original size:157 final size:155
Alignment explanation
Indices: 166550--166870 Score: 500
Period size: 157 Copynumber: 2.1 Consensus size: 155
166540 TTGTTTTTAA
*
166550 AGAAGATTTTATCTGCTTGAGATAGTTTTCCTCGAAACATAAGATTTTATCTCGCTTGAGATAGT
1 AGAAGATTTTATCTGCTTGAGATAGTTTTCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGT
* * * *
166615 TTCCCTCAAAACATAAGATTTTATCTCGCTTGAGATAGTTTTCCTGGAAACATAATATTTTGTCT
66 TTCCCTCAAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAATATTTTGTCT
* *
166680 CGCTTGAGATAGTTTCCCTTGAAAT
131 CGCTTGAGATAGTTTCCCTCGAAAC
*
166705 AGAAGATTTTATCTCGCTTGAGATAG-TTTCTCTCGAAACAGAATATTTTTATCTCGCTTGAGAT
1 AGAAGATTTTATCT-GCTTGAGATAGTTTTC-CTCGAAACAGAAGA-TTTTATCTCGCTTGAGAT
*
166769 AGTTTCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAATATTTTG
63 AGTTTCCCTCAAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAATATTTTG
* *
166834 TCTCGCTTGCGATAGTTTCGCTCGAAAC
128 TCTCGCTTGAGATAGTTTCCCTCGAAAC
*
166862 AAAAGATTT
1 AGAAGATTT
166871 AAAGAAACTA
Statistics
Matches: 151, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
155 18 0.12
156 23 0.15
157 110 0.73
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (155 bp):
AGAAGATTTTATCTGCTTGAGATAGTTTTCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGT
TTCCCTCAAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAATATTTTGTCT
CGCTTGAGATAGTTTCCCTCGAAAC
Found at i:167003 original size:21 final size:21
Alignment explanation
Indices: 166979--167032 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
166969 CTATAAGTCT
166979 TTCGGGCAAGATAATAAGACC
1 TTCGGGCAAGATAATAAGACC
*
167000 TTCGGGC-A-ATCCATAAGACC
1 TTCGGGCAAGAT-AATAAGACC
*
167020 TTCGGGCAGGATA
1 TTCGGGCAAGATA
167033 TTTTTAACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 2 0.07
20 16 0.59
21 7 0.26
22 2 0.07
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.20
Consensus pattern (21 bp):
TTCGGGCAAGATAATAAGACC
Found at i:167562 original size:27 final size:28
Alignment explanation
Indices: 167510--167562 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
167500 CCTATTAAAC
167510 CCCACCATCCCACATTTCAACACCAATG
1 CCCACCATCCCACATTTCAACACCAATG
* *
167538 CCCATCATCCCATA-TTCAACACCAA
1 CCCACCATCCCACATTTCAACACCAA
167563 ATACCCCCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.34, C:0.45, G:0.02, T:0.19
Consensus pattern (28 bp):
CCCACCATCCCACATTTCAACACCAATG
Found at i:168838 original size:16 final size:17
Alignment explanation
Indices: 168799--168840 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
168789 TTATTATTTG
168799 TAATTT-TTATTTTATT
1 TAATTTATTATTTTATT
*
168815 CAATTTTATTA-TTTATT
1 TAA-TTTATTATTTTATT
168832 TAATTTATT
1 TAATTTATT
168841 TTGTAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 8 0.36
17 11 0.50
18 3 0.14
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (17 bp):
TAATTTATTATTTTATT
Found at i:168851 original size:22 final size:22
Alignment explanation
Indices: 168794--168854 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
168784 TTCCTTTATT
*
168794 ATTTGTAATTTTTATTTTATTCA
1 ATTTGTAA-TTTTATTTAATTCA
* *
168817 ATTT-TATTATTTATTTAATTTA
1 ATTTGTAAT-TTTATTTAATTCA
*
168839 TTTTGTAATTTTATTT
1 ATTTGTAATTTTATTT
168855 CTTAATTAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
21 1 0.03
22 23 0.74
23 7 0.23
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.69
Consensus pattern (22 bp):
ATTTGTAATTTTATTTAATTCA
Found at i:170646 original size:13 final size:14
Alignment explanation
Indices: 170623--170655 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
170613 CAGCAAAAAT
170623 AATAGAAAAAG-GAA
1 AATA-AAAAAGAGAA
170637 AATAAAAAAGAGAA
1 AATAAAAAAGAGAA
170651 AATAA
1 AATAA
170656 CCTCAGTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (14 bp):
AATAAAAAAGAGAA
Found at i:170832 original size:41 final size:41
Alignment explanation
Indices: 170787--170927 Score: 212
Period size: 41 Copynumber: 3.5 Consensus size: 41
170777 ATTCGCGTTG
*
170787 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* ** **
170828 CATTTCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
170868 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGGGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
170909 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
170928 CTACAGTTGT
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
40 34 0.39
41 53 0.61
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:170837 original size:20 final size:20
Alignment explanation
Indices: 170812--170924 Score: 154
Period size: 20 Copynumber: 5.6 Consensus size: 20
170802 TAGTTGAAAA
*
170812 TCGCGTTGCGCTTTTCCATT
1 TCGCGTTGCGATTTTCCATT
170832 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
170852 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
170872 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
*
170893 TCGCGTTGGGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
170913 TCGCGTTGCGAT
1 TCGCGTTGCGAT
170925 AGTCTACAGT
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
20 65 0.82
21 14 0.18
ACGTcount: A:0.12, C:0.23, G:0.24, T:0.41
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:171068 original size:6 final size:6
Alignment explanation
Indices: 171057--171082 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
171047 AGACACGTAT
171057 GACCAC GACCAC GACCAC GACCAC GA
1 GACCAC GACCAC GACCAC GACCAC GA
171083 GACGAGACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.46, G:0.19, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:171595 original size:6 final size:6
Alignment explanation
Indices: 171584--171632 Score: 80
Period size: 6 Copynumber: 8.2 Consensus size: 6
171574 CTCGTCTCGT
* *
171584 GGTCGG GGTCGG GGTCGG GGTCGG GGTCGG GGTCGT GGTCGT GGTCGG
1 GGTCGG GGTCGG GGTCGG GGTCGG GGTCGG GGTCGG GGTCGG GGTCGG
171632 G
1 G
171633 CTGGTGCTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.00, C:0.16, G:0.63, T:0.20
Consensus pattern (6 bp):
GGTCGG
Found at i:179471 original size:12 final size:12
Alignment explanation
Indices: 179454--179479 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
179444 TTCAACCTTG
179454 AATCACCCCAAT
1 AATCACCCCAAT
179466 AATCACCCCAAT
1 AATCACCCCAAT
179478 AA
1 AA
179480 AGCAGCGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.38, G:0.00, T:0.15
Consensus pattern (12 bp):
AATCACCCCAAT
Found at i:180704 original size:55 final size:55
Alignment explanation
Indices: 180627--180766 Score: 190
Period size: 55 Copynumber: 2.5 Consensus size: 55
180617 TAGAGACCTT
* * *
180627 AGTGGTAAAAGAATTGTCGTTATTCTTTGATATAGAGCATAAATTAAGTGACATC
1 AGTGGTAAAAGAATTATTGTTATTCTTTGATATAGAGCATAAATCAAGTGACATC
* * * *
180682 ATTGGTAAAAAAATTATTGTTATTCTTTGATATAGAGCATGAATCAAGTGACCTC
1 AGTGGTAAAAGAATTATTGTTATTCTTTGATATAGAGCATAAATCAAGTGACATC
* * *
180737 AGTGATAAAAGAATTTTTATTATTCTTTGA
1 AGTGGTAAAAGAATTATTGTTATTCTTTGA
180767 GGCATTAAGT
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 73 1.00
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (55 bp):
AGTGGTAAAAGAATTATTGTTATTCTTTGATATAGAGCATAAATCAAGTGACATC
Found at i:183095 original size:33 final size:32
Alignment explanation
Indices: 183047--183187 Score: 99
Period size: 33 Copynumber: 4.5 Consensus size: 32
183037 AAAAATGATA
183047 AATATATATATAATAAAATAAAATAATAATAGT
1 AATATATA-ATAATAAAATAAAATAATAATAGT
183080 AATATATAATGAAT--AAT---AT-AT-ATA-T
1 AATATATAAT-AATAAAATAAAATAATAATAGT
183105 -ATATAT-ATAATAAAATAATAA-AATAATAGT
1 AATATATAATAATAAAATAA-AATAATAATAGT
* *
183135 AATATATAATAAATAATATATATATATATAAT-GAT
1 AATATATAAT-AATAAAATA-AAATA-ATAATAG-T
183170 AAATATATAATATATAAA
1 -AATATATAATA-ATAAA
183188 TATGCTATAT
Statistics
Matches: 86, Mismatches: 3, Indels: 35
0.69 0.02 0.28
Matches are distributed among these distances:
22 3 0.03
23 2 0.02
24 9 0.10
25 1 0.01
26 3 0.03
27 2 0.02
28 5 0.06
29 3 0.03
30 1 0.01
31 9 0.10
32 4 0.05
33 20 0.23
34 3 0.03
35 7 0.08
36 14 0.16
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (32 bp):
AATATATAATAATAAAATAAAATAATAATAGT
Found at i:183100 original size:2 final size:2
Alignment explanation
Indices: 183095--183452 Score: 261
Period size: 2 Copynumber: 187.5 Consensus size: 2
183085 ATAATGAATA
* *
183095 AT AT AT AT AT AT AT AT AT A- AT A- AA AT A- AT A- AA AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
183132 AGT A- AT AT AT A- AT AA AT A- AT AT AT AT AT AT AT A- AT GAT AA
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
* * * * *
183172 AT AT AT A- AT AT AT AA AT AT GCT AT AT CAT AT AT A- AT GT AC AA
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT -AT AT AT AT AT AT AT AT
* *
183214 AT AT AT A- AT GAT AT A- AT AT AT AT AC AT -T AT AC AT AT AT AT
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
183254 AT ACT AT AT A- AT AT AA AT AT ACT AT AT A- AT AT AT AT AA AT AT
1 AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
*
183296 AT A- AT A- AT AT AT AT AT AT AT AG A- AT AT A- AGT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A-T AT AT
*
183336 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
183377 AT AT AT A- AT AT AT ACT AT AT A- AT AT AA AT AT ACT AT A- AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT
183418 A- AT AT A- AT AT AT AT AT -T A- AT AT A- AT AT ACT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A
183453 AAAAGGGCCA
Statistics
Matches: 287, Mismatches: 28, Indels: 82
0.72 0.07 0.21
Matches are distributed among these distances:
1 29 0.10
2 236 0.82
3 22 0.08
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (2 bp):
AT
Found at i:183176 original size:71 final size:70
Alignment explanation
Indices: 183044--183454 Score: 266
Period size: 78 Copynumber: 5.5 Consensus size: 70
183034 CAAAAAAATG
* * *
183044 ATAAATATATATATAATAAAATAA-A-ATAATAATAGTAATATATA-ATGA-ATAATATATATAT
1 ATAAA-ATATATAAAATAATATAATATATAATAA-A-TAATATATATAT-ATATAATATAAATAT
183105 ATATATATA
62 ATATATATA
183114 ATAAAATA-ATAAAATAATAGTAATATATAATAAATAATATATATATATATAATGATAAATATAT
1 ATAAAATATATAAAATAATA-TAATATATAATAAATAATATATATATATATAAT-ATAAATATAT
183178 AATATATAA
64 -ATATAT-A
*** * * * *
183187 ATATGCTATATCATATATAATGTACAAATATATAATGATATAATATATATACATTATACATAT--
1 ATAAAATATAT-A-AAATAA--TA-TAATATATAAT-AAATAATATATATATA-TATA-ATATAA
183250 ATATATACTATATA
58 ATATATA-TATATA
* *
183264 ATATAAATATACTATATAATATATATAAATATATAAT-AAT-ATATATATATATAGAATATAAGT
1 ATA-AAATATA-TA-A-AATA-ATAT-AATATATAATAAATAATATATATATATATAATATAAAT
183327 ATACTATATATA
60 ATA-TATATATA
* *
183339 TATATATATATATAATATATATATATATATATATAAATATATATAATATATA-CTATATAATATA
1 -ATA-AAATATATAA-A-ATA-ATATA-ATATAT-AATA-A-ATAATATATATATATATAATATA
183403 AATATACTATAATATA
57 AATATA-TAT-ATATA
* * *
183419 ATATAATATATATATTAATATAATATACTATATAAA
