Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008041.1 Hibiscus syriacus cultivar Beakdansim tig00110528_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: 4970990
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 21
Found at i:305299 original size:25 final size:26
Alignment explanation
Indices: 305271--305325 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
305261 TTAATAAAAA
305271 AATAT-TTATCTAATGA-AAAATATTT
1 AATATATT-TCTAATGATAAAATATTT
* *
305296 AATATATTTCTAATGATAATATTTTT
1 AATATATTTCTAATGATAAAATATTT
305322 AATA
1 AATA
305326 ACTAATGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 13 0.50
26 13 0.50
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (26 bp):
AATATATTTCTAATGATAAAATATTT
Found at i:305488 original size:7 final size:7
Alignment explanation
Indices: 305472--305533 Score: 53
Period size: 7 Copynumber: 9.4 Consensus size: 7
305462 TTTTGTAATG
*
305472 AACCCCA
1 AACCCTA
305479 AACCCTA
1 AACCCTA
*
305486 AA-CCAA
1 AACCCTA
*
305492 AGACAC-A
1 A-ACCCTA
305499 AA-CCTA
1 AACCCTA
305505 AACCCT-
1 AACCCTA
305511 AACCCT-
1 AACCCTA
305517 AACCCTA
1 AACCCTA
305524 AACCCTA
1 AACCCTA
305531 AAC
1 AAC
305534 TATTAATCCG
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
5 1 0.02
6 20 0.43
7 24 0.52
8 1 0.02
ACGTcount: A:0.47, C:0.42, G:0.02, T:0.10
Consensus pattern (7 bp):
AACCCTA
Found at i:305517 original size:13 final size:14
Alignment explanation
Indices: 305472--305533 Score: 53
Period size: 13 Copynumber: 4.7 Consensus size: 14
305462 TTTTGTAATG
*
305472 AACCCCAAACCCTA
1 AACCCTAAACCCTA
* *
305486 AA-CCAAAGACAC-A
1 AACCCTAA-ACCCTA
305499 AA-CCTAAACCCT-
1 AACCCTAAACCCTA
305511 AACCCT-AACCCTA
1 AACCCTAAACCCTA
305524 AACCCTAAAC
1 AACCCTAAAC
305534 TATTAATCCG
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
12 11 0.28
13 20 0.51
14 8 0.21
ACGTcount: A:0.47, C:0.42, G:0.02, T:0.10
Consensus pattern (14 bp):
AACCCTAAACCCTA
Found at i:307198 original size:18 final size:18
Alignment explanation
Indices: 307162--307214 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
307152 TCAAACTAAT
*
307162 CAAAATGATTAAA-CTAAC
1 CAAAATGATCAAATC-AAC
* * *
307180 CAGAATGGTCGAATCAAC
1 CAAAATGATCAAATCAAC
307198 CAAAATGATCAAATCAA
1 CAAAATGATCAAATCAA
307215 TCTCCTTTCT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
18 26 0.96
19 1 0.04
ACGTcount: A:0.51, C:0.19, G:0.11, T:0.19
Consensus pattern (18 bp):
CAAAATGATCAAATCAAC
Found at i:309791 original size:17 final size:17
Alignment explanation
Indices: 309769--309804 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
309759 TTCGATCAAT
*
309769 ATCTCAGTTTTTGTGCC
1 ATCTCAGTTTTTATGCC
309786 ATCTCAGTTTTTATGCC
1 ATCTCAGTTTTTATGCC
309803 AT
1 AT
309805 ATCGATCGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.22, G:0.14, T:0.47
Consensus pattern (17 bp):
ATCTCAGTTTTTATGCC
Found at i:315678 original size:13 final size:13
Alignment explanation
Indices: 315660--315691 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
315650 ACATTATTTT
315660 CACATAACTTAAC
1 CACATAACTTAAC
315673 CACATAACTTAAC
1 CACATAACTTAAC
315686 CACATA
1 CACATA
315692 TCTGCATCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (13 bp):
CACATAACTTAAC
Found at i:320501 original size:226 final size:228
Alignment explanation
Indices: 320104--320611 Score: 715
Period size: 226 Copynumber: 2.2 Consensus size: 228
320094 TGTGTTGCTG
* * * * * * *
320104 ATTCGAAGTGATGTGAATCGAG-AAAAGGAAATGTGAACCCCTCTGGTGGGGCGTTGTTGATTCA
1 ATTCGAAGTGTTGTGAATTGAGCCATAGGAAATGTTAACCCCTCTGGTGGGGCATTGCTGATTCA
**
320168 AAGTGTTGTGAATCAAGTAAAGGAAATGTTGAAAACATCCTGCCCGAAGGTCTTTAGGATGGCCC
66 AAGTGCAGTGAATCAAGTAAAGGAAATGTTGAAAACATCCTGCCCGAAGGTCTTTAGGATGGCCC
* * * * *
320233 GAAGGACTTATCATCTTGCTCGAGAGACTTATAGGAGACCCGAAGGATTTAAGCATCTTGCTTAA
131 AAAGGACTTATCATCTTGCTCGAAAGACTTATAGGAGACCCGAAAGATTTAAGCATCATGCTCAA
* *
320298 AAGACTT-ACTGATGGCCTGAAGGATTTAAGCTA
196 AAGACTTGA-TGATGGCCCGAAGGACTTAAGCTA
*
320331 ATTCGAAGTGTTGTGAATTGAGCCATAGGAAATGTTAA-CCCTCTGGTGGGGTATTGCTGATTCC
1 ATTCGAAGTGTTGTGAATTGAGCCATAGGAAATGTTAACCCCTCTGGTGGGGCATTGCTGATT-C
* *
320395 AAA-TGCAGTGAATCAAG-CAAGGAAATGTTGAAAACATCCTGCTCGAAGGTCTTGT-GGATGGC
65 AAAGTGCAGTGAATCAAGTAAAGGAAATGTTGAAAACATCCTGCCCGAAGGTCTT-TAGGATGGC
*
320457 CTAAAGGACTTATCATCTTGCTCGAAAGACTTATA-GATGACCCGAAAGATTTAAGCATCATGCT
129 CCAAAGGACTTATCATCTTGCTCGAAAGACTTATAGGA-GACCCGAAAGATTTAAGCATCATGCT
* * *
320521 CGAAAGACTTGATGATGGCCCGAAGGACTTAATCTG
193 CAAAAGACTTGATGATGGCCCGAAGGACTTAAGCTA
*
320557 ATTCGAAGTGTTATGAATTGAGCCATAGGAAATGTTAACCCCTCTGGTGGGGCAT
1 ATTCGAAGTGTTGTGAATTGAGCCATAGGAAATGTTAACCCCTCTGGTGGGGCAT
320612 CATTGATTCG
Statistics
Matches: 250, Mismatches: 25, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
225 2 0.01
226 162 0.65
227 70 0.28
228 16 0.06
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (228 bp):
ATTCGAAGTGTTGTGAATTGAGCCATAGGAAATGTTAACCCCTCTGGTGGGGCATTGCTGATTCA
AAGTGCAGTGAATCAAGTAAAGGAAATGTTGAAAACATCCTGCCCGAAGGTCTTTAGGATGGCCC
AAAGGACTTATCATCTTGCTCGAAAGACTTATAGGAGACCCGAAAGATTTAAGCATCATGCTCAA
AAGACTTGATGATGGCCCGAAGGACTTAAGCTA
Found at i:320844 original size:42 final size:41
Alignment explanation
Indices: 320726--320844 Score: 103
Period size: 42 Copynumber: 2.8 Consensus size: 41
320716 ATGTTGCCCG
* ** * * * *
320726 AAGGACTTATGGATGGCCTAAAAGACTTATCATCTTTCTCGA
1 AAGG-CTTATAGATGGCCCGAAGGACTTATCATCATGCTCAA
* * * *
320768 AAGACTTATAGATGACCCGAAGGATTTAAGCATCATGCTCAA
1 AAGGCTTATAGATGGCCCGAAGGACTT-ATCATCATGCTCAA
*
320810 AAGGCTTATTGATGGCCCGAAGGACTTACTCATCA
1 AAGGCTTATAGATGGCCCGAAGGACTTA-TCATCA
320845 AATAAACCTT
Statistics
Matches: 59, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
41 18 0.31
42 41 0.69
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (41 bp):
AAGGCTTATAGATGGCCCGAAGGACTTATCATCATGCTCAA
Found at i:321049 original size:55 final size:58
Alignment explanation
Indices: 320897--321087 Score: 187
Period size: 58 Copynumber: 3.4 Consensus size: 58
320887 TTTTCAATTG
* **
320897 TCATCAAGAATCCCCTAAAAATTAGGCTTAACTTCTTTTAAAAATTCTTTGGAGATAA
1 TCATCAAGAAACCCCTAAAAATTAGGCTTAACTTCTTTTAAAAACCCTTTGGAGATAA
* * ** * *
320955 TCATAAAGAAACCTCTAAAAAGCAGGCTT-A-GT-TTTTAAAAACCCTTTTGA-A-AA
1 TCATCAAGAAACCCCTAAAAATTAGGCTTAACTTCTTTTAAAAACCCTTTGGAGATAA
* *** * *
321008 -CATCAATAAACCCCTAAAAATTAGGCTTAACTTCTTTTAAAAAATTATTTGGAAATCA
1 TCATCAAGAAACCCCTAAAAATTAGGCTTAACTTCTTTT-AAAAACCCTTTGGAGATAA
*
321066 TCATTAAGAAACCCCTAAAAAT
1 TCATCAAGAAACCCCTAAAAAT
321088 CATGCTTAGT
Statistics
Matches: 104, Mismatches: 22, Indels: 13
0.75 0.16 0.09
Matches are distributed among these distances:
52 23 0.22
53 3 0.03
54 2 0.02
55 19 0.18
56 11 0.11
57 2 0.02
58 25 0.24
59 19 0.18
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (58 bp):
TCATCAAGAAACCCCTAAAAATTAGGCTTAACTTCTTTTAAAAACCCTTTGGAGATAA
Found at i:321096 original size:111 final size:110
Alignment explanation
Indices: 320898--321234 Score: 390
Period size: 110 Copynumber: 3.0 Consensus size: 110
320888 TTTCAATTGT
* * * * *
320898 CATCAAGAATCCCCTAAAAATTAGGCTTAACTTCTTTTAAAAATTCTTTGGAGATAATCATAAAG
1 CATCAAAAAACCCCTAAAAATTAGGCTTAACTTCTTTTAAAAATTATTTGGAAATCATCATAAAG
* *