1 ATAAAATATATAAAATAATATAATATA-TA-ATAAA
183455 AAGGGCCAGA
Statistics
Matches: 277, Mismatches: 28, Indels: 69
0.74 0.07 0.18
Matches are distributed among these distances:
68 9 0.03
69 16 0.06
70 14 0.05
71 16 0.06
72 6 0.02
73 11 0.04
74 16 0.06
75 46 0.17
76 24 0.09
77 6 0.02
78 50 0.18
79 42 0.15
80 19 0.07
81 2 0.01
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (70 bp):
ATAAAATATATAAAATAATATAATATATAATAAATAATATATATATATATAATATAAATATATAT
ATATA
Found at i:183274 original size:134 final size:130
Alignment explanation
Indices: 183079--183454 Score: 396
Period size: 134 Copynumber: 2.8 Consensus size: 130
183069 ATAATAATAG
* * *
183079 TAATATATAATGA-ATAATATATATATATATATATAATAAAATAATAAAATAATAGT-AATATA-
1 TAATATATAATGATATAATATATATA-ATATATATAAT-ATATACT-ATATAATA-TAAATATAC
*
183141 TAATAAATAATATATATATATATAATGATAAATATATAATATATAAATATGCTATATCATATATA
62 T-ATAAATAATATA-ATATATATAAT-ATAAATATATAATATATAAATATACTATAT-ATATATA
*
183206 -ATGTACA
123 TATATACA
*
183213 -AATATATAATGATATAATATATATACATTATACATATATATATACTATATAATATAAATATACT
1 TAATATATAATGATATAATATATATA-A-TATATATA-ATATATACTATATAATATAAATATACT
*
183277 ATATAATATATATAAATATATAATAATATATATATATATAGA-ATATAAGTATACTATATATATA
63 ATA-AATA-ATAT-AATATAT-ATAATATA-A-ATATATA-ATATATAAATATACTATATATATA
*
183341 TATATATATA
121 TATATATACA
183351 TAATATAT-AT-ATAT-ATATATATAAATATATATAATATATACTATATAATATAAATATACTAT
1 TAATATATAATGATATAATATATAT-AATATATATAATATATACTATATAATATAAATATACTAT
*
183413 AATATAATATAATATATAT-AT-TAATATAATATACTATATAAA
65 AA-ATAATATAATATATATAATATAA-AT-ATATAATATATAAA
183455 AAGGGCCAGA
Statistics
Matches: 212, Mismatches: 12, Indels: 41
0.80 0.05 0.15
Matches are distributed among these distances:
128 4 0.02
129 13 0.06
130 2 0.01
131 2 0.01
132 7 0.03
133 18 0.08
134 62 0.29
135 24 0.11
136 24 0.11
137 19 0.09
138 29 0.14
139 8 0.04
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (130 bp):
TAATATATAATGATATAATATATATAATATATATAATATATACTATATAATATAAATATACTATA
AATAATATAATATATATAATATAAATATATAATATATAAATATACTATATATATATATATATACA
Found at i:183453 original size:55 final size:52
Alignment explanation
Indices: 183044--183453 Score: 268
Period size: 55 Copynumber: 7.7 Consensus size: 52
183034 CAAAAAAATG
*
183044 ATAAATATATATATAATAAAATAA-A-ATA-ATAATAGTAATATA-TAATGAATAAT
1 ATAAATATATATAT-ATAATATAATATATATATAATA-TAATATACT-AT--ATAAT
* * *
183097 ATATATATATATATATAATAAAATA-ATAAAATAATAGTAATATA-TA-ATAA-
1 ATAAATATATATATATAATATAATATAT-ATATAATA-TAATATACTATATAAT
**
183147 ATAATATATATATATATAATGATAAATATATAATATATAAATATGCTATATCATATATAATGT
1 ATAA-ATATATATATATAAT-AT--A-ATAT-ATATAT-AATATAATATA-C-TATATAA--T
* *
183210 ACAAATATATAATGATATAATAT-ATATACATTATACATATATATATACTATATAAT
1 ATAAATATAT-AT-ATATAATATAATATATA-TATA-ATATA-ATATACTATATAAT
*
183266 ATAAATATACTATATAATATATATAA-ATATATAATAATATATATATA-TATAGAAT
1 ATAAATATA-TATAT-ATA-ATATAATATATAT-ATAATATA-ATATACTATATAAT
*
183321 ATAAGTATACTATATAT-ATAT-ATATATATATAATAT-ATATA-TATATATAT
1 ATAAATATA-TATATATAATATAATATATATATAATATAATATACTATATA-AT
* *
183371 ATAAATATATATA-AT-ATATACTATATAATATAAATATACTATA--ATATAAT
1 ATAAATATATATATATAATATAATATAT-ATAT-AATATAATATACTATATAAT
183421 AT-AATATATATAT-TAATATAATATACTATATAA
1 ATAAATATATATATATAATATAATATA-TATATAA
183454 AAAGGGCCAG
Statistics
Matches: 299, Mismatches: 21, Indels: 78
0.75 0.05 0.20
Matches are distributed among these distances:
48 6 0.02
49 32 0.11
50 34 0.11
51 38 0.13
52 22 0.07
53 16 0.05
54 5 0.02
55 41 0.14
56 34 0.11
57 18 0.06
58 11 0.04
59 14 0.05
60 8 0.03
62 6 0.02
63 7 0.02
64 7 0.02
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (52 bp):
ATAAATATATATATATAATATAATATATATATAATATAATATACTATATAAT
Found at i:184102 original size:72 final size:72
Alignment explanation
Indices: 183971--184132 Score: 261
Period size: 72 Copynumber: 2.2 Consensus size: 72
183961 CGTTGCAGAC
* * * *
183971 GACTCATTCGTTGTGAAGTTAAGTCGATCTCTTGGGCACGATATCTTTCTTCGTAAAGTTGAAAT
1 GACTCATTCGTCGTGAAGTTAAATCGATCTCTTGGGCACGATATCCTTCATCGTAAAGTTGAAAT
184036 CATGGGT
66 CATGGGT
*
184043 GACTCATTCGTCGTGAAGTTAAATCGATCTCTTGGGCACGATATCCTTCATCGTGAAGTTGAAAT
1 GACTCATTCGTCGTGAAGTTAAATCGATCTCTTGGGCACGATATCCTTCATCGTAAAGTTGAAAT
**
184108 TGTGGGT
66 CATGGGT
184115 GACTCATTCGTCGTGAAG
1 GACTCATTCGTCGTGAAG
184133 CTGAGTCCAA
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 83 1.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (72 bp):
GACTCATTCGTCGTGAAGTTAAATCGATCTCTTGGGCACGATATCCTTCATCGTAAAGTTGAAAT
CATGGGT
Found at i:184549 original size:22 final size:22
Alignment explanation
Indices: 184521--184598 Score: 104
Period size: 22 Copynumber: 3.6 Consensus size: 22
184511 AAGAGGTGCG
184521 ATACCCCTATGAATGGGTATCA
1 ATACCCCTATGAATGGGTATCA
* *
184543 ATACCCCCATGAATGGGTACCA
1 ATACCCCTATGAATGGGTATCA
* **
184565 ATGCCCCTATGAAAAGGTATCA
1 ATACCCCTATGAATGGGTATCA
184587 ATACCCC-ATGAA
1 ATACCCCTATGAA
184599 GGCTCAAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
21 5 0.10
22 43 0.90
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.22
Consensus pattern (22 bp):
ATACCCCTATGAATGGGTATCA
Found at i:187779 original size:21 final size:24
Alignment explanation
Indices: 187753--187796 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 24
187743 ATTGGTAACA
187753 ATTGGTAT-C-TTT-TTAACAATG
1 ATTGGTATCCTTTTGTTAACAATG
187774 ATTGGTATCCTTTTGTTAACAAT
1 ATTGGTATCCTTTTGTTAACAAT
187797 TGATATCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.40
22 1 0.05
23 3 0.15
24 8 0.40
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (24 bp):
ATTGGTATCCTTTTGTTAACAATG
Found at i:187798 original size:21 final size:20
Alignment explanation
Indices: 187748--187808 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
187738 CAACAATTGG
187748 TAACAATTGGTAT-C-TTTT
1 TAACAATTGGTATCCTTTTT
187766 TAACAATGATTGGTATCCTTTTGT
1 TAAC-A--ATTGGTATCCTTTT-T
*
187790 TAACAATTGATAT-CTTTTT
1 TAACAATTGGTATCCTTTTT
187809 CATTAAACAT
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
18 4 0.11
19 2 0.06
20 5 0.14
21 15 0.42
22 1 0.03
23 4 0.11
24 5 0.14
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.49
Consensus pattern (20 bp):
TAACAATTGGTATCCTTTTT
Found at i:188054 original size:22 final size:22
Alignment explanation
Indices: 188029--188102 Score: 87
Period size: 22 Copynumber: 3.3 Consensus size: 22
188019 AGAGGTACCG
188029 ATACCCCTATGAATAGGTATCA
1 ATACCCCTATGAATAGGTATCA
* * *
188051 ATACCCCCTATGAATGGGTACCG
1 ATA-CCCCTATGAATAGGTATCA
*
188074 ATACCCTTATGAA-AGGGTATCA
1 ATACCCCTATGAATA-GGTATCA
188096 ATACCCC
1 ATACCCC
188103 GTGAAGGCTC
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
22 23 0.55
23 19 0.45
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (22 bp):
ATACCCCTATGAATAGGTATCA
Found at i:188062 original size:23 final size:23
Alignment explanation
Indices: 188032--188102 Score: 83
Period size: 23 Copynumber: 3.1 Consensus size: 23
188022 GGTACCGATA
188032 CCCCTATGAATAGGTATCAATAC
1 CCCCTATGAATAGGTATCAATAC
* * *
188055 CCCCTATGAATGGGTACCGATA-
1 CCCCTATGAATAGGTATCAATAC
*
188077 CCCTTATGAA-AGGGTATCAATAC
1 CCCCTATGAATA-GGTATCAATAC
188100 CCC
1 CCC
188103 GTGAAGGCTC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
22 17 0.44
23 22 0.56
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (23 bp):
CCCCTATGAATAGGTATCAATAC
Found at i:189025 original size:23 final size:23
Alignment explanation
Indices: 188967--189037 Score: 83
Period size: 23 Copynumber: 3.1 Consensus size: 23
188957 GAGCCTTCAT
*
188967 GGGGTATTGATACCC-TTTCAT-T
1 GGGGTATTGATACCCATTT-ATAG
* *
188989 GGGGTATCGGTACCCATTTATAG
1 GGGGTATTGATACCCATTTATAG
*
189012 GGGGTATTGATACCCATTCATAG
1 GGGGTATTGATACCCATTTATAG
189035 GGG
1 GGG
189038 TATAGGTACC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
22 15 0.37
23 26 0.63
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (23 bp):
GGGGTATTGATACCCATTTATAG
Found at i:189047 original size:22 final size:22
Alignment explanation
Indices: 188962--189040 Score: 97
Period size: 22 Copynumber: 3.6 Consensus size: 22
188952 AATTTGAGCC
*
188962 TTCAT-GGGGTATTGATACCCT
1 TTCATAGGGGTATTGATACCCA
* * *
188983 TTCATTGGGGTATCGGTACCCA
1 TTCATAGGGGTATTGATACCCA
*
189005 TTTATAGGGGGTATTGATACCCA
1 TTCATA-GGGGTATTGATACCCA
189028 TTCATAGGGGTAT
1 TTCATAGGGGTAT
189041 AGGTACCTCT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
21 5 0.10
22 24 0.50
23 19 0.40
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (22 bp):
TTCATAGGGGTATTGATACCCA
Found at i:189306 original size:16 final size:16
Alignment explanation
Indices: 189282--189312 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
189272 AATTGTTTAC
189282 AAAAGGATACCAATTA
1 AAAAGGATACCAATTA
*
189298 AAAATGATACCAATT
1 AAAAGGATACCAATT
189313 GTTGAAAATA
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:0.55, C:0.13, G:0.10, T:0.23
Consensus pattern (16 bp):
AAAAGGATACCAATTA
Found at i:201347 original size:54 final size:54
Alignment explanation
Indices: 201282--201942 Score: 827
Period size: 54 Copynumber: 12.2 Consensus size: 54
201272 TTTTTTAAGA
* * * * * *
201282 TGCACAGATAGTGCCTATATGGTCGTTCATCAACTCATGATGAATTCCGTTG-GT
1 TGCACACATAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTTCG-TGAGT
* * * * *
201336 TGCACACATAGTTCCTGTACGATTCTTCATCGACTCATGATGAA-TTCTGTGAGT
1 TGCACACATAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTTC-GTGAGT
** * *
201390 TAAACACATAGTGCTTGTACAGTTGTTCATCAA-TACATGATGAATTTCGTGAGT
1 TGCACACATAGTGCATGTACGGTTGTTCATCAACT-CATGATGAATTTCGTGAGT
* * * *
201444 TGCACACATAGTGCCTGTACGGTTGTTCATCAACACATGATGAATTCCATGAGT
1 TGCACACATAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTTCGTGAGT
* *
201498 TGCACACATAGTGCATGTACGGTAGTTCATCAACAT-ATGATGAATTTTGTGAGT
1 TGCACACATAGTGCATGTACGGTTGTTCATCAAC-TCATGATGAATTTCGTGAGT
* *
201552 TGCACACATAGTGCATGTACGGCTGTTCATCAACTCATGATGAATTCCGTG-GAT
1 TGCACACATAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTTCGTGAG-T
* *
201606 TGTACACATAGTGTATGTACGGTTGTTCATCAACTCATGATGAATTTCGTG-GAT
1 TGCACACATAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTTCGTGAG-T
* * *
201660 TGCACACATAGTGCTTGTACAGTTGTTCATCAACACATGATGAATTTCGTGAGT
1 TGCACACATAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTTCGTGAGT
* * *
201714 TGCACACATAGTGCCTGTACGGTTGTTCATCAACACATGATGAA-TTCTATGAGT
1 TGCACACATAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTTC-GTGAGT
* *
201768 TGCACACATAGTGCATGTACGGTAGTTCATCAACACATGATGAATTTCGTGAGT
1 TGCACACATAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTTCGTGAGT
**
201822 TGCACACATAGTGCATGTACGACTGTTCATCAACTCATGATGAATTTCGTG-GAT
1 TGCACACATAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTTCGTGAG-T
* * * *
201876 TGCACACATAGTGCTTGTACGATTGATCATCAACTCATGATGAATTCCGTG-GAT
1 TGCACACATAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTTCGTGAG-T
201930 TGCACACATAGTG
1 TGCACACATAGTG
201943 TCTGTAGTAC
Statistics
Matches: 538, Mismatches: 57, Indels: 24
0.87 0.09 0.04
Matches are distributed among these distances:
53 11 0.02
54 520 0.97
55 7 0.01
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (54 bp):
TGCACACATAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTTCGTGAGT
Found at i:202330 original size:19 final size:21
Alignment explanation
Indices: 202290--202341 Score: 72
Period size: 19 Copynumber: 2.5 Consensus size: 21
202280 TACCCTTACA
202290 ATGGTATCGATACTACTATATT
1 ATGGTATCGATACTAC-ATATT
202312 ATGGTATCGATACT-C-TATT
1 ATGGTATCGATACTACATATT
*
202331 ACGGTATCGAT
1 ATGGTATCGAT
202342 GCCATTTCTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 14 0.48
21 1 0.03
22 14 0.48
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.38
Consensus pattern (21 bp):
ATGGTATCGATACTACATATT
Found at i:203768 original size:54 final size:54
Alignment explanation
Indices: 203387--203769 Score: 513
Period size: 54 Copynumber: 7.1 Consensus size: 54
203377 GTACTACAGA
* * * *
203387 CACTATGTGTGCAATCCACGGAATTCATCATGAGTTGATGATCAATCGTACAAG
1 CACTATGTGTGCAATCCACGAAATTCATCATGAGTTGATGAACAACCGTACATG
**
203441 CACTATGTGTGCAATCCACGAAATTCATCATGAGTTGATGAACAGTCGTACATG
1 CACTATGTGTGCAATCCACGAAATTCATCATGAGTTGATGAACAACCGTACATG
* *
203495 CACTATGTGTGCAA-CTCACGAAATTCATCATGTGTTGATGAACTACCGTACATG
1 CACTATGTGTGCAATC-CACGAAATTCATCATGAGTTGATGAACAACCGTACATG
* * *
203549 CACTATGTGTGCAA-CTCA-TAGAATTCATCATGTGTTGATGAACAACCGTACAGG
1 CACTATGTGTGCAATC-CACGA-AATTCATCATGAGTTGATGAACAACCGTACATG
* ** *
203603 CACTATGTGTGCAA-CTCACGAAATTCATCATGTGTTGATGAACAACTATACAAG
1 CACTATGTGTGCAATC-CACGAAATTCATCATGAGTTGATGAACAACCGTACATG
*
203657 CACTATGTGTGCAATCCACGAAATTCATCATGAGTTGATGAACAACTGTACATG
1 CACTATGTGTGCAATCCACGAAATTCATCATGAGTTGATGAACAACCGTACATG
* * * * *
203711 CACTATGTGTACAATCCACGGAATTCATCATGAGTTGATGAACGACCGTATAGG
1 CACTATGTGTGCAATCCACGAAATTCATCATGAGTTGATGAACAACCGTACATG
203765 CACTA
1 CACTA
203770 CGCATCTTAA
Statistics
Matches: 301, Mismatches: 24, Indels: 8
0.90 0.07 0.02
Matches are distributed among these distances:
53 2 0.01
54 297 0.99
55 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (54 bp):
CACTATGTGTGCAATCCACGAAATTCATCATGAGTTGATGAACAACCGTACATG
Found at i:206923 original size:2 final size:2
Alignment explanation
Indices: 206918--207209 Score: 159
Period size: 2 Copynumber: 154.5 Consensus size: 2
206908 AAAATGATAA
* * *
206918 AT AT AT AT GT AT A- AT A- AA AT A- AT AT AT A- AT AA AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
206955 AT AT AT AT GT AT ACC AT AT -T AC ACT AT AT A- AT AT A- AA AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
* *
206996 AT A- AT AT AT A- AT AT AT AA AT AT ACT AT AT CAT AT AT A- AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT -AT AT AT AT AT AT
*
207037 AT AA AT AT AT A- AT GAT AT A- AT AT AT AT AT AT AT AT AT ACT AT
1 AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* *
207079 AT A- AT AT A- AGT AT ACT AT A- AT AT AT AG A- AT AT AT AA AT AT
1 AT AT AT AT AT A-T AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
207119 AC A- AT AT AT AA AT AT AT AT AT AT AC AT -T AT AT A- AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
207158 AT AT ACT AT AT A- AT AT A- AT AT AA AA AT AT AT A- AT A- AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
207197 A- AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT A
207210 AAAAGGGTCG
Statistics
Matches: 225, Mismatches: 30, Indels: 70
0.69 0.09 0.22
Matches are distributed among these distances:
1 26 0.12
2 184 0.82
3 15 0.07
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (2 bp):
AT
Found at i:206948 original size:7 final size:7
Alignment explanation
Indices: 206917--207209 Score: 224
Period size: 7 Copynumber: 39.9 Consensus size: 7
206907 AAAAATGATA
206917 AATATAT
1 AATATAT
*
206924 -ATGTAT
1 AATATAT
*
206930 AATAAAAT
1 AAT-ATAT
206938 AATATAT
1 AATATAT
*
206945 AATAAAT
1 AATATAT
206952 AATATAT
1 AATATAT
*
206959 ATATGTAT
1 A-ATATAT
206967 ACCATAT-T
1 A--ATATAT
206975 ACACTATAT
1 A-A-TATAT
*
206984 AATATAA
1 AATATAT
206991 AATATAT
1 AATATAT
206998 AATATAT
1 AATATAT
207005 AATATAT
1 AATATAT
207012 AA-ATAT
1 AATATAT
*
207018 ACTATAT
1 AATATAT
*
207025 CATATAT
1 AATATAT
*
207032 AATGTAT
1 AATATAT
207039 AAATATAT
1 -AATATAT
207047 AATGATAT
1 AAT-ATAT
207055 AATATAT
1 AATATAT
207062 -ATATAT
1 AATATAT
207068 -ATATAT
1 AATATAT
*
207074 ACTATAT
1 AATATAT
207081 AATATA-
1 AATATAT
207087 AGTATACTAT
1 A--ATA-TAT
207097 AATATAT
1 AATATAT
207104 AGAATATAT
1 --AATATAT
*
207113 AAATATAC
1 -AATATAT
207121 AATATAT
1 AATATAT
207128 AA-ATAT
1 AATATAT
207134 ATATATAT
1 A-ATATAT
207142 ACATTATAT
1 A-A-TATAT
207151 AATATA-
1 AATATAT
207157 AATATACT
1 AATATA-T
207165 ATATAATAT
1 A-AT-ATAT
*
207174 AATATAAA
1 AATAT-AT
207182 AATATAT
1 AATATAT
207189 AATAATAT
1 AAT-ATAT
207197 AATATAT
1 AATATAT
*
207204 TATATA
1 AATATA
207210 AAAAGGGTCG
Statistics
Matches: 235, Mismatches: 26, Indels: 50
0.76 0.08 0.16
Matches are distributed among these distances:
6 34 0.14
7 108 0.46
8 65 0.28
9 24 0.10
10 4 0.02
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (7 bp):
AATATAT
Found at i:206967 original size:6 final size:6
Alignment explanation
Indices: 206918--207209 Score: 159
Period size: 5 Copynumber: 51.5 Consensus size: 6
206908 AAAATGATAA
* * *
206918 ATATAT ATGTAT A-ATA- AAATA- ATATAT A-ATAA ATA-AT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* * * *
206961 ATGTAT ACCATAT -TACACT ATATA- ATATA- AAATAT ATA-AT ATATA-
1 ATATAT A-TATAT ATATA-T ATATAT ATATAT ATATAT ATATAT ATATAT
* * *
207006 ATATAT AAATAT ACTATAT CATATAT A-ATGT ATAAAT ATATA- ATGATAT
1 ATATAT ATATAT A-TATAT -ATATAT ATATAT ATATAT ATATAT AT-ATAT
207055 A-ATAT ATATAT ATATAT ATACTAT ATA-AT ATA-AGT ATACTAT A-ATAT
1 ATATAT ATATAT ATATAT ATA-TAT ATATAT ATATA-T ATA-TAT ATATAT
* * * * *
207102 ATAGA- ATATAT AAATAT ACA-AT ATATAA ATATAT ATATAT ACAT-T
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* * *
207147 ATATA- ATATAA ATATACT ATATA- ATATA- ATATAA AAATAT ATA-AT
1 ATATAT ATATAT ATATA-T ATATAT ATATAT ATATAT ATATAT ATATAT
207192 A-ATAT A-ATAT AT-TAT ATA
1 ATATAT ATATAT ATATAT ATA
207210 AAAAGGGTCG
Statistics
Matches: 224, Mismatches: 32, Indels: 60
0.71 0.10 0.19
Matches are distributed among these distances:
4 2 0.01
5 102 0.46
6 89 0.40
7 29 0.13
8 2 0.01
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (6 bp):
ATATAT
Found at i:207005 original size:23 final size:23
Alignment explanation
Indices: 206927--207202 Score: 189
Period size: 23 Copynumber: 11.8 Consensus size: 23
206917 AATATATATG
* *
206927 TATAATA-AAATAATATATAATA
1 TATAATATATATAATATAAAATA
* * **
206949 AATAATATATATATGTATACCATA
1 TATAATATATATA-ATATAAAATA
*
206973 T-TACA-CTATATAATATAAAATA
1 TATA-ATATATATAATATAAAATA
206995 TAT-A-ATATATAATATATAAATA
1 TATAATATATATAATATA-AAATA
*
207017 TACTATATCATATATAATGTATAAATA
1 TA-TA-AT-ATATATAATATA-AAATA
* *
207044 TATAAT-GATATAATATATATATA
1 TATAATATATATAATATA-AAATA
*
207067 TATATATACTATATAATATAAGTATA
1 TATA-ATA-TATATAATATAA-AATA
*
207093 CTATAATATATAGAATATATAAATA
1 -TATAATATATATAATATA-AAATA
* *
207118 TACAATATATA-AATAT-ATATA
1 TATAATATATATAATATAAAATA
207139 TATACAT-TATATAATAT-AAATA
1 TATA-ATATATATAATATAAAATA
207161 TACT-ATATAATATAATATAAAAATA
1 TA-TAATAT-ATATAATAT-AAAATA
207186 TATAATA-ATATAATATA
1 TATAATATATATAATATA
207203 TTATATAAAA
Statistics
Matches: 208, Mismatches: 22, Indels: 48
0.75 0.08 0.17
Matches are distributed among these distances:
21 25 0.12
22 36 0.17
23 56 0.27
24 21 0.10
25 27 0.13
26 20 0.10
27 23 0.11
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (23 bp):
TATAATATATATAATATAAAATA
Found at i:209639 original size:16 final size:16
Alignment explanation
Indices: 209618--209652 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
209608 ATTATTATAA
209618 AATTTAAAATTAAATT
1 AATTTAAAATTAAATT
209634 AATTTAAAATTAAATT
1 AATTTAAAATTAAATT
209650 AAT
1 AAT
209653 AATGAGCGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATTTAAAATTAAATT
Found at i:218399 original size:28 final size:29
Alignment explanation
Indices: 218345--218399 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
218335 GGGGACGAGT
*
218345 ACAAAAATAAATGCGTTTTAGATGAAACG
1 ACAAAAATAAATGCGTTTGAGATGAAACG
218374 ACAAAAATAAATGCGTTTGAG-TGAAA
1 ACAAAAATAAATGCGTTTGAGATGAAA
218400 GAGTTATACG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.49, C:0.09, G:0.18, T:0.24
Consensus pattern (29 bp):
ACAAAAATAAATGCGTTTGAGATGAAACG
Found at i:219894 original size:2 final size:2
Alignment explanation
Indices: 219889--219944 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
219879 ATATATGAGA
219889 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
219931 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
219945 GGGCAACTAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:220889 original size:15 final size:16
Alignment explanation
Indices: 220869--220905 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
220859 TAATTTAATA
220869 AAAATATAA-AAATTT
1 AAAATATAAGAAATTT
220884 AAAATATAAGTAAATTT
1 AAAATATAAG-AAATTT
220901 AAAAT
1 AAAAT
220906 TTGTAAGAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 9 0.45
17 11 0.55
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AAAATATAAGAAATTT
Found at i:222719 original size:107 final size:104
Alignment explanation
Indices: 222606--222816 Score: 386
Period size: 104 Copynumber: 2.0 Consensus size: 104
222596 GATTTACCTC
222606 AAATATCAATCGATGAGCTTGTGGGTTCACTTCAAGCCCATGAGTAGAGAAGATAAAAAAAATGA
1 AAATATCAATCGATGAGCTTGTGGGTTCACTTCAAGCCCATGAGT--AGAAGAT-AAAAAAATGA
222671 AAATACTGAAAATTTAGAGCAAGCCTTGCAAAGAAAAATGAA
63 AAATACTGAAAATTTAGAGCAAGCCTTGCAAAGAAAAATGAA
222713 AAATATCAATCGATGAGCTTGTGGGTTCACTTCAAGCCCATGAGTAGAAGATAAAAAAATGAAAA
1 AAATATCAATCGATGAGCTTGTGGGTTCACTTCAAGCCCATGAGTAGAAGATAAAAAAATGAAAA
*
222778 TATTGAAAATTTAGAGCAAGCCTTGCAAAGAAAAATGAA
66 TACTGAAAATTTAGAGCAAGCCTTGCAAAGAAAAATGAA
222817 CATCCACGAA
Statistics
Matches: 103, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
104 51 0.50
105 7 0.07
107 45 0.44
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.22
Consensus pattern (104 bp):
AAATATCAATCGATGAGCTTGTGGGTTCACTTCAAGCCCATGAGTAGAAGATAAAAAAATGAAAA
TACTGAAAATTTAGAGCAAGCCTTGCAAAGAAAAATGAA
Found at i:223683 original size:24 final size:24
Alignment explanation
Indices: 223630--223684 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
223620 CACCACAACT
* *
223630 CATATAAAATGCACCAAAGTGCCG
1 CATAGAAAATGCACCAAAGTGCCA
* * *
223654 CGTAGAAAATGCATCGAAGTGCCA
1 CATAGAAAATGCACCAAAGTGCCA
223678 CATAGAA
1 CATAGAA