320963 AAACCTCTAAAAAGCAGGCTTAGTTTTTAAAAACCCTTTTGAAAA
66 AAACCCCTAAAAATCAGGCTTAGTTTTTAAAAACCCTTTTGAAAA
* *
321008 CATCAATAAACCCCTAAAAATTAGGCTTAACTTCTTTTAAAAAATTATTTGGAAATCATCATTAA
1 CATCAAAAAACCCCTAAAAATTAGGCTTAACTTCTTTT-AAAAATTATTTGGAAATCATCATAAA
* * * * *
321073 GAAACCCCTAAAAATCATGCTTAGTTTCTAAAAACTCATTTG-AAT
65 GAAACCCCTAAAAATCAGGCTTAGTTTTTAAAAACCCTTTTGAAAA
* ** ** * *
321118 CGTCAAAAAACTGCTAAAAATTAGGCTTAGTTTCTTTTAAAAATTCA-TTGAAAATCATCATCAA
1 CATCAAAAAACCCCTAAAAATTAGGCTTAACTTCTTTTAAAAATT-ATTTGGAAATCATCATAAA
* * * *
321182 GAAACCCCTTAAAGTAAGGCTTAGTTTCTTTAAAAATCCTTTTGAAAA
65 GAAACCCCTAAAAATCAGGCTTAG-TT-TTTAAAAACCCTTTTGAAAA
*
321230 TATCA
1 CATCA
321235 TGTTGTTTGG
Statistics
Matches: 190, Mismatches: 32, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
109 42 0.22
110 73 0.38
111 70 0.37
112 5 0.03
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.32
Consensus pattern (110 bp):
CATCAAAAAACCCCTAAAAATTAGGCTTAACTTCTTTTAAAAATTATTTGGAAATCATCATAAAG
AAACCCCTAAAAATCAGGCTTAGTTTTTAAAAACCCTTTTGAAAA
Found at i:323245 original size:17 final size:16
Alignment explanation
Indices: 323168--323249 Score: 58
Period size: 17 Copynumber: 4.9 Consensus size: 16
323158 ATTTGATATG
*
323168 TTTTCTTTCTTTATTT-
1 TTTTTTTTCTTT-TTTA
**
323184 TTTTTTTTCTTTTTCC
1 TTTTTTTTCTTTTTTA
* *
323200 TTTGTTTTCCTTTTTTCC
1 TTT-TTTTTCTTTTTT-A
* *
323218 TTTTCTATCTTTTTTA
1 TTTTTTTTCTTTTTTA
323234 TGTTTTTTTCTTTTTT
1 T-TTTTTTTCTTTTTT
323250 GCCATGTCTT
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
15 2 0.04
16 15 0.29
17 31 0.60
18 4 0.08
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (16 bp):
TTTTTTTTCTTTTTTA
Found at i:323696 original size:15 final size:15
Alignment explanation
Indices: 323676--323706 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
323666 CCTTTTATTT
323676 TTTCTTCATTCATTC
1 TTTCTTCATTCATTC
*
323691 TTTCTTCTTTCATTC
1 TTTCTTCATTCATTC
323706 T
1 T
323707 CTCCTAGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.26, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTCTTCATTCATTC
Found at i:329099 original size:21 final size:21
Alignment explanation
Indices: 329058--329105 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
329048 TGAACAATAA
329058 CGATACCATATGGAAAGGGTAT
1 CGATACCATATGG-AAGGGTAT
329080 CGATACCCATATGG-AGGGTAT
1 CGATA-CCATATGGAAGGGTAT
*
329101 TGATA
1 CGATA
329106 ACTGGAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 11 0.46
22 5 0.21
23 8 0.33
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (21 bp):
CGATACCATATGGAAGGGTAT
Found at i:331006 original size:15 final size:15
Alignment explanation
Indices: 330986--331059 Score: 148
Period size: 15 Copynumber: 4.9 Consensus size: 15
330976 TGATCGAGGG
330986 TTGCAGAAATTGGTC
1 TTGCAGAAATTGGTC
331001 TTGCAGAAATTGGTC
1 TTGCAGAAATTGGTC
331016 TTGCAGAAATTGGTC
1 TTGCAGAAATTGGTC
331031 TTGCAGAAATTGGTC
1 TTGCAGAAATTGGTC
331046 TTGCAGAAATTGGT
1 TTGCAGAAATTGGT
331060 AATTACTTTG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 59 1.00
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (15 bp):
TTGCAGAAATTGGTC
Found at i:331821 original size:17 final size:18
Alignment explanation
Indices: 331801--331860 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
331791 TGAAACATAT
331801 AAATATA-AATTATAATA
1 AAATATACAATTATAATA
* *
331818 AAATA-ACAAATACAAATA
1 AAATATACAATTA-TAATA
*
331836 AAA-ATATAATTATAATAA
1 AAATATACAATTATAAT-A
331854 AAATATA
1 AAATATA
331861 TTTTTATAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 1 0.03
17 13 0.39
18 16 0.48
19 3 0.09
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
AAATATACAATTATAATA
Found at i:331872 original size:19 final size:17
Alignment explanation
Indices: 331801--331860 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
331791 TGAAACATAT
331801 AAATATAAATTATAAT-A
1 AAATAT-AATTATAATAA
* * *
331818 AAATAACAAATACAAATAA
1 AAAT-ATAATTA-TAATAA
331837 AAATATAATTATAATAA
1 AAATATAATTATAATAA
331854 AAATATA
1 AAATATA
331861 TTTTTATAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 20 0.59
18 9 0.26
19 5 0.15
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.28
Consensus pattern (17 bp):
AAATATAATTATAATAA
Found at i:332796 original size:39 final size:39
Alignment explanation
Indices: 332735--332853 Score: 141
Period size: 39 Copynumber: 3.1 Consensus size: 39
332725 TAAAATTTTT
* * *
332735 ATTCCTAA-TTATAAAATAATTTCACCATAACATTCTAA
1 ATTCTTAATTTATTAAATTATTTCACCATAACATTCTAA
* * *
332773 ATTCTTAATTTATTAAATTATTTCACTACACCATTCTAA
1 ATTCTTAATTTATTAAATTATTTCACCATAACATTCTAA
* * * *
332812 ATTATTAATTTATTAAATTATTTTACCCTAACAATCTAA
1 ATTCTTAATTTATTAAATTATTTCACCATAACATTCTAA
332851 ATT
1 ATT
332854 ATTTATTTTA
Statistics
Matches: 67, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
38 7 0.10
39 60 0.90
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (39 bp):
ATTCTTAATTTATTAAATTATTTCACCATAACATTCTAA
Found at i:332922 original size:14 final size:14
Alignment explanation
Indices: 332886--332934 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
332876 ATTTTAAATA
*
332886 TAATTATATTTATT
1 TAATTATATTTTTT
332900 TAATTTTATATTTTTT
1 TAA--TTATATTTTTT
* *
332916 TAATTATGTATTTT
1 TAATTATATTTTTT
332930 TAATT
1 TAATT
332935 TTTTAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 17 0.57
16 13 0.43
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TAATTATATTTTTT
Found at i:332927 original size:16 final size:16
Alignment explanation
Indices: 332890--332930 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
332880 TAAATATAAT
* *
332890 TATATTTATTTAATTT
1 TATATTTTTTTAATTA
332906 TATATTTTTTTAATTA
1 TATATTTTTTTAATTA
*
332922 TGTATTTTT
1 TATATTTTT
332931 AATTTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (16 bp):
TATATTTTTTTAATTA
Found at i:334908 original size:20 final size:20
Alignment explanation
Indices: 334871--334909 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
334861 TTTATATGTA
* *
334871 TGATATATTGACTTTATGAG
1 TGATATATTAACTCTATGAG
*
334891 TGATATGTTAACTCTATGA
1 TGATATATTAACTCTATGA
334910 TAATTATATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.44
Consensus pattern (20 bp):
TGATATATTAACTCTATGAG
Found at i:341678 original size:26 final size:24
Alignment explanation
Indices: 341649--341699 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 24
341639 ATTTGCTATG
341649 AATTCATCAACCATTACATAATACAT
1 AATTCATCAACCATTACA-AA-ACAT
341675 AATTCATCAACCATTACAAAACAT
1 AATTCATCAACCATTACAAAACAT
341699 A
1 A
341700 CATCCTAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 5 0.20
25 2 0.08
26 18 0.72
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (24 bp):
AATTCATCAACCATTACAAAACAT
Found at i:341756 original size:40 final size:43
Alignment explanation
Indices: 341670--341759 Score: 105
Period size: 46 Copynumber: 2.1 Consensus size: 43
341660 CATTACATAA
* *
341670 TACATAATTCATCAACCATTACAAAACATACATCCTAAACTTCCAT
1 TACATAATTCATCAACCATTAC-AAACAT--ATACTAAACTGCCAT
*
341716 TACATAATTCATCAACTATTAC-AACAT-TAC-AAACTGCCAT
1 TACATAATTCATCAACCATTACAAACATATACTAAACTGCCAT
341756 TACA
1 TACA
341760 AGAAAAAACT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