223685 TGTCCCGAAG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.16
Consensus pattern (24 bp):
CATAGAAAATGCACCAAAGTGCCA
Found at i:223748 original size:21 final size:21
Alignment explanation
Indices: 223718--223794 Score: 102
Period size: 21 Copynumber: 3.6 Consensus size: 21
223708 TATCTCGTAA
223718 GACCACATATATGTTCCAAAG
1 GACCACATATATGTTCCAAAG
*
223739 GACCAAATATATG-TCCAAAAAG
1 GACCACATATATGTTCC--AAAG
*
223761 GACCGCATATATGTTCCAAAG
1 GACCACATATATGTTCCAAAG
*
223782 GATCACATATATG
1 GACCACATATATG
223795 CCCCGAAGGA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
20 3 0.06
21 27 0.56
22 15 0.31
23 3 0.06
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (21 bp):
GACCACATATATGTTCCAAAG
Found at i:232150 original size:4 final size:4
Alignment explanation
Indices: 232141--234820 Score: 2895
Period size: 4 Copynumber: 669.0 Consensus size: 4
232131 TATATAACAT
* * *
232141 TACA TACA TACA TACA TACA TACA TGCA TACA TGCA TACA TGCA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * * *
232189 TGCA TACA TGCA TACA TGCA TACA TGCA TACA TGCA TACA TGCA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * * *
232237 TGCA TACA TGCA TACA TGCA TACA TGCA TGCACA TACA TGCA TGCA TACA
1 TACA TACA TACA TACA TACA TACA TACA T--ACA TACA TACA TACA TACA
* * * * * * *
232287 TGCA TGCA TGCA TGCACA TACA TGCA TGCA TGCA TGCACA TACA TGCA
1 TACA TACA TACA T--ACA TACA TACA TACA TACA T--ACA TACA TACA
* * * * * * *
232335 TGCA TGCA TGCACA TACA TGCA TGCA TGCA TGCACA TACA TGCA TGCA
1 TACA TACA T--ACA TACA TACA TACA TACA T--ACA TACA TACA TACA
* * * *
232383 TGCA TGCACA TACA TACA TACA TGCA TGCA TGCA TGCACA TACA TACA
1 TACA T--ACA TACA TACA TACA TACA TACA TACA T--ACA TACA TACA
232431 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
232479 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
232527 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
232575 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
232623 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
232671 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA T--A
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * *
232717 TACA TACA TACA TACA TACA TATA CACA TACA TACA TACA TATA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
232765 TACA TAC- -ACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
232811 TACA TACA TACA TACA TACA TAGA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
232859 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* *
232907 TACA TACA TAGA TACA TACA TAGA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
232955 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * *
233003 TGCA TACA TGCA TACA TACA TACA TGCA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* ** ** ** ** ** ** ** * **
233051 TACA TACA TATGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGCA TGTA
1 TACA TACA TA--CA TACA TACA TACA TACA TACA TACA TACA TACA TACA
** ** * ** * ** ** ** ** ** ** **
233101 TGTA TGTA TGCA TGTA TGCA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
** ** ** ** ** ** ** ** ** ** *
233149 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T-C- TATG TATG TATA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
** ** * ** * ** ** ** ** ** ** **
233195 TGTA TGTA TGCA TGTA TGCA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
** ** ** ** ** ** ** ** ** ** **
233243 TGTA TGTA TATG TATG TATG TATG TATG TATG TATC- TATG TATG TATG
1 TACA TACA TACA TACA TACA TACA TACA TACA TA-CA TACA TACA TACA
** ** ** ** ** *
233291 TATG TATG TATG TATG TATGT TACA TACA TAGA TACA TACA TACA TACA
1 TACA TACA TACA TACA TA-CA TACA TACA TACA TACA TACA TACA TACA
*
233340 TACA TACA TACA TACA TACAA CACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TAC-A TACA TACA TACA TACA TACA TACA TACA
*
233389 TGCA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC-
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
233436 -ACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * *
233483 TATA TACA TACA TACA TACA TATA TACA TACA TACA TACA TGCA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
233531 TGCA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
233579 T--A TACA TACA TACA TACA TAC- -ACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
233623 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
233671 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
233719 TACA TACA TACA TACA TACA TACA TACA TACA TACA TATA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
233767 TACA T--A TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
233813 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC-
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
233860 -ACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
233907 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* ** ** ** ** **
233955 TACA TATA TACA TACA TACA TACA TATGCA TGTA TGTA TGTA TGTA T-GT
1 TACA TACA TACA TACA TACA TACA TA--CA TACA TACA TACA TACA TACA
*
234004 TACA TACA TAGA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * *
234052 TACA TACA TGCA TACA TGCA TACA TACA TATA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
234100 TACA TACA TACA TACA TACA TACA TACA TATA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * *
234148 TACA TATA TACA TACA TACA TACA TGCA TACA TGCA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
234196 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
234244 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
234292 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
234340 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
234388 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * *
234436 TACA TACA TACA TACA TACA TACA AACTC TTC- TGGCA TGCA TACA TACA
1 TACA TACA TACA TACA TACA TACA TAC-A TACA T-ACA TACA TACA TACA
234485 TACA TACA TACA TACA TACA TACA TACA T--A TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * *
234531 TACA TACA TGCA TACA TACG TACA TGCA TACA TACG TACA TGCA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * *
234579 TACG TACA TACG TACA TACG TACA TACG TACA TACG TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * * * *
234627 TACA TACA AACTC TTC- TGGCA TACA TACA TACA TACA TACA AACTC TTC-
1 TACA TACA TAC-A TACA T-ACA TACA TACA TACA TACA TACA TAC-A TACA
* * * * * * *
234676 TGGCA TGCA TACA TACA TACA TACA TACA TGCA TGCA TGCA TGCA TGCA
1 T-ACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* ** * * ** * * *
234725 TGCA TACA TATG TACA TACG TACA TACG TACA TATG TATA TACG TATA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * * *
234773 TGCG TACA TACG TACA TACG TACA TACG TACA TACG TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
234821 AACTCTTCTG
Statistics
Matches: 2436, Mismatches: 190, Indels: 100
0.89 0.07 0.04
Matches are distributed among these distances:
2 17 0.01
3 4 0.00
4 2378 0.98
5 11 0.00
6 26 0.01
ACGTcount: A:0.44, C:0.22, G:0.06, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:234657 original size:33 final size:33
Alignment explanation
Indices: 234615--234700 Score: 163
Period size: 33 Copynumber: 2.6 Consensus size: 33
234605 CGTACATACG
234615 TACATACATACATACATACAAACTCTTCTGGCA
1 TACATACATACATACATACAAACTCTTCTGGCA
234648 TACATACATACATACATACAAACTCTTCTGGCA
1 TACATACATACATACATACAAACTCTTCTGGCA
*
234681 TGCATACATACATACATACA
1 TACATACATACATACATACA
234701 TACATGCATG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.41, C:0.27, G:0.06, T:0.27
Consensus pattern (33 bp):
TACATACATACATACATACAAACTCTTCTGGCA
Found at i:235257 original size:170 final size:168
Alignment explanation
Indices: 234896--235284 Score: 521
Period size: 169 Copynumber: 2.3 Consensus size: 168
234886 ATGATAAGAA
* * * * * * *
234896 AATCTCTGCCATTCCATAGTGTCTAATCTCATCAAACATAATAGGTCTTGACGTGAATAGTTTCT
1 AATCTCTACCATACCATAGTGTCTCATCCCATCAAACATAATAGGTGTTGACGTAAATAGTTCCT
* * * *
234961 TGATGGGGAACATCATTTAGGGTTATTATTAATTGAAAAATACAGAGATCTCTGACGAAAAAGGA
66 TGACGAGAAACATCATTTAGGGTTATTATTAACTGAAAAATACAGAGATCTCTGACGAAAAAGGA
*
235026 AGGATCATCCCACAAGAAATGCTTTCACCTTTTTTAGAT
131 AGGATCA-CCCACAAGAAATGCTTTCACCTTTGTTAGAT
*
235065 AATCTCTACCATACCATAGTGTCTCGTCCCATCAAACATAATAGGTGTTGACGTAAATAGTTCCT
1 AATCTCTACCATACCATAGTGTCTCATCCCATCAAACATAATAGGTGTTGACGTAAATAGTTCCT
* * *
235130 TGACGAGAAACATC-TATTAGGGTTATTATTAACTGAAAAATGCAGAGAATCTTTGACGAAAAGG
66 TGACGAGAAACATCAT-TTAGGGTTATTATTAACTGAAAAATACAGAG-ATCTCTGACGAAAAAG
* *
235194 GAAGGTGTGC-CCCACAAGAAGTGCTTTCACCTTTGTTAGAT
129 GAAGG-AT-CACCCACAAGAAATGCTTTCACCTTTGTTAGAT
* * * *
235235 AATCTCTACCATGCCATAGTGTCTCATCCTATAAAAAATAATAGGTGTTG
1 AATCTCTACCATACCATAGTGTCTCATCCCATCAAACATAATAGGTGTTG
235285 TTATGAATGG
Statistics
Matches: 193, Mismatches: 23, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
168 1 0.01
169 97 0.50
170 93 0.48
171 1 0.01
172 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (168 bp):
AATCTCTACCATACCATAGTGTCTCATCCCATCAAACATAATAGGTGTTGACGTAAATAGTTCCT
TGACGAGAAACATCATTTAGGGTTATTATTAACTGAAAAATACAGAGATCTCTGACGAAAAAGGA
AGGATCACCCACAAGAAATGCTTTCACCTTTGTTAGAT
Found at i:235370 original size:94 final size:94
Alignment explanation
Indices: 235203--235393 Score: 265
Period size: 94 Copynumber: 2.0 Consensus size: 94
235193 GGAAGGTGTG
** * *
235203 CCCCACAAGAAGTGCTTTCACCTTTGTTAGATAATCTCTACCATGCCATAGTGTCTCATCCTATA
1 CCCCACAAGAAGCACTTTCACCTTTGTCAGATAATCTCTACCATGCCATAGTGTCTCATCCCATA
* *
235268 AAAAATAATAGGTGTTGTTATGAATGGTT
66 AAAAATAATAGGTGTTGATATGAATAGTT
* * ** *
235297 CCCCACAAGAAGCACTTTCACCTTTGTCAGATAATCTTTGCCATGTTATAGTGTCTCATCCCATC
1 CCCCACAAGAAGCACTTTCACCTTTGTCAGATAATCTCTACCATGCCATAGTGTCTCATCCCATA
* *
235362 AAACATAATAGGTGTTGATGTGAATAGTT
66 AAAAATAATAGGTGTTGATATGAATAGTT
235391 CCC
1 CCC
235394 TGATGGGGAA
Statistics
Matches: 84, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
94 84 1.00
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.33
Consensus pattern (94 bp):
CCCCACAAGAAGCACTTTCACCTTTGTCAGATAATCTCTACCATGCCATAGTGTCTCATCCCATA
AAAAATAATAGGTGTTGATATGAATAGTT
Found at i:235504 original size:264 final size:264
Alignment explanation
Indices: 235047--235563 Score: 683
Period size: 264 Copynumber: 2.0 Consensus size: 264
235037 ACAAGAAATG
* * *
235047 CTTTCACCTTTTTTAGATAATCTCTACCATACCATAGTGTCTCGTCCCATCAAACATAATAGGTG
1 CTTTCACCTTTGTCAGATAATCTCTACCATACCATAGTGTCTCATCCCATCAAACATAATAGGTG
* * * * * *
235112 TTGACGTAAATAGTTCCTTGACGAGAAACATCTATTAGGGTTATTATTAACTGAAAAATGCAGAG
66 TTGACGTAAATAGTTCCCTGACGAGAAACATCAATTAAGGCTATTATTAACTAAAAAATGCAGAA
* * ** * * * *
235177 AATCTTTGACGAAAAGGGAAGGTGTGCCCCACAAGAAGTGCTTTCACCTTTGTTAGATAATCTCT
131 AATCTCTAACGAAAAGGGAAGACGCGCCCCACAAGAAGCGATTTCACCTTTGTCAGATAATCTCT
* ** *
235242 ACCATGCCATAGTGTCTCATCCTATAAAAAATAATAGGTGTTGTTATGAATGGTTCCCCACAAGA
196 ACCATGCCATAGTGTCTCATCCCATAAAAAATAATAGGTGTTGACATGAATAGTTCCCCACAAGA
235307 AGCA
261 AGCA
* * ***
235311 CTTTCACCTTTGTCAGATAATCTTTGCCATGTTATAGTGTCTCATCCCATCAAACATAATAGGTG
1 CTTTCACCTTTGTCAGATAATCTCTACCATACCATAGTGTCTCATCCCATCAAACATAATAGGTG
* * * * * *
235376 TTGATGTGAATAGTTCCCTGATGGGGAACATCAATTAAGGCTATTATTAACTAAAAAATGTAGAA
66 TTGACGTAAATAGTTCCCTGACGAGAAACATCAATTAAGGCTATTATTAACTAAAAAATGCAGAA
* *
235441 AATCTCTAACGAAAAGGGAAGACGCGTCTCACAAGAAGCGATTTCACCTTTGTCAGATAATCTCT
131 AATCTCTAACGAAAAGGGAAGACGCGCCCCACAAGAAGCGATTTCACCTTTGTCAGATAATCTCT
* ** * *
235506 ACCTTGTTATAGTGTCTCATCCCATCAAACATAATAGGTGTTGACATGAATAGTTCCC
196 ACCATGCCATAGTGTCTCATCCCATAAAAAATAATAGGTGTTGACATGAATAGTTCCC
235564 TGAAGGGGAA
Statistics
Matches: 214, Mismatches: 39, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
264 214 1.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (264 bp):
CTTTCACCTTTGTCAGATAATCTCTACCATACCATAGTGTCTCATCCCATCAAACATAATAGGTG
TTGACGTAAATAGTTCCCTGACGAGAAACATCAATTAAGGCTATTATTAACTAAAAAATGCAGAA
AATCTCTAACGAAAAGGGAAGACGCGCCCCACAAGAAGCGATTTCACCTTTGTCAGATAATCTCT
ACCATGCCATAGTGTCTCATCCCATAAAAAATAATAGGTGTTGACATGAATAGTTCCCCACAAGA
AGCA
Found at i:235718 original size:434 final size:433
Alignment explanation
Indices: 234911--235732 Score: 1072
Period size: 434 Copynumber: 1.9 Consensus size: 433
234901 CTGCCATTCC
* * *
234911 ATAGTGTCTAATCTCATCAAACATAATAGGTCTTGACGTGAATAGTTTCTTGATGGGGAACATCA
1 ATAGTGTCTAATCCCATCAAACATAATAGGTCTTGACGTGAATAGTTCCCTGATGGGGAACATCA
* * * * * * * *
234976 TTTAGGGTTATTATTAATTGAAAAATACAGAGATCTCTGACGAAAAAGGAAGGATCATCCCACAA
66 ATTAAGGCTATTATTAACTAAAAAATACAGAAATCTCTAACGAAAAAGGAAGGAGCATCCCACAA
* * * * *
235041 GAAATGCTTTCACCTTTTTTAGATAATCTCTACCATACCATAGTGTCTCGTCCCATCAAACATAA
131 GAAACGATTTCACCTTTGTCAGATAATCTCTACCATACCATAGTGTCTCATCCCATCAAACATAA
* * * *
235106 TAGGTGTTGACGTAAATAGTTCCTTGACGAGAAACATCTATTAGGGTTATTATTAACTGAAAAAT
196 TAGGTGTTGACATAAATAGTTCCCTGAAGAGAAACATCTATTAGGGCTATTATTAACTGAAAAAT
* * *** ** * *
235171 GCAGAGAATCTTTGACGAAAAGGGAAGGTGTGCCCCACAAGAAGTGCTTTCACCTTTGTTAGATA
261 ACAGAGAATCTCTGACGAAAAGGGAAGGAACGCCCCACAAGAAGCACTTTCACCCTTGTCAGATA
* * * *
235236 ATCTCTACCATGCCATAGTGTCTCATCCTATAAAAAATAATAGGTGTTGTTATGAATGGTTCCCC
326 ATCTCTACCATGCCATAGTGTCTCATCCCATAAAAAATAAAAGGTGTTGATATGAATAGTTCCCC
235301 ACAAGAAGCACTTTCACCTTTGTCAGATAATCTTTGCCATGTT
391 ACAAGAAGCACTTTCACCTTTGTCAGATAATCTTTGCCATGTT
* * *
235344 ATAGTGTCTCATCCCATCAAACATAATAGGTGTTGATGTGAATAGTTCCCTGATGGGGAACATCA
1 ATAGTGTCTAATCCCATCAAACATAATAGGTCTTGACGTGAATAGTTCCCTGATGGGGAACATCA
** * * *
235409 ATTAAGGCTATTATTAACTAAAAAATGTAGAAAATCTCTAACGAAAAGGGAA-GACGCGTCTCAC
66 ATTAAGGCTATTATTAACTAAAAAATACAG-AAATCTCTAACGAAAAAGGAAGGA-GCATCCCAC
* * ***
235473 AAGAAGCGATTTCACCTTTGTCAGATAATCTCTACCTTGTTATAGTGTCTCATCCCATCAAACAT
129 AAGAAACGATTTCACCTTTGTCAGATAATCTCTACCATACCATAGTGTCTCATCCCATCAAACAT
* * *
235538 AATAGGTGTTGACATGAATAGTTCCCTGAAGGGGAACAT-TAATTAGGGCTATTATTAACTGAAA
194 AATAGGTGTTGACATAAATAGTTCCCTGAAGAGAAACATCT-ATTAGGGCTATTATTAACTGAAA
* * *
235602 AATATAGAGAATCTCTGATGAAAAGGGAAGGAACGTCCCACAAGAAGCACTTTCACCCTTGTCAG
258 AATACAGAGAATCTCTGACGAAAAGGGAAGGAACGCCCCACAAGAAGCACTTTCACCCTTGTCAG
* *** * * *
235667 ATAATCTCTGCCATGTTGTAGTGTCTCATCCCATCAAACATAAAAGGTGTTGATGTGAATAGTTC
323 ATAATCTCTACCATGCCATAGTGTCTCATCCCATAAAAAATAAAAGGTGTTGATATGAATAGTTC
235732 C
388 C
235733 ATGACGGGGA
Statistics
Matches: 327, Mismatches: 59, Indels: 5
0.84 0.15 0.01
Matches are distributed among these distances:
433 85 0.26
434 242 0.74
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (433 bp):
ATAGTGTCTAATCCCATCAAACATAATAGGTCTTGACGTGAATAGTTCCCTGATGGGGAACATCA
ATTAAGGCTATTATTAACTAAAAAATACAGAAATCTCTAACGAAAAAGGAAGGAGCATCCCACAA
GAAACGATTTCACCTTTGTCAGATAATCTCTACCATACCATAGTGTCTCATCCCATCAAACATAA
TAGGTGTTGACATAAATAGTTCCCTGAAGAGAAACATCTATTAGGGCTATTATTAACTGAAAAAT
ACAGAGAATCTCTGACGAAAAGGGAAGGAACGCCCCACAAGAAGCACTTTCACCCTTGTCAGATA
ATCTCTACCATGCCATAGTGTCTCATCCCATAAAAAATAAAAGGTGTTGATATGAATAGTTCCCC
ACAAGAAGCACTTTCACCTTTGTCAGATAATCTTTGCCATGTT
Found at i:235860 original size:169 final size:168
Alignment explanation
Indices: 235298--236067 Score: 922
Period size: 170 Copynumber: 4.6 Consensus size: 168
235288 TGAATGGTTC
* *
235298 CCCACAAGAAGCACTTTCA-CCTTTGTCAGATAATCTTTGCCATGTTATAGTGTCTCATCCCATC
1 CCCACAAGAAGCGCTTTCACCCTTT-TCAGATAATCTCTGCCATGTTATAGTGTCTCATCCCATC
* * * *
235362 AAACATAATAGGTGTTGATGTGAATAGTTCCCTGATGGGGAACATCAATTAAGGCTATTATTAAC
65 AAACATAATAGGTGTTGACGTGAATAGTTCCATGACGGGGAACATCAATTAGGGCTATTATTAAC
* * * * *
235427 TAAAAAATGTAGAAAATCTCTAACGAAAAGGGAAGACGCGT
130 TGAAAAATATAGAGAATCTCTGACGAAAAGGGAAG--GCAT
* * * *
235468 CTCACAAGAAGCGATTTCA-CCTTTGTCAGATAATCTCTACCTTGTTATAGTGTCTCATCCCATC
1 CCCACAAGAAGCGCTTTCACCCTTT-TCAGATAATCTCTGCCATGTTATAGTGTCTCATCCCATC
* * * *
235532 AAACATAATAGGTGTTGACATGAATAGTTCCCTGAAGGGGAACATTAATTAGGGCTATTATTAAC
65 AAACATAATAGGTGTTGACGTGAATAGTTCCATGACGGGGAACATCAATTAGGGCTATTATTAAC
* *
235597 TGAAAAATATAGAGAATCTCTGATGAAAAGGGAAGGAACGT
130 TGAAAAATATAGAGAATCTCTGACGAAAAGGGAAGG--CAT
* * *
235638 CCCACAAGAAGCACTTTCACCCTTGTCAGATAATCTCTGCCATGTTGTAGTGTCTCATCCCATCA
1 CCCACAAGAAGCGCTTTCACCCTTTTCAGATAATCTCTGCCATGTTATAGTGTCTCATCCCATCA
* *
235703 AACATAAAAGGTGTTGATGTGAATAGTTCCATGACGGGGAACATCAATTAGGGCTATTATTAACT
66 AACATAATAGGTGTTGACGTGAATAGTTCCATGACGGGGAACATCAATTAGGGCTATTATTAACT
*
235768 -AAAAATACAGAGAATCTCTGACGAAAAGGGAACGTGCAT
131 GAAAAATATAGAGAATCTCTGACGAAAAGGGAA-G-GCAT
* * * ** *
235807 CCCACAAGAAGTGTTTTCACCCTTTTCAGATAATCTATGCCATGCCATAGTGTCTCGTCCCATCA
1 CCCACAAGAAGCGCTTTCACCCTTTTCAGATAATCTCTGCCATGTTATAGTGTCTCATCCCATCA
* * * * *
235872 AACATAATAGGTGTTGACGTGAATATTTCCATGACAGAGAACATCAATTAGGCCTATT-TTAATT
66 AACATAATAGGTGTTGACGTGAATAGTTCCATGACGGGGAACATCAATTAGGGCTATTATTAACT
* *
235936 GAAAAATATAGAGAATCTCTGA-AAAAAAGGAAGGCATGT
131 GAAAAATATAGAGAATCTCTGACGAAAAGGGAAGGCA--T
* * ** * * * * * *
235975 CCCATAAGAAGTGCTTAAACCTTTTTCATATAATCTCTACCATGTCATAGTGTCTCGTCTCATCA
1 CCCACAAGAAGCGCTTTCACCCTTTTCAGATAATCTCTGCCATGTTATAGTGTCTCATCCCATCA
* * *
236040 AACATATTA-TTGGTTGACATGAATAGTT
66 AACATAATAGGT-GTTGACGTGAATAGTT
236068 TAGATGAATA
Statistics
Matches: 526, Mismatches: 65, Indels: 20
0.86 0.11 0.03
Matches are distributed among these distances:
166 3 0.01
167 2 0.00
168 92 0.17
169 160 0.30
170 264 0.50
171 5 0.01
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (168 bp):
CCCACAAGAAGCGCTTTCACCCTTTTCAGATAATCTCTGCCATGTTATAGTGTCTCATCCCATCA
AACATAATAGGTGTTGACGTGAATAGTTCCATGACGGGGAACATCAATTAGGGCTATTATTAACT
GAAAAATATAGAGAATCTCTGACGAAAAGGGAAGGCAT
Found at i:236162 original size:16 final size:17
Alignment explanation
Indices: 236140--236201 Score: 56
Period size: 16 Copynumber: 3.7 Consensus size: 17
236130 CAAATTTCAA
236140 AACACTCAAATTCTCTC
1 AACACTCAAATTCTCTC
**
236157 AA-ACTCTCATTCTCTC
1 AACACTCAAATTCTCTC
* *
236173 AATCTCTCAAATTCTC-A
1 AA-CACTCAAATTCTCTC
*
236190 AACTCTCAAATT
1 AACACTCAAATT
236202 GATATCTCTA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
16 24 0.65
17 4 0.11
18 9 0.24
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (17 bp):
AACACTCAAATTCTCTC
Found at i:236165 original size:8 final size:8
Alignment explanation
Indices: 236152--236199 Score: 60
Period size: 8 Copynumber: 6.0 Consensus size: 8
236142 CACTCAAATT
236152 CTCTCAAA
1 CTCTCAAA
**
236160 CTCTCATT
1 CTCTCAAA
*
236168 CTCTCAAT
1 CTCTCAAA
236176 CTCTCAAA
1 CTCTCAAA
*
236184 TTCTCAAA
1 CTCTCAAA
236192 CTCTCAAA
1 CTCTCAAA
236200 TTGATATCTC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.33
Consensus pattern (8 bp):
CTCTCAAA
Found at i:236183 original size:24 final size:24
Alignment explanation
Indices: 236151--236198 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
236141 ACACTCAAAT
**
236151 TCTCTCAAACTCTCATTCTCTCAA
1 TCTCTCAAACTCTCAAACTCTCAA
*
236175 TCTCTCAAATTCTCAAACTCTCAA
1 TCTCTCAAACTCTCAAACTCTCAA
236199 ATTGATATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (24 bp):
TCTCTCAAACTCTCAAACTCTCAA
Found at i:237754 original size:30 final size:30
Alignment explanation
Indices: 237720--237782 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
237710 TTGTAGTATT
237720 CATTTCTACTATACAATCACAATATGGATA
1 CATTTCTACTATACAATCACAATATGGATA
237750 CATTTCTACTATACAATCACAATATGGATA
1 CATTTCTACTATACAATCACAATATGGATA
237780 CAT
1 CAT
237783 CGTCTCCTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.33
Consensus pattern (30 bp):
CATTTCTACTATACAATCACAATATGGATA
Found at i:239426 original size:27 final size:26
Alignment explanation
Indices: 239389--239456 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 26
239379 TGCATAATAT
*
239389 TATTTTATAATATTTCAATAT-ATATG
1 TATTTTCTAATATTTCAATATAAT-TG
* *
239415 TTTGTTTCTAATATTTCAATGTAATTG
1 TAT-TTTCTAATATTTCAATATAATTG
239442 TATTTTCTAATATTT
1 TATTTTCTAATATTT
239457 TTAAATGTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 14 0.39
27 20 0.56
28 2 0.06
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (26 bp):
TATTTTCTAATATTTCAATATAATTG
Found at i:239472 original size:28 final size:26
Alignment explanation
Indices: 239419--239479 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 26
239409 TATATGTTTG
*
239419 TTTCTAATATTTCAATGTAATTGTAT
1 TTTCTAATATTTAAATGTAATTGTAT
239445 TTTCTAATATTTTTAAATGT-ATGTGTAT
1 TTTCTAATA--TTTAAATGTAAT-TGTAT
239473 TTTCTAA
1 TTTCTAA
239480 AAAAAGTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 9 0.29
27 2 0.06
28 20 0.65
ACGTcount: A:0.30, C:0.07, G:0.08, T:0.56
Consensus pattern (26 bp):
TTTCTAATATTTAAATGTAATTGTAT
Found at i:239589 original size:24 final size:24
Alignment explanation
Indices: 239530--239639 Score: 132
Period size: 25 Copynumber: 4.5 Consensus size: 24
239520 TTCATTTTAA
**
239530 TTTAACCT-AAAACCTTAAACCAC
1 TTTAACCTAAAAACCCAAAACCAC
*
239553 TTTAACTTAAAAACCCCAAAACCAC
1 TTTAACCTAAAAA-CCCAAAACCAC
*
239578 TTTAACCTAAAAACCCAAGACCAC
1 TTTAACCTAAAAACCCAAAACCAC
* *
239602 TTTCACCTAAAAAACTCAAAACCAC
1 TTTAACCT-AAAAACCCAAAACCAC
*
239627 TTTGACCTAAAAA
1 TTTAACCTAAAAA
239640 AACCTTAAAC
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
23 7 0.09
24 26 0.35
25 42 0.56
ACGTcount: A:0.46, C:0.30, G:0.02, T:0.22
Consensus pattern (24 bp):
TTTAACCTAAAAACCCAAAACCAC
Found at i:239602 original size:49 final size:49
Alignment explanation
Indices: 239530--239639 Score: 143
Period size: 49 Copynumber: 2.3 Consensus size: 49
239520 TTCATTTTAA
* * *
239530 TTTAACCT-AAAACCTTAAACCACTTTAACTTAAAAACCCCAAAACCAC
1 TTTAACCTAAAAACCTCAAACCACTTTAACCTAAAAAACCCAAAACCAC
* *
239578 TTTAACCTAAAAACC-CAAGACCACTTTCACCTAAAAAACTCAAAACCAC
1 TTTAACCTAAAAACCTCAA-ACCACTTTAACCTAAAAAACCCAAAACCAC
*
239627 TTTGACCTAAAAA
1 TTTAACCTAAAAA
239640 AACCTTAAAC
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