40 13 0.32
41 2 0.05
44 5 0.12
46 21 0.51
ACGTcount: A:0.43, C:0.27, G:0.01, T:0.29
Consensus pattern (43 bp):
TACATAATTCATCAACCATTACAAACATATACTAAACTGCCAT
Found at i:349709 original size:12 final size:12
Alignment explanation
Indices: 349694--349726 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
349684 TGTATAAACT
*
349694 ACCTGATTTGAA
1 ACCTGATTCGAA
349706 ACCTGATTCGAA
1 ACCTGATTCGAA
349718 ACCTGATTC
1 ACCTGATTC
349727 CTGATTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (12 bp):
ACCTGATTCGAA
Found at i:351247 original size:30 final size:30
Alignment explanation
Indices: 351211--351270 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
351201 CTCATATTAG
351211 ACTCCTCTTTACTCACAGTAATTGCATCAT
1 ACTCCTCTTTACTCACAGTAATTGCATCAT
351241 ACTCCTCTTTACTCACAGTAATTGCATCAT
1 ACTCCTCTTTACTCACAGTAATTGCATCAT
351271 CCACCAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.30, G:0.07, T:0.37
Consensus pattern (30 bp):
ACTCCTCTTTACTCACAGTAATTGCATCAT
Found at i:352220 original size:31 final size:31
Alignment explanation
Indices: 352182--352258 Score: 82
Period size: 32 Copynumber: 2.5 Consensus size: 31
352172 TAAGGCGACC
* * * *
352182 CTTGGGTAGGCTCTGCGGCTCCGAGATTTTT
1 CTTGGGTAGCCTCTGCGGCCCCGAGAATTGT
* * *
352213 CTTGGGTAAGTCTCCGTGGCCCCGAGAATTGT
1 CTTGGGT-AGCCTCTGCGGCCCCGAGAATTGT
352245 CTTGGGTAGCCTCT
1 CTTGGGTAGCCTCT
352259 TAGGCCCCAA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
31 12 0.32
32 25 0.68
ACGTcount: A:0.12, C:0.25, G:0.31, T:0.32
Consensus pattern (31 bp):
CTTGGGTAGCCTCTGCGGCCCCGAGAATTGT
Found at i:355147 original size:22 final size:23
Alignment explanation
Indices: 355121--355167 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
355111 TGATCGCTAC
*
355121 ATATGATGTTTATCATGAAT-AT
1 ATATGATATTTATCATGAATGAT
355143 ATATGATATTTATCATGAATGAT
1 ATATGATATTTATCATGAATGAT
355166 AT
1 AT
355168 TTAGGGTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.45
Consensus pattern (23 bp):
ATATGATATTTATCATGAATGAT
Found at i:355369 original size:40 final size:40
Alignment explanation
Indices: 355314--355392 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
355304 TATCGATTAA
*
355314 GCACTTCGATGCATATGGTGGGTACAACCTTATGTGTAAT
1 GCACTTCGATGCATATGGTGGGCACAACCTTATGTGTAAT
* **
355354 GCACTTCGGTGCATATGGTGGGCATGACCTTATGTGTAA
1 GCACTTCGATGCATATGGTGGGCACAACCTTATGTGTAA
355393 GAACTACGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.32
Consensus pattern (40 bp):
GCACTTCGATGCATATGGTGGGCACAACCTTATGTGTAAT
Found at i:356825 original size:127 final size:127
Alignment explanation
Indices: 356599--356853 Score: 510
Period size: 127 Copynumber: 2.0 Consensus size: 127
356589 CAAATTATCC
356599 CTAATCGAACATGTATTGAACAAAAACGAAAGAAGGATCATTACAAAGAATATGTCTGCAAACAA
1 CTAATCGAACATGTATTGAACAAAAACGAAAGAAGGATCATTACAAAGAATATGTCTGCAAACAA
356664 GAGGATGTACCATATGAAGTTATGATGAAAGTGAATAGAGAATCATTAAGATTAATGAATTT
66 GAGGATGTACCATATGAAGTTATGATGAAAGTGAATAGAGAATCATTAAGATTAATGAATTT
356726 CTAATCGAACATGTATTGAACAAAAACGAAAGAAGGATCATTACAAAGAATATGTCTGCAAACAA
1 CTAATCGAACATGTATTGAACAAAAACGAAAGAAGGATCATTACAAAGAATATGTCTGCAAACAA
356791 GAGGATGTACCATATGAAGTTATGATGAAAGTGAATAGAGAATCATTAAGATTAATGAATTT
66 GAGGATGTACCATATGAAGTTATGATGAAAGTGAATAGAGAATCATTAAGATTAATGAATTT
356853 C
1 C
356854 AAGTCAAGTA
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
127 128 1.00
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.25
Consensus pattern (127 bp):
CTAATCGAACATGTATTGAACAAAAACGAAAGAAGGATCATTACAAAGAATATGTCTGCAAACAA
GAGGATGTACCATATGAAGTTATGATGAAAGTGAATAGAGAATCATTAAGATTAATGAATTT
Found at i:363605 original size:20 final size:21
Alignment explanation
Indices: 363580--363627 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
363570 TAATGGTGTC
* * *
363580 TTTAAATGAATTT-ATAATGT
1 TTTAAATAAATTTGAAAAGGT
363600 TTTAAATAAATTTGAAAAGGT
1 TTTAAATAAATTTGAAAAGGT
363621 TTTAAAT
1 TTTAAAT
363628 TTTAGTAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (21 bp):
TTTAAATAAATTTGAAAAGGT
Found at i:365785 original size:18 final size:20
Alignment explanation
Indices: 365747--365785 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
365737 CCTAAGGCAA
365747 GAATCTTCACTAAAAATCAT
1 GAATCTTCACTAAAAATCAT
365767 GAATCTTCA-TAAAAA-CAT
1 GAATCTTCACTAAAAATCAT
365785 G
1 G
365786 TGTTTTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
19 6 0.32
20 9 0.47
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (20 bp):
GAATCTTCACTAAAAATCAT
Found at i:369258 original size:11 final size:11
Alignment explanation
Indices: 369242--369272 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
369232 TGATTATATG
369242 ATATGTTTATT
1 ATATGTTTATT
369253 ATATGTTTATT
1 ATATGTTTATT
369264 ATATGTTTA
1 ATATGTTTA
369273 GCATGCATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (11 bp):
ATATGTTTATT
Found at i:384838 original size:21 final size:20
Alignment explanation
Indices: 384812--384851 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
384802 AATACTGGTA
384812 TTGGTATCAATATTGCGGGTG
1 TTGGTATCAATATTG-GGGTG
*
384833 TTGGTATCTATATTGGGGT
1 TTGGTATCAATATTGGGGT
384852 ATTTTTTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.17, C:0.07, G:0.33, T:0.42
Consensus pattern (20 bp):
TTGGTATCAATATTGGGGTG
Found at i:390236 original size:77 final size:78
Alignment explanation
Indices: 390144--390289 Score: 206
Period size: 77 Copynumber: 1.9 Consensus size: 78
390134 TTCAAATTAA
* *
390144 TTAAACTCTTTTTTAATTAATTCAAATTAAATATCCATT-AAAGACTTATAATCCA-AATTACAA
1 TTAAACTCTTATTTAATTAATTCAAATTAAAAATCCATTAAAAGACTTATAAT-CAGAATTACAA
390207 TCTTTACTTTTTAT
65 TCTTTACTTTTTAT
* * * * *
390221 TTAAACTCTTATTTAATTATTTCGAATTAAAAATCCATTAAAAGAGTTGTAATCAGAATTACATT
1 TTAAACTCTTATTTAATTAATTCAAATTAAAAATCCATTAAAAGACTTATAATCAGAATTACAAT
390286 CTTT
66 CTTT
390290 TAATATTTAC
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
77 37 0.62
78 23 0.38
ACGTcount: A:0.39, C:0.13, G:0.04, T:0.44
Consensus pattern (78 bp):
TTAAACTCTTATTTAATTAATTCAAATTAAAAATCCATTAAAAGACTTATAATCAGAATTACAAT
CTTTACTTTTTAT
Found at i:392342 original size:28 final size:27
Alignment explanation
Indices: 392270--392345 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 27
392260 ATAAAGTAGG
392270 TATATCATTTATGATAAAACAAGGCTCC
1 TATATCATTTATGATAAAACAAGGCT-C
* * *
392298 TACTAGC-TTTCTTATAAACACAAGGCT-
1 TA-TATCATTTATGATAAA-ACAAGGCTC
392325 TATATTCATTTATGATAAAAC
1 TATA-TCATTTATGATAAAAC
392346 CAAACCCTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
26 2 0.05
27 5 0.13
28 20 0.53
29 11 0.29
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (27 bp):
TATATCATTTATGATAAAACAAGGCTC
Found at i:398594 original size:20 final size:20
Alignment explanation
Indices: 398569--398608 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
398559 TATTAAAATA
398569 TGCATTATAGAATATGCATT
1 TGCATTATAGAATATGCATT
*
398589 TGCATTCTAGAATATGCATT
1 TGCATTATAGAATATGCATT
398609 ATTAACGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (20 bp):
TGCATTATAGAATATGCATT
Found at i:400288 original size:35 final size:35
Alignment explanation
Indices: 400235--400348 Score: 140
Period size: 35 Copynumber: 3.3 Consensus size: 35
400225 TCGTCTAAAG
* *
400235 TAGAAC-GAAGGGAGGCATCACACTTTTGATTCAAG
1 TAGAACGGAA-GGAAGCATCACACTTTTGATTCAAC
* * * * *
400270 AAGAACGGAATGAAGCATCGCACTTTCGATTCAAT
1 TAGAACGGAAGGAAGCATCACACTTTTGATTCAAC
*
400305 TAGAACGGAAGGAAGCATCACATTTTTGATTCAAC
1 TAGAACGGAAGGAAGCATCACACTTTTGATTCAAC
400340 TAGAACGGA
1 TAGAACGGA
400349 TGGTTTACTA
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
35 63 0.95
36 3 0.05
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.23
Consensus pattern (35 bp):
TAGAACGGAAGGAAGCATCACACTTTTGATTCAAC
Found at i:413616 original size:20 final size:20
Alignment explanation
Indices: 413578--413628 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
413568 TGTAACCCTT
413578 TGAAAATACAT-GATTTTAA
1 TGAAAATACATGGATTTTAA
* *
413597 TGAATATACATGGTTTTTAA
1 TGAAAATACATGGATTTTAA
413617 TGAAAATACATG
1 TGAAAATACATG
413629 CTCTTGACCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGGATTTTAA
Found at i:414604 original size:120 final size:120
Alignment explanation
Indices: 414386--414631 Score: 483
Period size: 120 Copynumber: 2.0 Consensus size: 120
414376 TGGAGATGAT
*
414386 ATAAAAGCTAAAGTAAACAATGTATACCATAACATATGCATGAATTAAGCTAATCATAATCATGA
1 ATAATAGCTAAAGTAAACAATGTATACCATAACATATGCATGAATTAAGCTAATCATAATCATGA
414451 CATAAAGATGTGGACTTAGGTTATGCATGAATATCATATAATATTCAAGTGAATG
66 CATAAAGATGTGGACTTAGGTTATGCATGAATATCATATAATATTCAAGTGAATG
414506 ATAATAGCTAAAGTAAACAATGTATACCATAACATATGCATGAATTAAGCTAATCATAATCATGA
1 ATAATAGCTAAAGTAAACAATGTATACCATAACATATGCATGAATTAAGCTAATCATAATCATGA
414571 CATAAAGATGTGGACTTAGGTTATGCATGAATATCATATAATATTCAAGTGAATG
66 CATAAAGATGTGGACTTAGGTTATGCATGAATATCATATAATATTCAAGTGAATG
414626 ATAATA
1 ATAATA
414632 TATGGTAATT
Statistics
Matches: 125, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 125 1.00
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (120 bp):
ATAATAGCTAAAGTAAACAATGTATACCATAACATATGCATGAATTAAGCTAATCATAATCATGA
CATAAAGATGTGGACTTAGGTTATGCATGAATATCATATAATATTCAAGTGAATG
Found at i:414988 original size:19 final size:16
Alignment explanation
Indices: 414936--414989 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 16
414926 TTTTCAATGT
*
414936 TTATAATAATCATATAA
1 TTATAATAA-AATATAA
414953 TTATAATAAAATCATAA
1 TTATAATAAAAT-ATAA
414970 TTAATAATCAAAACTATAA
1 TT-ATAAT-AAAA-TATAA
414989 T
1 T
414990 ATTAAAACTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 2 0.06
17 15 0.47
18 5 0.16
19 9 0.28
20 1 0.03
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (16 bp):
TTATAATAAAATATAA
Found at i:416013 original size:37 final size:37
Alignment explanation
Indices: 415958--416033 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
415948 TTGGAAGAAA
* *
415958 TTCCATATATTTCATTTAAATTGGATCAATATGAGTC
1 TTCCATATATTTCATTTAAATTAGATCAACATGAGTC
*
415995 TTCCTTATATTTCATTTAAATTAGATCAACATGAGTC
1 TTCCATATATTTCATTTAAATTAGATCAACATGAGTC
416032 TT
1 TT
416034 TTCTCAGATC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (37 bp):
TTCCATATATTTCATTTAAATTAGATCAACATGAGTC
Found at i:417005 original size:24 final size:24
Alignment explanation
Indices: 416978--417025 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
416968 GTTCAGATAC
*
416978 CAGAATAGAATCCAAGTCAGGTAT
1 CAGAACAGAATCCAAGTCAGGTAT
* * *
417002 CAGAACATAATCCAGGTTAGGTAT
1 CAGAACAGAATCCAAGTCAGGTAT
417026 TATAACAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.23
Consensus pattern (24 bp):
CAGAACAGAATCCAAGTCAGGTAT
Found at i:435093 original size:25 final size:25
Alignment explanation
Indices: 435065--435121 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
435055 CCTTTTAATG
*
435065 AATATTTAAACTGAAATAATTAAAT
1 AATATTTAAACTAAAATAATTAAAT
***
435090 AATATTTATTTTAAAATAATTAAAT
1 AATATTTAAACTAAAATAATTAAAT
*
435115 AAGATTT
1 AATATTT
435122 TAATTAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (25 bp):
AATATTTAAACTAAAATAATTAAAT
Found at i:438125 original size:140 final size:140
Alignment explanation
Indices: 437873--438153 Score: 553
Period size: 140 Copynumber: 2.0 Consensus size: 140
437863 GAATAGTAGC
437873 AAAGCCTAAGGGTAATGGCAAGCCCAAACCTAAAGGAAAGGATGCACTGAAACCCAAAGGGGGAG
1 AAAGCCTAAGGGTAATGGCAAGCCCAAACCTAAAGGAAAGGATGCACTGAAACCCAAAGGGGGAG
*
437938 TTAGCAAGGAATGAAAAAAAATTGATTGCGAAAGAACCAGACACTGGAAAAGAAAATGTATTATT
66 TTAGCAAGGAAGGAAAAAAAATTGATTGCGAAAGAACCAGACACTGGAAAAGAAAATGTATTATT
438003 TAGCTTGAAG
131 TAGCTTGAAG
438013 AAAGCCTAAGGGTAATGGCAAGCCCAAACCTAAAGGAAAGGATGCACTGAAACCCAAAGGGGGAG
1 AAAGCCTAAGGGTAATGGCAAGCCCAAACCTAAAGGAAAGGATGCACTGAAACCCAAAGGGGGAG
438078 TTAGCAAGGAAGGAAAAAAAATTGATTGCGAAAGAACCAGACACTGGAAAAGAAAATGTATTATT
66 TTAGCAAGGAAGGAAAAAAAATTGATTGCGAAAGAACCAGACACTGGAAAAGAAAATGTATTATT
438143 TAGCTTGAAG
131 TAGCTTGAAG
438153 A
1 A
438154 GGTCAAGAAG
Statistics
Matches: 140, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.44, C:0.14, G:0.25, T:0.16
Consensus pattern (140 bp):
AAAGCCTAAGGGTAATGGCAAGCCCAAACCTAAAGGAAAGGATGCACTGAAACCCAAAGGGGGAG
TTAGCAAGGAAGGAAAAAAAATTGATTGCGAAAGAACCAGACACTGGAAAAGAAAATGTATTATT
TAGCTTGAAG
Found at i:442295 original size:26 final size:26
Alignment explanation
Indices: 442266--442324 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
442256 TAAATGAATA
*
442266 TTTAATTCATAATAACTAAATAAGAT
1 TTTAATTCAAAATAACTAAATAAGAT
* **
442292 TTTATTTCAAAATATTTAAATAAGAT
1 TTTAATTCAAAATAACTAAATAAGAT
442318 TTTAATT
1 TTTAATT
442325 AATTCAGAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (26 bp):
TTTAATTCAAAATAACTAAATAAGAT
Found at i:444023 original size:19 final size:19
Alignment explanation
Indices: 443976--444016 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
443966 ATTAAAAACA
443976 AAACATGATGATATGTAAC
1 AAACATGATGATATGTAAC
443995 AAACATGATGATATGTAAC
1 AAACATGATGATATGTAAC
444014 AAA
1 AAA
444017 TGTGATGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.24
Consensus pattern (19 bp):
AAACATGATGATATGTAAC
Found at i:444411 original size:2 final size:2
Alignment explanation
Indices: 444404--444439 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
444394 CAAAACATTA
444404 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
444440 CTTATCTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:444479 original size:12 final size:12
Alignment explanation
Indices: 444450--444486 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
444440 CTTATCTATT
* *
444450 TATCTATCTATC
1 TATCTCTCTCTC
444462 TATCTCTCTCTC
1 TATCTCTCTCTC
444474 TATCTCTCTCTC
1 TATCTCTCTCTC
444486 T
1 T
444487 CCATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.14, C:0.35, G:0.00, T:0.51
Consensus pattern (12 bp):
TATCTCTCTCTC
Found at i:444483 original size:16 final size:16
Alignment explanation
Indices: 444442--444487 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
444432 ATATATATCT
* * *
444442 TATCTATTTATCTATC
1 TATCTATCTCTCTCTC
444458 TATCTATCTCTCTCTC
1 TATCTATCTCTCTCTC
*
444474 TATCTCTCTCTCTC
1 TATCTATCTCTCTC
444488 CATATATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.15, C:0.33, G:0.00, T:0.52
Consensus pattern (16 bp):
TATCTATCTCTCTCTC
Found at i:447590 original size:23 final size:23
Alignment explanation