48 10 0.19
49 44 0.81
ACGTcount: A:0.46, C:0.30, G:0.02, T:0.22
Consensus pattern (49 bp):
TTTAACCTAAAAACCTCAAACCACTTTAACCTAAAAAACCCAAAACCAC
Found at i:240041 original size:34 final size:33
Alignment explanation
Indices: 239978--240048 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
239968 CATTTATAAC
* * *
239978 TCCCTAGTTTTTCAATGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACAAGGGATAAACTAGAACCTT
*
240011 TCCCTAGCTTTTACAAGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTACAAGGGATAAACTAGAACCTT
240045 TCCC
1 TCCC
240049 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 7 0.21
34 26 0.79
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (33 bp):
TCCCTAGTTTTACAAGGGATAAACTAGAACCTT
Found at i:240515 original size:63 final size:64
Alignment explanation
Indices: 240411--240532 Score: 210
Period size: 63 Copynumber: 1.9 Consensus size: 64
240401 CGTTGCATCC
* *
240411 AGGGGGTATCGGTACCCCTGGGGGGTATCGATACCCTCTTTGCATTCTGGAATTTTTGCCTTCA
1 AGGGGGTATAGATACCCCTGGGGGGTATCGATACCCTCTTTGCATTCTGGAATTTTTGCCTTCA
*
240475 AGGGGGTATAGATACCCCT-GGGGGTATCGGTACCCTCTTTGCATTCTGGAATTTTTGC
1 AGGGGGTATAGATACCCCTGGGGGGTATCGATACCCTCTTTGCATTCTGGAATTTTTGC
240533 TCAAATCCGA
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
63 38 0.69
64 17 0.31
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (64 bp):
AGGGGGTATAGATACCCCTGGGGGGTATCGATACCCTCTTTGCATTCTGGAATTTTTGCCTTCA
Found at i:241126 original size:19 final size:20
Alignment explanation
Indices: 241091--241137 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
241081 CTAAATCCTT
*
241091 TTTCAAAATTTTATTTTGGC
1 TTTCAAAATTATATTTTGGC
* *
241111 TTTCAAAA-TATATTTTTGT
1 TTTCAAAATTATATTTTGGC
241130 TTTCAAAA
1 TTTCAAAA
241138 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.53
Consensus pattern (20 bp):
TTTCAAAATTATATTTTGGC
Found at i:241490 original size:3 final size:3
Alignment explanation
Indices: 241482--241506 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
241472 TTGTCACTCA
241482 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
241507 TAGAGAAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:242514 original size:64 final size:64
Alignment explanation
Indices: 242433--242556 Score: 205
Period size: 64 Copynumber: 1.9 Consensus size: 64
242423 GGTGCCTCTG
*
242433 CAGGGGGTATTGGTACCCCTGGGGGGTATCGGTACCCTCTTTGCATTCTAGAATTTTTGCCTTC
1 CAGGAGGTATTGGTACCCCTGGGGGGTATCGGTACCCTCTTTGCATTCTAGAATTTTTGCCTTC
* *
242497 CAGGAGGTA-TGGATACCCCTGGGGGGTATCGGTGCCCTCTTTGCATTCTGGAATTTTTGC
1 CAGGAGGTATTGG-TACCCCTGGGGGGTATCGGTACCCTCTTTGCATTCTAGAATTTTTGC
242557 TCAAATGAGT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 3 0.05
64 53 0.95
ACGTcount: A:0.15, C:0.23, G:0.30, T:0.33
Consensus pattern (64 bp):
CAGGAGGTATTGGTACCCCTGGGGGGTATCGGTACCCTCTTTGCATTCTAGAATTTTTGCCTTC
Found at i:244330 original size:21 final size:24
Alignment explanation
Indices: 244295--244340 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
244285 ACCTTTTGGG
244295 TTTTCACTTTGTTTCC-CTCTTTT
1 TTTTCACTTTGTTTCCTCTCTTTT
*
244318 TTTTCA-TTT-TTTCCTTTCTTTT
1 TTTTCACTTTGTTTCCTCTCTTTT
244340 T
1 T
244341 CTTCCGGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 10 0.48
23 6 0.29
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.72
Consensus pattern (24 bp):
TTTTCACTTTGTTTCCTCTCTTTT
Found at i:248762 original size:2 final size:2
Alignment explanation
Indices: 248746--248794 Score: 82
Period size: 2 Copynumber: 24.5 Consensus size: 2
248736 CCAATAAACT
248746 TA TA -A TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
248788 TA TA TA T
1 TA TA TA T
248795 TAGTTTCAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 42 0.93
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:249855 original size:15 final size:16
Alignment explanation
Indices: 249835--249864 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
249825 TTTTTATCTT
249835 TTAAAAT-TATTTTTC
1 TTAAAATGTATTTTTC
249850 TTAAAATGTATTTTT
1 TTAAAATGTATTTTT
249865 TGGTATTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (16 bp):
TTAAAATGTATTTTTC
Found at i:250710 original size:14 final size:14
Alignment explanation
Indices: 250691--250719 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
250681 AGATCCATGT
250691 AGACGACTTCCTAA
1 AGACGACTTCCTAA
250705 AGACGACTTCCTAA
1 AGACGACTTCCTAA
250719 A
1 A
250720 CATCTTCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.21
Consensus pattern (14 bp):
AGACGACTTCCTAA
Found at i:262883 original size:36 final size:36
Alignment explanation
Indices: 262836--262909 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
262826 TTTAAAAACG
262836 TGATTTGGAAATTTTGAATCCTTAAAACCAGGAGGT
1 TGATTTGGAAATTTTGAATCCTTAAAACCAGGAGGT
* *
262872 TGATTTGGAAATTTTGAATCCTTAAAATCGGGAGGT
1 TGATTTGGAAATTTTGAATCCTTAAAACCAGGAGGT
262908 TG
1 TG
262910 TACCACATAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.31, C:0.09, G:0.24, T:0.35
Consensus pattern (36 bp):
TGATTTGGAAATTTTGAATCCTTAAAACCAGGAGGT
Found at i:263641 original size:54 final size:54
Alignment explanation
Indices: 263579--264033 Score: 705
Period size: 54 Copynumber: 8.4 Consensus size: 54
263569 TTTGGTTTTT
* * * * *
263579 CACACATAGTGTCAATACGATAATTCACAAACTCAATGTGAATTACGTAGGTTG
1 CACACATAGTGTCGATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTG
263633 CACACATAGTGTCGATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTG
1 CACACATAGTGTCGATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTG
* * *
263687 CACACATAATGTCGATAGGGTAATTAACAAACTCATTATGAATTACTTAGGTTG
1 CACACATAGTGTCGATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTG
* * *
263741 CACATATAGTGCCGATACGGTAATTTACAAACTCATTATGAATTACTTAGGTTG
1 CACACATAGTGTCGATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTG
263795 CACACATAGTGTCGATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTG
1 CACACATAGTGTCGATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTG
*
263849 CACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTG
1 CACACATAGTGTCGATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTG
* * * *
263903 CACACATAGTGTTGATGCGGTAATTCACAAATTCATTATGAATTA-TGTGGGTTG
1 CACACATAGTGTCGATACGGTAATTCACAAACTCATTATGAATTACT-TAGGTTG
* * * *
263957 CATACATAGTGTCGATATGGTAATTCACTAACTCGTTATGAATTACTTAGGTTG
1 CACACATAGTGTCGATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTG
*
264011 CACACATAGTGCCGATACGGTAA
1 CACACATAGTGTCGATACGGTAA
264034 ATACAACATA
Statistics
Matches: 366, Mismatches: 33, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
53 1 0.00
54 364 0.99
55 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Consensus pattern (54 bp):
CACACATAGTGTCGATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTG
Found at i:270600 original size:54 final size:53
Alignment explanation
Indices: 270503--270983 Score: 606
Period size: 54 Copynumber: 8.9 Consensus size: 53
270493 TGAATATTAC
* * * *
270503 AACTCATTATAAATTATGT-GGATTTTCACACATAGTACCGATACGGTAATTCAGA
1 AACTCATTATGAATTAT-TAGG--TTGCACACATAGTGCCGATACGGTAATTCACA
* * **
270558 AACTCATTGTGAATTATGTAGGTTGCACACATAGTGTCGATACAATAATTCACA
1 AACTCATTATGAATTAT-TAGGTTGCACACATAGTGCCGATACGGTAATTCACA
* *
270612 AACTCATTATGAATTACTTAGGTTGCACGCATAGTGCCGATATGGTAATTCACA
1 AACTCATTATGAATTA-TTAGGTTGCACACATAGTGCCGATACGGTAATTCACA
* * **
270666 AACTCATTGTGAATTACTTAGGTTGCACACATAGTGTCGATACCATAATTCACA
1 AACTCATTATGAATTA-TTAGGTTGCACACATAGTGCCGATACGGTAATTCACA
*
270720 AACTCATTATGAATTACTTAGGTTGCACACATAGTGTCGATACGGTAATTCACA
1 AACTCATTATGAATTA-TTAGGTTGCACACATAGTGCCGATACGGTAATTCACA
270774 AACTCATTATGAATTATTTAGGTTGCACACATAGTGCCGATACGGTAATTCACA
1 AACTCATTATGAATTA-TTAGGTTGCACACATAGTGCCGATACGGTAATTCACA
* * * * *
270828 AACTCATTATGAATTCCTCAGGTTGCACACATAGTGCCGATATGGTTATTCAAA
1 AACTCATTATGAATT-ATTAGGTTGCACACATAGTGCCGATACGGTAATTCACA
* * *
270882 AACTAATTATGAATTATGT-GTGTTGCACACATAGTGCCAATACAGTAATTCACA
1 AACTCATTATGAATTAT-TAG-GTTGCACACATAGTGCCGATACGGTAATTCACA
* **
270936 AACTCATTATGAATTACTTAGGTTACACACATAGTGTAGATACGGTAA
1 AACTCATTATGAATTA-TTAGGTTGCACACATAGTGCCGATACGGTAA
270984 ATACAACATA
Statistics
Matches: 375, Mismatches: 44, Indels: 15
0.86 0.10 0.03
Matches are distributed among these distances:
53 2 0.01
54 351 0.94
55 20 0.05
56 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (53 bp):
AACTCATTATGAATTATTAGGTTGCACACATAGTGCCGATACGGTAATTCACA
Found at i:270797 original size:162 final size:162
Alignment explanation
Indices: 270529--270983 Score: 671
Period size: 162 Copynumber: 2.8 Consensus size: 162
270519 TGTGGATTTT
* * *
270529 CACACATAGTACCGATACGGTAATTCAGAAACTCATTGTGAATTATGTAGGTTGCACACATAGTG
1 CACACATAGTGCCGATACGGTAATTCAAAAACTCATTATGAATTATGTAGGTTGCACACATAGTG
* * *
270594 TCGATACAATAATTCACAAACTCATTATGAATTACTTAGGTTGCACGCATAGTGCCGATATGGTA
66 TCGATACAGTAATTCACAAACTCATTATGAATTACTTAGGTTGCACACATAGTGCCGATACGGTA
* *
270659 ATTCACAAACTCATTGTGAATTACTTAGGTTG
131 ATTCACAAACTCATTATGAATTACTCAGGTTG
* ** *
270691 CACACATAGTGTCGATACCATAATTCACAAACTCATTATGAATTACT-TAGGTTGCACACATAGT
1 CACACATAGTGCCGATACGGTAATTCAAAAACTCATTATGAATTA-TGTAGGTTGCACACATAGT
* *
270755 GTCGATACGGTAATTCACAAACTCATTATGAATTATTTAGGTTGCACACATAGTGCCGATACGGT
65 GTCGATACAGTAATTCACAAACTCATTATGAATTACTTAGGTTGCACACATAGTGCCGATACGGT
*
270820 AATTCACAAACTCATTATGAATTCCTCAGGTTG
130 AATTCACAAACTCATTATGAATTACTCAGGTTG
* * *
270853 CACACATAGTGCCGATATGGTTATTCAAAAACTAATTATGAATTATGT-GTGTTGCACACATAGT
1 CACACATAGTGCCGATACGGTAATTCAAAAACTCATTATGAATTATGTAG-GTTGCACACATAGT
* * * **
270917 GCCAATACAGTAATTCACAAACTCATTATGAATTACTTAGGTTACACACATAGTGTAGATACGGT
65 GTCGATACAGTAATTCACAAACTCATTATGAATTACTTAGGTTGCACACATAGTGCCGATACGGT
270982 AA
130 AA
270984 ATACAACATA
Statistics
Matches: 262, Mismatches: 28, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
161 2 0.01
162 259 0.99
163 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (162 bp):
CACACATAGTGCCGATACGGTAATTCAAAAACTCATTATGAATTATGTAGGTTGCACACATAGTG
TCGATACAGTAATTCACAAACTCATTATGAATTACTTAGGTTGCACACATAGTGCCGATACGGTA
ATTCACAAACTCATTATGAATTACTCAGGTTG
Found at i:276687 original size:289 final size:289
Alignment explanation
Indices: 276158--276738 Score: 761
Period size: 289 Copynumber: 2.0 Consensus size: 289
276148 GCTTTCTCTT
* * * * * *
276158 TGATCTTTTATCTTCACATATGACTTGGAATCTTGTTTTTATATTCCCTCTATTTATTCTAATCG
1 TGATCTCTTATCTTCACATATAACTTGGAATCTTATTTTTATACTCCCTCGATTAATTCTAATCG
* * * * * *
276223 TTTGGGTTGTTATGGAAGTAAATAGAGTCATTGGGAGGTAGTTTTTCGCAATAAATGTTGCCCTG
66 TTTGGGTTGTTATGGAAGTAAATAGAGTCATTGGAAGGTAGTTTCTCACAATAAATGCTACCCAG
* * * * * *
276288 ATGCTTATAGTATTGGTGCTCGGGCTTTGGGTATCAATACTCCTTGTATTAAATAAAAAAATATA
131 ATGCTTATAGTATCGGTACTCAGGCTTTGGATATCAATACTCCCTGCATTAAATAAAAAAATATA
* * * * * * *
276353 GTCGTTGGGGAAAGGTAGTATTGATACTCGTACAAGGGGTATCGATACT-ACTTTTATAAGTAAT