Indices: 447564--447610 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
447554 AAGATGTGGG
447564 TCTATTTAACAATTTTGAAAAGT
1 TCTATTTAACAATTTTGAAAAGT
447587 TCTATTTAACAATTTTGAAAAGT
1 TCTATTTAACAATTTTGAAAAGT
447610 T
1 T
447611 ATGGGGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.45
Consensus pattern (23 bp):
TCTATTTAACAATTTTGAAAAGT
Found at i:447698 original size:19 final size:20
Alignment explanation
Indices: 447655--447700 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
447645 TGATATGCTG
* *
447655 GAAATTTATGTTAGAGTGTT
1 GAAATTGATGTTAGAATGTT
447675 GAAATTGATGTTAGAATG-T
1 GAAATTGATGTTAGAATGTT
447694 GAAATTG
1 GAAATTG
447701 GTTATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.39
Consensus pattern (20 bp):
GAAATTGATGTTAGAATGTT
Found at i:455751 original size:22 final size:21
Alignment explanation
Indices: 455714--455754 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
455704 CCATCTCCAT
455714 TTCATCATCAACACCATCATC
1 TTCATCATCAACACCATCATC
*
455735 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
455755 ATTCCGCAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.37, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACCATCATC
Found at i:456142 original size:27 final size:26
Alignment explanation
Indices: 456087--456143 Score: 71
Period size: 29 Copynumber: 2.1 Consensus size: 26
456077 AGAAAAGACA
*
456087 AAAAGAAAAAAATTTCAGAAAATGAAG
1 AAAAGAAAAAAATTTCAAAAAAT-AAG
456114 AAAAGAAAAGAAAATTTCAAAAAAT-AG
1 AAAAG-AAA-AAAATTTCAAAAAATAAG
456141 AAA
1 AAA
456144 GCAAGCCAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 10 0.37
28 3 0.11
29 14 0.52
ACGTcount: A:0.70, C:0.04, G:0.12, T:0.14
Consensus pattern (26 bp):
AAAAGAAAAAAATTTCAAAAAATAAG
Found at i:467463 original size:12 final size:13
Alignment explanation
Indices: 467437--467466 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
467427 CTTTCATCTT
467437 TTTAATTCTTTAA
1 TTTAATTCTTTAA
467450 TTTAATTC-TTAA
1 TTTAATTCTTTAA
467462 TTTAA
1 TTTAA
467467 ATAGTAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTAATTCTTTAA
Found at i:472704 original size:2 final size:2
Alignment explanation
Indices: 472692--472768 Score: 131
Period size: 2 Copynumber: 39.5 Consensus size: 2
472682 TTTTCAATTA
*
472692 TG TG TG CG TG TG TG TG TG TG TG TG TG TG TG TG TG T- TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
472733 TG TG TG TG TG TG TG -G TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
472769 TTAACATAAA
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
1 2 0.03
2 69 0.97
ACGTcount: A:0.00, C:0.01, G:0.49, T:0.49
Consensus pattern (2 bp):
TG
Found at i:479105 original size:55 final size:55
Alignment explanation
Indices: 478732--479110 Score: 449
Period size: 55 Copynumber: 6.9 Consensus size: 55
478722 ATATACGGAA
* * * ** * * *
478732 ATTCATCAACTCACGATGAATTCCATGGGT-TGCACATATAGTGCCTGTACGGTG
1 ATTCATCAACCCATGATGAATTCCGTGAATATGCACACAAAGTGCTTGTACGGTG
* * * * * * ** *
478786 ATTCATCAACTCATGATGAATTCCATGAGTTTTCACACAAAGTTCTTGTACATTA
1 ATTCATCAACCCATGATGAATTCCGTGAATATGCACACAAAGTGCTTGTACGGTG
* *
478841 ACTT-ATCAACCCATGATGAATTCCGTGAATTTGCACACAAAATG-TCTGTACGGTG
1 A-TTCATCAACCCATGATGAATTCCGTGAATATGCACACAAAGTGCT-TGTACGGTG
*
478896 ATTCATCAACCCATGATGAATTCCGTGAATATGCACACAAAGTGCTTATACGGTG
1 ATTCATCAACCCATGATGAATTCCGTGAATATGCACACAAAGTGCTTGTACGGTG
* * * * *
478951 ATTCATCAACCTATGATGAATTACGTGAATATGCACACAAAGTGCCTATACAGTG
1 ATTCATCAACCCATGATGAATTCCGTGAATATGCACACAAAGTGCTTGTACGGTG
* *
479006 ATTCATCAACACATGATGAATTCAGTGAATATGCACACAAAGTGCTTGTACGGTG
1 ATTCATCAACCCATGATGAATTCCGTGAATATGCACACAAAGTGCTTGTACGGTG
* * *
479061 ATTCATCGACCCATGATGAATTTCGTGAATATGCACACAAAGTGCATGTA
1 ATTCATCAACCCATGATGAATTCCGTGAATATGCACACAAAGTGCTTGTA
479111 GTACACATAG
Statistics
Matches: 282, Mismatches: 38, Indels: 9
0.86 0.12 0.03
Matches are distributed among these distances:
54 31 0.11
55 248 0.88
56 3 0.01
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (55 bp):
ATTCATCAACCCATGATGAATTCCGTGAATATGCACACAAAGTGCTTGTACGGTG
Found at i:479144 original size:2 final size:2
Alignment explanation
Indices: 479139--479198 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
479129 TATCAATGCA
479139 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
479181 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
479199 TCACTTACCT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:479537 original size:63 final size:61
Alignment explanation
Indices: 479445--479565 Score: 188
Period size: 63 Copynumber: 2.0 Consensus size: 61
479435 TGGCTCCATA
*
479445 GTATCGATACTACTACCATGGTACCGATACCCCCTTCCGGTGTCGATACCAAAATTAGTTG
1 GTATCGATACTACTACCATGGTACCGATACCCCCTTCCGGTATCGATACCAAAATTAGTTG
* * *
479506 GTATCGATACTACCATACTATGGTACCGATACCCCCTTCTGGTATCGATATCAAAATTAG
1 GTATCGATACTA-C-TACCATGGTACCGATACCCCCTTCCGGTATCGATACCAAAATTAG
479566 ATTTGATGTC
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
61 12 0.22
62 1 0.02
63 41 0.76
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (61 bp):
GTATCGATACTACTACCATGGTACCGATACCCCCTTCCGGTATCGATACCAAAATTAGTTG
Found at i:483030 original size:15 final size:15
Alignment explanation
Indices: 482998--483031 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
482988 AATTGTTTCG
* *
482998 GCTTGGGCGTTCGTA
1 GCTTGGGCGTCCGCA
483013 GCTTGGGCGTCCGCA
1 GCTTGGGCGTCCGCA
483028 GCTT
1 GCTT
483032 AGGCAAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.26, G:0.38, T:0.29
Consensus pattern (15 bp):
GCTTGGGCGTCCGCA
Found at i:487104 original size:2 final size:2
Alignment explanation
Indices: 487097--487141 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
487087 AATACGTCTT
487097 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
487139 TA T
1 TA T
487142 TATGCTCGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:487517 original size:23 final size:22
Alignment explanation
Indices: 487487--487529 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
487477 GCAGCTAAAG
487487 TTGGTTAGGGTTAAGGTTTTGTT
1 TTGGTTAGGG-TAAGGTTTTGTT
*
487510 TTGGTTAGGGTATGGTTTTG
1 TTGGTTAGGGTAAGGTTTTG
487530 GGTTTGGGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.12, C:0.00, G:0.37, T:0.51
Consensus pattern (22 bp):
TTGGTTAGGGTAAGGTTTTGTT
Found at i:487535 original size:23 final size:23
Alignment explanation
Indices: 487487--487536 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
487477 GCAGCTAAAG
*
487487 TTGGTTAGGGTTAAGGTTTTGTT
1 TTGGTTAGGGTTAAGGTTTTGGT
*
487510 TTGGTTAGGG-TATGGTTTTGGGT
1 TTGGTTAGGGTTAAGGTTTT-GGT
487533 TTGG
1 TTGG
487537 GCCTGTAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.10, C:0.00, G:0.40, T:0.50
Consensus pattern (23 bp):
TTGGTTAGGGTTAAGGTTTTGGT
Found at i:488103 original size:41 final size:41
Alignment explanation
Indices: 488058--488151 Score: 102
Period size: 42 Copynumber: 2.3 Consensus size: 41
488048 ATGGATTGCT
* *
488058 CGAAGGACTT-GTCATCTTGCTTGAAAGACTTA-TAGATGACC
1 CGAAGGACTTAG-CATCATGCTCGAAAGACTTACT-GATGACC
* *
488099 CGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCC
1 CGAAGGACTT-AGCATCATGCTCGAAAGACTTACTGATGACC
*
488141 CAAAGGACTTA
1 CGAAGGACTTA
488152 CTTATCAAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