196 GCCATTGGGGAAAGATAGTATCGACACTCGTACAAGGGCTATCGATA-TAACTCTTATAAGTAAT
*
276417 ATTGATACTCGGACTAGTATCGGTACCAAA
260 ATCGATACTCGGACTAGTATCGGTACCAAA
*
276447 TGATCTCTTATCTTCACATATAACTTGGAATCTTATTTTTATACTCCCTCGATTAATTCTAATTG
1 TGATCTCTTATCTTCACATATAACTTGGAATCTTATTTTTATACTCCCTCGATTAATTCTAATCG
* * ** *
276512 TTTGGGTTGTTGTGGGAGTAAATAGAGTTGTTGGAAGGTAGTTTC-CTATAATAAATGCTACCCA
66 TTTGGGTTGTTATGGAAGTAAATAGAGTCATTGGAAGGTAGTTTCTC-ACAATAAATGCTACCCA
* * ** *
276576 GATGCTTGTAGTATCGGTACTTAGGCTTTGGATATTGATACTCCCTGCATTAAATACAAAAATAT
130 GATGCTTATAGTATCGGTACTCAGGCTTTGGATATCAATACTCCCTGCATTAAATAAAAAAATAT
* *
276641 AGCCATTGGGGAAAGATAGTATCGACACTGGTACAAGGGCTATCGATATAACTCTTATAAGTAGT
195 AGCCATTGGGGAAAGATAGTATCGACACTCGTACAAGGGCTATCGATATAACTCTTATAAGTAAT
* *
276706 ATCGATACTGGGACTAGTATTGGTACCAAA
260 ATCGATACTCGGACTAGTATCGGTACCAAA
276736 TGA
1 TGA
276739 GTATACTAGA
Statistics
Matches: 249, Mismatches: 41, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
288 2 0.01
289 247 0.99
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.36
Consensus pattern (289 bp):
TGATCTCTTATCTTCACATATAACTTGGAATCTTATTTTTATACTCCCTCGATTAATTCTAATCG
TTTGGGTTGTTATGGAAGTAAATAGAGTCATTGGAAGGTAGTTTCTCACAATAAATGCTACCCAG
ATGCTTATAGTATCGGTACTCAGGCTTTGGATATCAATACTCCCTGCATTAAATAAAAAAATATA
GCCATTGGGGAAAGATAGTATCGACACTCGTACAAGGGCTATCGATATAACTCTTATAAGTAATA
TCGATACTCGGACTAGTATCGGTACCAAA
Found at i:281359 original size:14 final size:15
Alignment explanation
Indices: 281311--281369 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
281301 AAATGAGATA
281311 ATCTATGTGACTATG
1 ATCTATGTGACTATG
* * *
281326 AGCTATATGAGTACAT-
1 ATCTATGTGACT--ATG
281342 ATCTATGTGA-TATG
1 ATCTATGTGACTATG
*
281356 ATCTTTGTGACTAT
1 ATCTATGTGACTAT
281370 ATGAAAATGT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
13 2 0.06
14 9 0.26
15 13 0.38
16 8 0.24
17 2 0.06
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.41
Consensus pattern (15 bp):
ATCTATGTGACTATG
Found at i:281603 original size:23 final size:22
Alignment explanation
Indices: 281559--281635 Score: 75
Period size: 23 Copynumber: 3.5 Consensus size: 22
281549 GAGTCGAGGG
* **
281559 TTCTACGCGGTCCTTCAAGACAA
1 TTCTACGTGGTCCTTCGGGAC-A
281582 TTCTACGTGGTCCTTCGGGACA
1 TTCTACGTGGTCCTTCGGGACA
* *
281604 -TCTATGTGGTCCTTTGCGGACA
1 TTCTACGTGGTCCTTCG-GGACA
*
281626 TTCTATGTGG
1 TTCTACGTGG
281636 CACTTCGATG
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 14 0.30
22 6 0.13
23 27 0.57
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.34
Consensus pattern (22 bp):
TTCTACGTGGTCCTTCGGGACA
Found at i:281612 original size:21 final size:23
Alignment explanation
Indices: 281581--281635 Score: 78
Period size: 21 Copynumber: 2.5 Consensus size: 23
281571 CTTCAAGACA
*
281581 ATTCTACGTGGTCCTTCG-GGAC
1 ATTCTATGTGGTCCTTCGCGGAC
*
281603 A-TCTATGTGGTCCTTTGCGGAC
1 ATTCTATGTGGTCCTTCGCGGAC
281625 ATTCTATGTGG
1 ATTCTATGTGG
281636 CACTTCGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 14 0.48
22 6 0.21
23 9 0.31
ACGTcount: A:0.15, C:0.22, G:0.27, T:0.36
Consensus pattern (23 bp):
ATTCTATGTGGTCCTTCGCGGAC
Found at i:281911 original size:23 final size:23
Alignment explanation
Indices: 281862--281912 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
281852 TGATTCAGGT
* * **
281862 ATGTTATGAATGTATGTATCTGT
1 ATGTTATGAAAGTATGTAACTAC
281885 ATGTTATGAAAGTATGTAACTAC
1 ATGTTATGAAAGTATGTAACTAC
281908 ATGTT
1 ATGTT
281913 TCATTAGTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.43
Consensus pattern (23 bp):
ATGTTATGAAAGTATGTAACTAC
Found at i:285462 original size:21 final size:21
Alignment explanation
Indices: 285420--285483 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
285410 TCTACACGGT
* *
285420 CCTTCGGGATAATTCTACGTGG
1 CCTTCGGGA-CATTCTATGTGG
285442 ACCTTCGGGACA-TCTATGTGG
1 -CCTTCGGGACATTCTATGTGG
* *
285463 TCTTTGGGACATTCTATGTGG
1 CCTTCGGGACATTCTATGTGG
285484 TACTTTGGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.25
21 17 0.47
22 1 0.03
23 9 0.25
ACGTcount: A:0.17, C:0.20, G:0.28, T:0.34
Consensus pattern (21 bp):
CCTTCGGGACATTCTATGTGG
Found at i:285473 original size:20 final size:22
Alignment explanation
Indices: 285431--285491 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
285421 CTTCGGGATA
* *
285431 ATTCTACGTGG-ACCTTCGGGAC
1 ATTCTATGTGGTA-CTTTGGGAC
285453 A-TCTATGTGGT-CTTTGGGAC
1 ATTCTATGTGGTACTTTGGGAC
285473 ATTCTATGTGGTACTTTGG
1 ATTCTATGTGGTACTTTGG
285492 TGAATTTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 9 0.26
21 18 0.53
22 7 0.21
ACGTcount: A:0.16, C:0.18, G:0.28, T:0.38
Consensus pattern (22 bp):
ATTCTATGTGGTACTTTGGGAC
Found at i:285735 original size:23 final size:23
Alignment explanation
Indices: 285708--285759 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
285698 ACGATTCAGG
* *
285708 TATGTTGTGAATGTATGTAACTA
1 TATGTTATGAAAGTATGTAACTA
285731 TATGTTATGAAAGTATGTAACTA
1 TATGTTATGAAAGTATGTAACTA
*
285754 CATGTT
1 TATGTT
285760 TCATTAGTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (23 bp):
TATGTTATGAAAGTATGTAACTA
Found at i:288613 original size:18 final size:19
Alignment explanation
Indices: 288578--288613 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
288568 TACCTTCATA
288578 ATGATTATTTATATAAGAT
1 ATGATTATTTATATAAGAT
*
288597 ATGATTGTTTA-ATAAGA
1 ATGATTATTTATATAAGA
288614 CAACATGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (19 bp):
ATGATTATTTATATAAGAT
Found at i:300574 original size:309 final size:309
Alignment explanation
Indices: 300015--300635 Score: 1053
Period size: 309 Copynumber: 2.0 Consensus size: 309
300005 GAACTTTCAA
* *
300015 TTGAATCAATCAGACCATCCAACTATTTAATTGATTCAATCAAACCACCGACCGTTAATTTTTAA
1 TTGAATCAATCAGACCACCCAACTATTTAATTAATTCAATCAAACCACCGACCGTTAATTTTTAA
* * *
300080 CAGAGGTGGTGACGTATTCGTTAATAAAATTGGCATAATTATATATTTGGTCTTTATTATTTACA
66 CAGAGGTGGTGACGTATTCGTTAATAAAATTGGCATAATTATATATTTGATCCTTAATATTTACA
* * * *
300145 TATTTTATCAATTTAGTCACTCTTTTAATTTAATTAAATAACTTTAACTATCCAATTATAACGTG
131 TATTTTATCAATTTAGTCACTATTTTAATTCAATTAAATAAATTTAACTATCCAATTAGAACGTG
*
300210 ACACGTGTAAATACATAATTGGAAGATTTTATTTATGAATTTTAAATTATTTAATTAAATGATTT
196 ACACGTGTAAATACATAATTAGAAGATTTTATTTATGAATTTTAAATTATTTAATTAAATGATTT
* * *
300275 TTCATCGTGTCACCACTCAATTGAAATGAAAATAAAGGGACAAACATGC
261 TTCATCGTGTCAACACCCAATTGAAATGAAAATAAAAGGACAAACATGC
* * *
300324 TTGAATCAATCAGACCACCCTACTATTTAATTAATTCAATCAAATCACTGACCGTTAATTTTTAA
1 TTGAATCAATCAGACCACCCAACTATTTAATTAATTCAATCAAACCACCGACCGTTAATTTTTAA
* *
300389 CAGAGGTGGTGACGTGTTCGTTAATAAAATTGGCATAATTATATTTTTGATCCTTAATATTTACA
66 CAGAGGTGGTGACGTATTCGTTAATAAAATTGGCATAATTATATATTTGATCCTTAATATTTACA
*
300454 TATTTTATCAATTTAGTCACTATTTTAATTCAATTAAATAAATTTAATTATCCAATTAGAACGTG
131 TATTTTATCAATTTAGTCACTATTTTAATTCAATTAAATAAATTTAACTATCCAATTAGAACGTG
*
300519 ACACGTGTAAATACATGATTAGAAGATTTTATTTATGAATTTTAAATTATTTAATTAAATGATTT
196 ACACGTGTAAATACATAATTAGAAGATTTTATTTATGAATTTTAAATTATTTAATTAAATGATTT
*
300584 TTCATCGTGTCAACACCCAATTGAAATGAAAATAAAAGGACCAACATGC
261 TTCATCGTGTCAACACCCAATTGAAATGAAAATAAAAGGACAAACATGC
300633 TTG
1 TTG
300636 CAAGAGGAAT
Statistics
Matches: 291, Mismatches: 21, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
309 291 1.00
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (309 bp):
TTGAATCAATCAGACCACCCAACTATTTAATTAATTCAATCAAACCACCGACCGTTAATTTTTAA
CAGAGGTGGTGACGTATTCGTTAATAAAATTGGCATAATTATATATTTGATCCTTAATATTTACA
TATTTTATCAATTTAGTCACTATTTTAATTCAATTAAATAAATTTAACTATCCAATTAGAACGTG
ACACGTGTAAATACATAATTAGAAGATTTTATTTATGAATTTTAAATTATTTAATTAAATGATTT
TTCATCGTGTCAACACCCAATTGAAATGAAAATAAAAGGACAAACATGC
Found at i:301010 original size:29 final size:30
Alignment explanation
Indices: 300972--301040 Score: 104
Period size: 29 Copynumber: 2.3 Consensus size: 30
300962 GGTTATTTCA
* *
300972 GTTCGGTTAATAATTTTCAAATTAA-TTTG
1 GTTCGATTAATAATTTTCAAATAAACTTTG
*
301001 GTTCGATTAATATTTTTCAAATAAACTTTG
1 GTTCGATTAATAATTTTCAAATAAACTTTG
301031 GTTCGATTAA
1 GTTCGATTAA
301041 CCGAACCGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 22 0.61
30 14 0.39
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.46
Consensus pattern (30 bp):
GTTCGATTAATAATTTTCAAATAAACTTTG
Found at i:301140 original size:29 final size:29
Alignment explanation
Indices: 301105--301181 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 29
301095 TAAAAATCGG
301105 TTAATTCGGTTCGGTTAATAATTTTCAAA
1 TTAATTCGGTTCGGTTAATAATTTTCAAA
*
301134 TTAATTCGATTCGGTTAATAATTTTCAAA
1 TTAATTCGGTTCGGTTAATAATTTTCAAA
* * *
301163 TAAAATTTGGTTCGATTAA
1 T-TAATTCGGTTCGGTTAA
301182 CCAAAAAGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 29 0.69
30 13 0.31
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.44
Consensus pattern (29 bp):
TTAATTCGGTTCGGTTAATAATTTTCAAA
Found at i:301280 original size:140 final size:141
Alignment explanation
Indices: 300953--301298 Score: 480
Period size: 141 Copynumber: 2.5 Consensus size: 141
300943 TGGTTAAAGA
* * * *
300953 AAAAAAATCGGTTATTTCA-GTTCGGTTAATAATTTTCAAATTAATTTGGTTCGATTAATATTTT
1 AAAAAAATCGGTTAATT-AGGTTCGGTTAATAATTTTCAAATTAATTCGGTTCGGTTAATAATTT
* * ** * * *
301017 TCAAATAAACTTTGGTTCGATTAACCGAACCGAATTAACCGAATTGTTTTCTTCAATTAATTCAA
65 TCAAATAAAATTTGGTTCGATTAACCAAAAAGAAATAACCAAATTGTTTGCTTCAATTAATTCAA
* *
301082 TTAATATTTTTT
130 TTAATAATTTTC
** * *
301094 TTAAAAATCGGTTAATTCGGTTCGGTTAATAATTTTCAAATTAATTCGATTCGGTTAATAATTTT
1 AAAAAAATCGGTTAATTAGGTTCGGTTAATAATTTTCAAATTAATTCGGTTCGGTTAATAATTTT
* *
301159 CAAATAAAATTTGGTTCGATTAACCAAAAAGAAATAACCAAATT-TTTGCTTCGATTAATTCAGT
66 CAAATAAAATTTGGTTCGATTAACCAAAAAGAAATAACCAAATTGTTTGCTTCAATTAATTCAAT
301223 TAATAATTTTC
131 TAATAATTTTC
* *
301234 AAAAAAATTGGTTAATTAGGTTCGGTTAATAATTTTCAAAATAATTCGGTTCGGTTAATAATTTT
1 AAAAAAATCGGTTAATTAGGTTCGGTTAATAATTTTCAAATTAATTCGGTTCGGTTAATAATTTT
301299 GGTTCGATTA
Statistics
Matches: 179, Mismatches: 25, Indels: 3
0.86 0.12 0.01
Matches are distributed among these distances:
140 85 0.47
141 94 0.53
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.42
Consensus pattern (141 bp):
AAAAAAATCGGTTAATTAGGTTCGGTTAATAATTTTCAAATTAATTCGGTTCGGTTAATAATTTT
CAAATAAAATTTGGTTCGATTAACCAAAAAGAAATAACCAAATTGTTTGCTTCAATTAATTCAAT
TAATAATTTTC
Found at i:301333 original size:114 final size:114
Alignment explanation
Indices: 301193--301412 Score: 350
Period size: 114 Copynumber: 1.9 Consensus size: 114
301183 CAAAAAGAAA
* *
301193 TAACCAAATTTTTGCTTCGATTAATTCAGTTAATAATTTTCAAAAAAATTGGTTAATTAGGTTCG
1 TAACCAAATTTTTGCTTCGATTAATTCAGTTAATAATTTTAAAAAAAATCGGTTAATTAGGTTCG
301258 GTTAATAATTTTCAAAATAATTCGGTTCGGTTAATAATTTTGGTTCGAT
66 GTTAATAATTTTCAAAATAATTCGGTTCGGTTAATAATTTTGGTTCGAT
* * *
301307 TAACCGAATTTTTGCTTCGATTAATTCGGTTAATAATTTTAAAAAAAATCGGTTAATTCGGTTCG
1 TAACCAAATTTTTGCTTCGATTAATTCAGTTAATAATTTTAAAAAAAATCGGTTAATTAGGTTCG
* * * * *
301372 TTTAATCATTTTTAAATTAATTTGGTTCGGTTAATAATTTT
66 GTTAATAATTTTCAAAATAATTCGGTTCGGTTAATAATTTT
301413 CAAATAAATT
Statistics
Matches: 96, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 96 1.00
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.45
Consensus pattern (114 bp):
TAACCAAATTTTTGCTTCGATTAATTCAGTTAATAATTTTAAAAAAAATCGGTTAATTAGGTTCG
GTTAATAATTTTCAAAATAATTCGGTTCGGTTAATAATTTTGGTTCGAT
Found at i:301399 original size:29 final size:29
Alignment explanation
Indices: 301359--301435 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
301349 AAAAAATCGG
* * * *
301359 TTAATTCGGTTCGTTTAATCATTTTTAAA
1 TTAATTTGGTTCGATTAATAATTTTCAAA
*
301388 TTAATTTGGTTCGGTTAATAATTTTCAAA
1 TTAATTTGGTTCGATTAATAATTTTCAAA
*
301417 TAAATTTTGGTTCGATTAA
1 TTAA-TTTGGTTCGATTAA
301436 CCGAACCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 28 0.68
30 13 0.32
ACGTcount: A:0.30, C:0.08, G:0.13, T:0.49
Consensus pattern (29 bp):
TTAATTTGGTTCGATTAATAATTTTCAAA
Found at i:302255 original size:29 final size:30
Alignment explanation
Indices: 302211--302274 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 30
302201 TCGGTTAATC
*
302211 GAACCAAAATTTATTTGAAAATTAGTAACT
1 GAACCAAAATTAATTTGAAAATTAGTAACT
*
302241 GAACC-AAATTAATTTGAAAATTATTAACT
1 GAACCAAAATTAATTTGAAAATTAGTAACT
302270 GAACC
1 GAACC
302275 GATTAACCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 27 0.84
30 5 0.16
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.31
Consensus pattern (30 bp):
GAACCAAAATTAATTTGAAAATTAGTAACT
Found at i:302502 original size:111 final size:113
Alignment explanation
Indices: 302242--302504 Score: 392
Period size: 111 Copynumber: 2.4 Consensus size: 113
302232 TTAGTAACTG
*
302242 AACC-AAATTAATTTGAAAATTATTAACTGAACCG-ATTAACCGATTTTTTAAAAAAACTTATTA
1 AACCAAAATTTATTTGAAAATTATTAACTGAACCGAATTAACCGATTTTTTAAAAAAACTTATTA
* * *
302305 ACCGAATTAATTGAAGCAAAATTTTGGTTAATTTGGTTCGGTTAATCA
66 ACCGAATTAATCGAAGCAAAATTCTGGTTAATTCGGTTCGGTTAATCA
* * **
302353 AACCAAATTTTATTTGAAAATTATTAACTTAACCGAATTAACCGA-TTTTTATGAAAA-TTATTA
1 AACCAAAATTTATTTGAAAATTATTAACTGAACCGAATTAACCGATTTTTTAAAAAAACTTATTA
302416 ACCGAATTAATCGAAGCAAAAATTCT-GTTAATTCGGTTCGGTTAATCA
66 ACCGAATTAATCGAAGC-AAAATTCTGGTTAATTCGGTTCGGTTAATCA
* *
302464 AACCAAAATTTATTTGAAAATTATTAACCGAACTGAATTAA
1 AACCAAAATTTATTTGAAAATTATTAACTGAACCGAATTAA
302505 TTTGAAAATT
Statistics
Matches: 137, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
111 84 0.61
112 44 0.32
113 9 0.07
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (113 bp):
AACCAAAATTTATTTGAAAATTATTAACTGAACCGAATTAACCGATTTTTTAAAAAAACTTATTA
ACCGAATTAATCGAAGCAAAATTCTGGTTAATTCGGTTCGGTTAATCA
Found at i:302512 original size:29 final size:29
Alignment explanation
Indices: 302470--302533 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
302460 ATCAAACCAA
* *
302470 AATTTATTTGAAAATTATTAACCGAACTG
1 AATTAATTTGAAAATTATTAACCGAACCG
*
302499 AATTAATTTGAAAATTATTAACTGAACCG
1 AATTAATTTGAAAATTATTAACCGAACCG
302528 AATTAA
1 AATTAA
302534 CCAATTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (29 bp):
AATTAATTTGAAAATTATTAACCGAACCG
Found at i:302616 original size:138 final size:138
Alignment explanation
Indices: 302364--302682 Score: 523
Period size: 138 Copynumber: 2.3 Consensus size: 138
302354 ACCAAATTTT
* * * *
302364 ATTTGAAAATTATTAACTTAACCGAATTAACCGATTTTTATGAAAATTATTAACCGAATTAATCG
1 ATTTGAAAATTATTAACTGAACCGAATTAACCAATTTTT-TTAAAATTATTAACCGAATTAATCA
*
302429 AAGCAAAAATTCTGTTAATTCGGTTCGGTTAATCAAACCAAAATTTATTTGAAAATTATTAACCG
65 AAGCAAAAATTCGGTTAATTCGGTTCGGTTAATCAAACCAAAATTTATTTGAAAATTATTAACCG
302494 AACTGAATTA
130 AAC-GAATTA
*
302504 ATTTGAAAATTATTAACTGAACCGAATTAACCAATTTTTTTAAAATTATTAATCGAATTAATCAA
1 ATTTGAAAATTATTAACTGAACCGAATTAACCAATTTTTTTAAAATTATTAACCGAATTAATCAA
* *
302569 AGC-AAAATTCGGTTAATTCGGTTTGGTTAATTAAACCAAAATTTATTTGAAAATTATTAACCGA
66 AGCAAAAATTCGGTTAATTCGGTTCGGTTAATCAAACCAAAATTTATTTGAAAATTATTAACCGA
302633 ACGAATTA
131 ACGAATTA
*
302641 AATTGAAAATTATTAACTGAACCGAATTAACCGAATTTTTTT
1 ATTTGAAAATTATTAACTGAACCGAATTAACC-AATTTTTTT
302683 TCTTTAACTA
Statistics
Matches: 169, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
137 37 0.22
138 69 0.41
139 26 0.15
140 37 0.22
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (138 bp):
ATTTGAAAATTATTAACTGAACCGAATTAACCAATTTTTTTAAAATTATTAACCGAATTAATCAA
AGCAAAAATTCGGTTAATTCGGTTCGGTTAATCAAACCAAAATTTATTTGAAAATTATTAACCGA
ACGAATTA
Found at i:302646 original size:28 final size:29
Alignment explanation
Indices: 302615--302670 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
302605 CAAAATTTAT
302615 TTGAAAATTATTAACCGAA-CGAATTAAA
1 TTGAAAATTATTAACCGAACCGAATTAAA
*
302643 TTGAAAATTATTAACTGAACCGAATTAA
1 TTGAAAATTATTAACCGAACCGAATTAA
302671 CCGAATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30
Consensus pattern (29 bp):
TTGAAAATTATTAACCGAACCGAATTAAA
Found at i:302863 original size:16 final size:16
Alignment explanation
Indices: 302844--302880 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
302834 TTACAATTAA
*
302844 TTTAAAAAATAATTTG
1 TTTAAAAAACAATTTG
302860 TTTAAAAAACAATTTG
1 TTTAAAAAACAATTTG
302876 TTTAA
1 TTTAA
302881 TTTTTTATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (16 bp):
TTTAAAAAACAATTTG
Found at i:303856 original size:30 final size:29
Alignment explanation
Indices: 303815--303878 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 29
303805 TAACGGTCGA
*
303815 TGGTTTGATTGAATCAATTAAATAGTTGGG
1 TGGTCTGATTGAATCAATTAAA-AGTTGGG
* * * *
303845 TGGTCTGATTGATTCATTTGAAAGTTTGG
1 TGGTCTGATTGAATCAATTAAAAGTTGGG
303874 TGGTC
1 TGGTC
303879 ACATTGATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 11 0.38
30 18 0.62
ACGTcount: A:0.23, C:0.06, G:0.28, T:0.42
Consensus pattern (29 bp):
TGGTCTGATTGAATCAATTAAAAGTTGGG
Found at i:303875 original size:29 final size:30
Alignment explanation
Indices: 303815--303887 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 30
303805 TAACGGTCGA
* *
303815 TGGTTTGATTGAATCAATTAAATAGTTGGG
1 TGGTCTGATTGATTCAATTAAATAGTTGGG
* * *
303845 TGGTCTGATTGATTCATTTGAA-AGTTTGG
1 TGGTCTGATTGATTCAATTAAATAGTTGGG
**
303874 TGGTCACATTGATT
1 TGGTCTGATTGATT
303888 TCTAAGCATA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 18 0.50
30 18 0.50
ACGTcount: A:0.25, C:0.07, G:0.26, T:0.42
Consensus pattern (30 bp):
TGGTCTGATTGATTCAATTAAATAGTTGGG
Found at i:307149 original size:16 final size:16
Alignment explanation
Indices: 307128--307159 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
307118 ATGTCGTCAA
307128 ATTTTTAACAGAAAAT
1 ATTTTTAACAGAAAAT
*
307144 ATTTTTAATAGAAAAT
1 ATTTTTAACAGAAAAT
307160 GATGAGTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (16 bp):
ATTTTTAACAGAAAAT
Found at i:310081 original size:17 final size:17
Alignment explanation
Indices: 310061--310094 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
310051 ATATATAATA
310061 ATATAAAATTATTAAAT
1 ATATAAAATTATTAAAT
* *
310078 ATATGATATTATTAAAT
1 ATATAAAATTATTAAAT
310095 CGTGTTCCCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
ATATAAAATTATTAAAT
Found at i:310094 original size:25 final size:25
Alignment explanation
Indices: 310019--310094 Score: 100
Period size: 25 Copynumber: 3.1 Consensus size: 25
310009 ATAAAAGTTC
*
310019 ATAATTAAATATATGATATTGTT-A
1 ATAATTAAATATATGATATTATTAA
* * *
310043 ATAATTAAATATATAATAATATAAA
1 ATAATTAAATATATGATATTATTAA
*
310068 ATTATTAAATATATGATATTATTAA
1 ATAATTAAATATATGATATTATTAA
310093 AT
1 AT
310095 CGTGTTCCCA
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
24 19 0.44
25 24 0.56
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (25 bp):
ATAATTAAATATATGATATTATTAA
Found at i:310175 original size:24 final size:25
Alignment explanation
Indices: 310142--310192 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 25
310132 AATCGCGTCT
310142 TATTGATTAAAAATTAAATATATAA
1 TATTGATTAAAAATTAAATATATAA
*
310167 TATT-ATTAATAATTAAATATATAA
1 TATTGATTAAAAATTAAATATATAA
310191 TA
1 TA
310193 ATATAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
TATTGATTAAAAATTAAATATATAA
Found at i:316269 original size:148 final size:148
Alignment explanation
Indices: 315995--316287 Score: 516
Period size: 148 Copynumber: 2.0 Consensus size: 148
315985 AAATACTCAA
*
315995 TTCAATTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTC
1 TTCAATTTATAAAATAGTTGACTCGAAATTTTTTCAATTTGAGTTTATAAAATTTAAATCAAGTC
* *
316060 AAATTGAATTGAATTTTCAAGTTTCTGTTTAAATTTAATTATAAATATTTATCATATTATAATAT
66 AAATTAAATTGAATTTTCAAGTTTCTGTTTAAATTTAATTATAAATATTTATAATATTATAATAT
316125 TATTTGATTCTAATTCAG
131 TATTTGATTCTAATTCAG
*
316143 TTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCAATTTGAGTTTATAAAATTTAAATCAAGTC
1 TTCAATTTATAAAATAGTTGACTCGAAATTTTTTCAATTTGAGTTTATAAAATTTAAATCAAGTC
*
316208 CAATTAAAATTGAATTTTCAAGTTTCTGTTTAAATTTAATTATAAATATTTATAATA-TATAATA
66 AAATT-AAATTGAATTTTCAAGTTTCTGTTTAAATTTAATTATAAATATTTATAATATTATAATA
*
316272 TTATTTTATTCTAATT
130 TTATTTGATTCTAATT
316288 TAAGTAGTTT
Statistics
Matches: 138, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
148 89 0.64
149 49 0.36
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (148 bp):
TTCAATTTATAAAATAGTTGACTCGAAATTTTTTCAATTTGAGTTTATAAAATTTAAATCAAGTC
AAATTAAATTGAATTTTCAAGTTTCTGTTTAAATTTAATTATAAATATTTATAATATTATAATAT
TATTTGATTCTAATTCAG
Found at i:317143 original size:16 final size:18
Alignment explanation
Indices: 317109--317145 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
317099 AATAAAGTAA
*
317109 ATATAAAATGAATAGAAT
1 ATATAAAATGAATAAAAT
317127 ATATAAAAT-AA-AAAAT
1 ATATAAAATGAATAAAAT
317143 ATA
1 ATA
317146 ATAACACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
18 9 0.50
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (18 bp):
ATATAAAATGAATAAAAT
Found at i:317297 original size:37 final size:36
Alignment explanation
Indices: 317256--317329 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
317246 GGATAAAGAT
*
317256 AAAAAGAAAATAG-ATAAATAAATGAGTAAAATATATA
1 AAAAAGAAAA-AGCATAAATAAATAAGTAAAATA-ATA
* * *
317293 AAAAAGTAAAAGCATATATATATAAGTAAAATAATA
1 AAAAAGAAAAAGCATAAATAAATAAGTAAAATAATA
317329 A
1 A
317330 TAATAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 6 0.19
37 26 0.81
ACGTcount: A:0.66, C:0.01, G:0.09, T:0.23
Consensus pattern (36 bp):
AAAAAGAAAAAGCATAAATAAATAAGTAAAATAATA
Found at i:317311 original size:20 final size:20
Alignment explanation
Indices: 317286--317323 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
317276 AATGAGTAAA
317286 ATATATAAAAAAGTAAAAGC
1 ATATATAAAAAAGTAAAAGC
* *
317306 ATATATATATAAGTAAAA
1 ATATATAAAAAAGTAAAA
317324 TAATAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (20 bp):
ATATATAAAAAAGTAAAAGC
Done.