41 10 0.23
42 32 0.73
43 2 0.05
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (41 bp):
CGAAGGACTTAGCATCATGCTCGAAAGACTTACTGATGACC
Found at i:488221 original size:38 final size:40
Alignment explanation
Indices: 488148--488228 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 40
488138 GCCCAAAGGA
*
488148 CTTACTTATCAAGAAACCCGTGAAAATCAAGCTTAG-TTT
1 CTTACTTATCAAGAAACCCCTGAAAATCAAGCTTAGCTTT
* * * *
488187 CTTAGTTATCAAGGAACCCCT-AAAATTAGGCTTAGCTTT
1 CTTACTTATCAAGAAACCCCTGAAAATCAAGCTTAGCTTT
488226 CTT
1 CTT
488229 TTTTTTAAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
38 12 0.33
39 24 0.67
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (40 bp):
CTTACTTATCAAGAAACCCCTGAAAATCAAGCTTAGCTTT
Found at i:488540 original size:275 final size:274
Alignment explanation
Indices: 488045--488563 Score: 770
Period size: 275 Copynumber: 1.9 Consensus size: 274
488035 GCCCTAATGC
* * * * * *
488045 CTTATGGATTGCTCGAAGGACTTGTCATCTTGCTTGAAAGACTTATAGATGACCCGAAGGATTTA
1 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAAATGACCCAAAGGATTTA
*
488110 AGCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACTTATCAAGAAACCCGTGAAAAT
66 AGCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACTCATCAAGAAACCCGTGAAAAT
* ***
488175 CAAGCTTAGTTTCTTAGTTATCAAGGAACCCCTAAAATTAGGCTTAGCTTTCTTTTTTTTAAACT
131 CAAGCTTAGTTTCTTAGTTATCAAGGAACCCCTAAAATTAGGCTTAGCTTTCCTTTTAAAAAACT
* * * *
488240 CTTTGGAGATAATCATCAAGAAACCCCTGAAAATTAGGCTTAATTTCTAAAACTCATTTGAAATC
196 CATTGAAAATAATAATCAAGAAACCCCTGAAAA-TAGGCTTAATTTCTAAAACTCATTTGAAATC
488305 ATTCTACCCGAAGGT
260 ATTCTACCCGAAGGT
*
488320 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAGAGACTTATAAATGACCCAAAGGATTTA
1 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAAATGACCCAAAGGATTTA
* * * * *
488385 AGCATCATGCTCGAAAGATTTACTGATTGCCCTAAGGACTTACTCATTAAGAAACCCTTGAAAAT
66 AGCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACTCATCAAGAAACCCGTGAAAAT
* * *
488450 CAAGCTTAGTTTCTTAGTTGTCAAGTAACCCCTAAAAATTAGGCTTAG-TTTCCTTTTAAAAAAT
131 CAAGCTTAGTTTCTTAGTTATCAAGGAACCCCT-AAAATTAGGCTTAGCTTTCCTTTTAAAAAAC
* * *
488514 TCATTGAAAATCATAATCAGGAAACCCCTGAAAATAGGCTTAGTTTCTAA
195 TCATTGAAAATAATAATCAAGAAACCCCTGAAAATAGGCTTAATTTCTAA
488564 GTTGTTAATG
Statistics
Matches: 216, Mismatches: 27, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
274 15 0.07
275 187 0.87
276 14 0.06
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31
Consensus pattern (274 bp):
CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAAATGACCCAAAGGATTTA
AGCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACTCATCAAGAAACCCGTGAAAAT
CAAGCTTAGTTTCTTAGTTATCAAGGAACCCCTAAAATTAGGCTTAGCTTTCCTTTTAAAAAACT
CATTGAAAATAATAATCAAGAAACCCCTGAAAATAGGCTTAATTTCTAAAACTCATTTGAAATCA
TTCTACCCGAAGGT
Found at i:488695 original size:99 final size:98
Alignment explanation
Indices: 488428--488858 Score: 634
Period size: 98 Copynumber: 4.4 Consensus size: 98
488418 AAGGACTTAC
* * * *
488428 TCATTAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTGTCAAGTAACCCCTAAAAATTAGG
1 TCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTAAAAATTAGG
* *
488493 CTTAGTTTCCTTTTAAAAAATTCATTGAAAATCA
66 CTTAGCTTCCTTTT-AAAAACTCATTGAAAATCA
* * * * *
488527 TAATCAGGAAACCCCTGAAAAT-AGGCTTAGTTTCTAAGTTGTTAATGAACCCCTAAAAATTAGG
1 TCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTAAAAATTAGG
* *
488591 CTTAGCTTCCTTTGAAAAACTCATTGAAAATCT
66 CTTAGCTTCCTTTTAAAAACTCATTGAAAATCA
* * *
488624 TCATCACA-AAACCCCTGAAACTCAGGCTTAGTTTTTTTAGTTGTCAAGGAACCCCTAAATATTA
1 TCATCA-AGAAACCCCTGAAAATCAGGCTTAG-TTTCTTAGTTGTCAAGGAACCCCTAAAAATTA
488688 GGCTTAGCTTCCTTTTAAAAACTCATTGAAAATCA
64 GGCTTAGCTTCCTTTTAAAAACTCATTGAAAATCA
*
488723 TCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTAGTTGTCAAAGAACCCCTAAAAATTAGG
1 TCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTAAAAATTAGG
*
488788 CTTAGC-TCCTTTTAAAAACTCATTGAAAATAA
66 CTTAGCTTCCTTTTAAAAACTCATTGAAAATCA
*
488820 TCATCAAGAAACCCCTGAAAAATCATGCTTAGTTTCTTA
1 TCATCAAGAAACCCCTG-AAAATCAGGCTTAGTTTCTTA
488859 AAAACTCATT
Statistics
Matches: 298, Mismatches: 29, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
97 77 0.26
98 115 0.39
99 106 0.36
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (98 bp):
TCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTAAAAATTAGG
CTTAGCTTCCTTTTAAAAACTCATTGAAAATCA
Found at i:488888 original size:54 final size:55
Alignment explanation
Indices: 488771--488910 Score: 169
Period size: 53 Copynumber: 2.5 Consensus size: 55
488761 GTTGTCAAAG
* *
488771 AACCCCTAAAAATTAGGCTTAGCTCCTTTTAAAAACTCATTGAAAATAATCATCAAGA
1 AACCCCTAAAAATCAGGCTTAGCT--TCTTAAAAACTCATTG-AAATAATCATCAAGA
* *
488829 AACCCCTGAAAAATCATGCTTAGTTTCTTAAAAACTCATTTG-AA-AA-CATCAAGA
1 AACCCCT-AAAAATCAGGCTTAGCTTCTTAAAAACTCA-TTGAAATAATCATCAAGA
*
488883 AACCCCTAAAAATTAGGCTTAGCTTCTT
1 AACCCCTAAAAATCAGGCTTAGCTTCTT
488911 TTGAAAATTG
Statistics
Matches: 73, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
53 18 0.25
54 15 0.21
55 2 0.03
56 2 0.03
57 12 0.16
58 10 0.14
59 14 0.19
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (55 bp):
AACCCCTAAAAATCAGGCTTAGCTTCTTAAAAACTCATTGAAATAATCATCAAGA
Found at i:490261 original size:31 final size:31
Alignment explanation
Indices: 490226--490286 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
490216 ATGTCGTACG
*
490226 ATAAAACTACCCGAATAAAATTATGTTTTTA
1 ATAAAACTACCCAAATAAAATTATGTTTTTA
*
490257 ATAAAACTACCCAAATAAAGTTATGTTTTT
1 ATAAAACTACCCAAATAAAATTATGTTTTT
490287 TAATTTGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (31 bp):
ATAAAACTACCCAAATAAAATTATGTTTTTA
Found at i:494549 original size:15 final size:14
Alignment explanation
Indices: 494513--494551 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
494503 AATATAATTG
494513 ATATTTTATTTTAA
1 ATATTTTATTTTAA
*
494527 ATAATTTATCTTTAA
1 ATATTTTAT-TTTAA
*
494542 ATTTTTTATT
1 ATATTTTATT
494552 AATTTATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (14 bp):
ATATTTTATTTTAA
Found at i:495747 original size:16 final size:16
Alignment explanation
Indices: 495722--495759 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
495712 CACACCAAAC
495722 TAATAAATTATTAAAT
1 TAATAAATTATTAAAT
*
495738 TAATATATTATTAAAT
1 TAATAAATTATTAAAT
495754 TAATAA
1 TAATAA
495760 TTTAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATAAATTATTAAAT
Found at i:495753 original size:24 final size:24
Alignment explanation
Indices: 495725--495770 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
495715 ACCAAACTAA
*
495725 TAAATTATTAAATTAATATATTAT
1 TAAATTAATAAATTAATATATTAT
*
495749 TAAATTAATAATTTAATATATT
1 TAAATTAATAAATTAATATATT
495771 TCTTATTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TAAATTAATAAATTAATATATTAT
Found at i:495764 original size:8 final size:8
Alignment explanation
Indices: 495722--495766 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
495712 CACACCAAAC
495722 TAATAAAT
1 TAATAAAT
*
495730 TATTAAAT
1 TAATAAAT
*
495738 TAATATAT
1 TAATAAAT
*
495746 TATTAAAT
1 TAATAAAT
*
495754 TAATAATT
1 TAATAAAT
495762 TAATA
1 TAATA
495767 TATTTCTTAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
TAATAAAT
Found at i:496266 original size:60 final size:60
Alignment explanation
Indices: 496169--496345 Score: 318
Period size: 60 Copynumber: 3.0 Consensus size: 60
496159 CCCTCTTGAT
496169 AACAAGATAACAACAGCCATCCTCTCGTGCAATAGCCTTAAATCAGCTCAATTGAATTAG
1 AACAAGATAACAACAGCCATCCTCTCGTGCAATAGCCTTAAATCAGCTCAATTGAATTAG
* * *
496229 AGCAAGATAACAAAAGCCATCCTCTCGTGCAAAAGCCTTAAATCAGCTCAATTGAATTAG
1 AACAAGATAACAACAGCCATCCTCTCGTGCAATAGCCTTAAATCAGCTCAATTGAATTAG
*
496289 AACAAGATAACAACAGCCATCCTCTCGTGCAATAGCTTTAAATCAGCTCAATTGAAT
1 AACAAGATAACAACAGCCATCCTCTCGTGCAATAGCCTTAAATCAGCTCAATTGAAT
496346 CAAAACGGAA
Statistics
Matches: 110, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 110 1.00
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.23
Consensus pattern (60 bp):
AACAAGATAACAACAGCCATCCTCTCGTGCAATAGCCTTAAATCAGCTCAATTGAATTAG
Found at i:496641 original size:24 final size:21
Alignment explanation
Indices: 496614--496664 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 21
496604 TCCTTATCTT
496614 AAAAATTAAAGTTTTTCTATAGA
1 AAAAATTAAAGTTTTT-TA-AGA
*
496637 GAAAAATTGAAGTTTTTTAAGA
1 -AAAAATTAAAGTTTTTTAAGA
496659 AAAAAT
1 AAAAAT
496665 AAATATAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 6 0.23
22 3 0.12
23 2 0.08
24 15 0.58
ACGTcount: A:0.51, C:0.02, G:0.12, T:0.35
Consensus pattern (21 bp):
AAAAATTAAAGTTTTTTAAGA
Found at i:498172 original size:36 final size:35
Alignment explanation
Indices: 498071--498176 Score: 106
Period size: 36 Copynumber: 2.9 Consensus size: 35
498061 TCTTAGGTCC
* * * * *
498071 ATAAGAAATTACCAGCTGATTTGTGCTGAACCT-AT
1 ATAAGGAATTACCAGTTGA-TCGTGTTGAACCTGAA
* *
498106 ATAAGGAATTACCAGCTTGATCATAATTGAACCTGAA
1 ATAAGGAATTACCAG-TTGATCGT-GTTGAACCTGAA
498143 ATAAGGAATTACCAGTTGATCGGTGTTGAACCTG
1 ATAAGGAATTACCAGTTGATC-GTGTTGAACCTG
498177 TATAAACAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
35 16 0.28
36 25 0.43
37 17 0.29
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (35 bp):
ATAAGGAATTACCAGTTGATCGTGTTGAACCTGAA
Found at i:498188 original size:72 final size:72
Alignment explanation
Indices: 498071--498212 Score: 185
Period size: 72 Copynumber: 2.0 Consensus size: 72
498061 TCTTAGGTCC
** ** * *
498071 ATAAGAAATTACCAGCTGATTTGTGCTGAACCTATATAAGGAATTACCAGCTTGATCATAATTGA
1 ATAAGAAATTACCAGCTGATCGGTGCTGAACCTATATAAACAATTACCAGCTTGATCAGAACTGA
498136 ACCTGAA
66 ACCTGAA
* * * * *
498143 ATAAGGAATTACCAGTTGATCGGTGTTGAACCTGTATAAACAATTATCAGCTTGATCAGAACTGA
1 ATAAGAAATTACCAGCTGATCGGTGCTGAACCTATATAAACAATTACCAGCTTGATCAGAACTGA
498208 ACCTG
66 ACCTG
498213 TAGAGACTTC
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
72 59 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (72 bp):
ATAAGAAATTACCAGCTGATCGGTGCTGAACCTATATAAACAATTACCAGCTTGATCAGAACTGA
ACCTGAA
Found at i:498209 original size:36 final size:36
Alignment explanation
Indices: 498096--498214 Score: 123
Period size: 36 Copynumber: 3.3 Consensus size: 36
498086 CTGATTTGTG
* *
498096 CTGAACCTATATAAGGAATTACCAGCTTGATCATAA
1 CTGAACCTGTATAAGGAATTACCAGCTTGATCAGAA
* * * **
498132 TTGAACCTGAAATAAGGAATTACCAG-TTGATCGGTG
1 CTGAACCTG-TATAAGGAATTACCAGCTTGATCAGAA
* ** *
498168 TTGAACCTGTATAAACAATTATCAGCTTGATCAGAA
1 CTGAACCTGTATAAGGAATTACCAGCTTGATCAGAA
498204 CTGAACCTGTA
1 CTGAACCTGTA
498215 GAGACTTCAT
Statistics
Matches: 66, Mismatches: 15, Indels: 4
0.78 0.18 0.05
Matches are distributed among these distances:
35 12 0.18
36 39 0.59
37 15 0.23
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (36 bp):
CTGAACCTGTATAAGGAATTACCAGCTTGATCAGAA
Found at i:502452 original size:42 final size:41
Alignment explanation
Indices: 502371--502471 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 41
502361 AGGTTTTATG
* * * *
502371 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACA
1 GATGGCCCGAAGGACTTAGCATCATGCTCAAAAGACTTACA
* * *
502412 GATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACT
1 GATGGCCCGAAGGACTT-AGCATCATGCTCAAAAGACTTACA
502454 GATGGCCCGAAGGACTTA
1 GATGGCCCGAAGGACTTA
502472 TAAATTGTGA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 16 0.32
42 34 0.68
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTAGCATCATGCTCAAAAGACTTACA
Found at i:502873 original size:214 final size:215
Alignment explanation
Indices: 501776--503102 Score: 2169
Period size: 214 Copynumber: 6.2 Consensus size: 215
501766 CAACACTCTT
* * *
501776 CCGAAGGATTTAAACACCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAC
1 CCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAA
* * *
501841 ATTTTGAAAATCATATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATTA-TTTTTCATTTT
66 ATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTTCATTTC
* * *
501905 CAAATTCTTGTGAAAATATCCTACCCGAAGGTTTTATGGATGGCCCCAAGGACTTATCATCTTGC
131 CAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTGC
* *
501970 TTTAAAGGCTCACAGATGAC
196 TCTAAAGGCTTACAGATGAC
* * *
501990 CCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGGCCAAAGCACTTATAAATTGTGAA
1 CCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAA
*
502055 ATTTTGAAAATCACATTCTTCGTTTTCAAAAATTTCATCTTCTTAAAACATCATTTTTTCATTTT
66 ATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTTCA-TTT
* *
502120 TCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATAGATGGCCCGAAGGACTTATCATCTTG
130 CCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTG
502185 CTCTAAAGGCTTACAGATGAC
195 CTCTAAAGGCTTACAGATGAC
* * *
502206 CCGAAGAATTTAAGCATCACGCTCAAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAA
1 CCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAA
* * *
502271 ATTTTG-AAATCACATTCTT-GTTTTCAAAAATTCCATCTTCTTAAGACATCA-TTTTCCATTTT
66 ATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTTCATTTC
* *
502333 CAAATTCATTTGAAAATATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTGC
131 CAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTGC
502398 TCTAAAGGCTTACAGATGAC
196 TCTAAAGGCTTACAGATGAC
*
502418 CCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAA
1 CCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAA
*
502483 ATTTTGAAAATCACATTCTTCATTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTTTCATTT
66 ATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCA-TTTTTTCATTT
* * * * *
502548 CCAAATTCATGTGAAAACGTCCTACCTGAAGGTCTTATAGATGGCCCGAATGACTTATCATCTTG
130 CCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTG
*
502613 CTCTAAAGGCTTACAGATGAT
195 CTCTAAAGGCTTACAGATGAC
*
502634 CCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTAATGGCCCGAAGGACTTATAAATTGTGAA
1 CCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAA
**
502699 ATTTTGAAAATTGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTT-ATTTC
66 ATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTTCATTTC
*
502763 CAAATTCATGTGAAAATATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTGC
131 CAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTGC
502828 TCTAAAGGCTTACAGATGAC
196 TCTAAAGGCTTACAGATGAC
* * * *
502848 CCGAAGGATTTATGCATCATGCTCGAAAGACTTACTGATAGCCCGAATGACTTATAAATTATGAA
1 CCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAA
** *
502913 ATTTTGAAAATCGTATTCTTTGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTTCATTTC
66 ATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTTCATTTC
* * *
502978 CAAATTCATGTGAAAACGTCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTCC
131 CAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTGC
503043 TCTAAAGGCTTACAGATGAC
196 TCTAAAGGCTTACAGATGAC
*
503063 CCGAAGGATTTAAGCATCATGCTCGAAAGACTTAATGATG
1 CCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATG
503103 TGTTTTCTTC
Statistics
Matches: 1038, Mismatches: 68, Indels: 13
0.93 0.06 0.01
Matches are distributed among these distances:
212 155 0.15
213 19 0.02
214 368 0.35
215 149 0.14
216 347 0.33
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (215 bp):
CCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAA
ATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTTCATTTC
CAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTGC
TCTAAAGGCTTACAGATGAC
Found at i:502882 original size:42 final size:41
Alignment explanation
Indices: 502801--502902 Score: 116
Period size: 42 Copynumber: 2.5 Consensus size: 41
502791 AGGTTTTATG
* * * *
502801 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACA
1 GATGACCCGAAGGACTTATCATCATGCTCGAAAGACTTACA
* *
502842 GATGACCCGAAGGATTTATGCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGACTTAT-CATCATGCTCGAAAGACTTACA
*
502884 GAT-AGCCCGAATGACTTAT
1 GATGA-CCCGAAGGACTTAT
502903 AAATTATGAA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
41 18 0.35
42 33 0.65
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (41 bp):
GATGACCCGAAGGACTTATCATCATGCTCGAAAGACTTACA
Found at i:503156 original size:34 final size:35
Alignment explanation
Indices: 503118--503282 Score: 140
Period size: 37 Copynumber: 4.6 Consensus size: 35
503108 TCTTCTATAT
*
503118 TCTTCTGTGAAGGCTTAAGGTGG-TGCTTCACTAC
1 TCTTCTGTGAAGGCTTAAGATGGTTGCTTCACTAC
* * * *
503152 TCTTCGGTGAAGGTTTAAGATGGTTTGTTTCACTCC
1 TCTTCTGTGAAGGCTTAAGATGG-TTGCTTCACTAC
*
503188 TCTT-TGGTGAAGGCTTAAGATTGATTTGCTTCACT-C
1 TCTTCT-GTGAAGGCTTAAGA-TG-GTTGCTTCACTAC
* *
503224 -CTTCTTGGTGAAGGCTTAAGATTGATTTGCTTCACTCC
1 TCTTC-T-GTGAAGGCTTAAGA-TG-GTTGCTTCACTAC
* *
503262 TTTTCGGTGAAGGCTTAAGAT
1 TCTTCTGTGAAGGCTTAAGAT
503283 TGACTTTGCT
Statistics
Matches: 111, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
34 20 0.18
35 3 0.03
36 28 0.25
37 56 0.50
38 1 0.01
39 3 0.03
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (35 bp):
TCTTCTGTGAAGGCTTAAGATGGTTGCTTCACTAC
Found at i:503232 original size:37 final size:37
Alignment explanation
Indices: 503141--503292 Score: 218
Period size: 37 Copynumber: 4.1 Consensus size: 37
503131 CTTAAGGTGG
* * *
503141 TGCTTCACTACTCTTCGGTGAAGGTTTAAGA-TGGTT
1 TGCTTCACTCCTCTTCGGTGAAGGCTTAAGATTGATT
* *
503177 TGTTTCACTCCTCTTTGGTGAAGGCTTAAGATTGATT
1 TGCTTCACTCCTCTTCGGTGAAGGCTTAAGATTGATT
503214 TGCTTCACTCCTTCTT-GGTGAAGGCTTAAGATTGATT
1 TGCTTCACTCC-TCTTCGGTGAAGGCTTAAGATTGATT
*
503251 TGCTTCACTCCTTTTCGGTGAAGGCTTAAGATTGACTT
1 TGCTTCACTCCTCTTCGGTGAAGGCTTAAGATTGA-TT
503289 TGCT
1 TGCT
503293 CCAATCTCAT
Statistics
Matches: 105, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
36 30 0.29
37 65 0.62
38 10 0.10
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.41
Consensus pattern (37 bp):
TGCTTCACTCCTCTTCGGTGAAGGCTTAAGATTGATT
Found at i:505233 original size:2 final size:2
Alignment explanation
Indices: 505222--505259 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
505212 ATTGTATACC
505222 AT AT -T AT AT AT AT AT AT AT AT AT -T 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
505260 TGTTGGGTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:505246 original size:19 final size:19
Alignment explanation
Indices: 505222--505259 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
505212 ATTGTATACC
505222 ATATTATATATATATATAT
1 ATATTATATATATATATAT
505241 ATATTATATATATATATAT
1 ATATTATATATATATATAT
505260 TGTTGGGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATTATATATATATATAT
Found at i:507366 original size:6 final size:6
Alignment explanation
Indices: 507348--507396 Score: 73
Period size: 6 Copynumber: 8.2 Consensus size: 6
507338 AAATAAATAC
*
507348 ATGCAA A-GCAA ATGCAA ATGCAA ATGCAA ATGCTAA ATGCAA ATACAA
1 ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA ATGC-AA ATGCAA ATGCAA
507396 A
1 A
507397 AGGTGTCATT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
5 5 0.12
6 29 0.73
7 6 0.15
ACGTcount: A:0.53, C:0.16, G:0.14, T:0.16
Consensus pattern (6 bp):
ATGCAA
Found at i:507387 original size:19 final size:18
Alignment explanation
Indices: 507348--507396 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
507338 AAATAAATAC
507348 ATGCAAA-GCAAATGCAA
1 ATGCAAATGCAAATGCAA
507365 ATGCAAATGCAAATGCTAA
1 ATGCAAATGCAAATGC-AA
*
507384 ATGCAAATACAAA
1 ATGCAAATGCAAA
507397 AGGTGTCATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 7 0.24
18 8 0.28
19 14 0.48
ACGTcount: A:0.53, C:0.16, G:0.14, T:0.16
Consensus pattern (18 bp):
ATGCAAATGCAAATGCAA
Found at i:510385 original size:23 final size:23
Alignment explanation
Indices: 510359--510425 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
510349 CCACAGCTCA
510359 TATAATTGCACCGAAGTGCCACG
1 TATAATTGCACCGAAGTGCCACG
* * *
510382 TATAATTGCACTGGAGTGCCGCG
1 TATAATTGCACCGAAGTGCCACG
* *
510405 TAGAATTGTACC-ATAGTGCCA
1 TATAATTGCACCGA-AGTGCCA
510426 TATAATAATG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.25
Consensus pattern (23 bp):
TATAATTGCACCGAAGTGCCACG
Found at i:510605 original size:101 final size:102
Alignment explanation
Indices: 510444--510656 Score: 367
Period size: 101 Copynumber: 2.1 Consensus size: 102
510434 TGTCCATAAA
* *
510444 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAA-CATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
510509 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
65 TTCACACATGTTCCAAAGAATACATATATGTCCCGAA-G
*
510548 GACCACATATCATTCCTTAAG-A-ATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACT
1 GACCACATATCATTCCTTAAGAACATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACT
510611 TCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAG
510648 GACCACATA
1 GACCACATA
510657 GACCCTCGAC
Statistics
Matches: 106, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
100 10 0.09
101 74 0.70
103 1 0.01
104 21 0.20
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (102 bp):
GACCACATATCATTCCTTAAGAACATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACT
TCACACATGTTCCAAAGAATACATATATGTCCCGAAG
Found at i:511819 original size:64 final size:63
Alignment explanation
Indices: 511667--511828 Score: 159
Period size: 64 Copynumber: 2.5 Consensus size: 63
511657 TTCCCTATCG
* ** ** *
511667 GTGCATCGATGCACTACCTGTGCATC-AGTGCATAAAATACATTCGATGTTTGTTTATTACTGG
1 GTGCATCGATGCACTACTTGTGCATCGA-TGCACCAAATACATTCGATGTTTGTTTATTAAAGA
* * * *
511730 GATGCATCGATGCA-TGCCTTATGCATCGATGCACCAATTGCATTCGATGTTT-TTATATTAAAA
1 G-TGCATCGATGCACT-ACTTGTGCATCGATGCACCAAATACATTCGATGTTTGTT-TATT-AAA
511793 GA
62 GA
*
511795 GTGCATCGATGCACTACTTGTGCATCGATACACC
1 GTGCATCGATGCACTACTTGTGCATCGATGCACC
511829 TTCAAACAAT
Statistics
Matches: 80, Mismatches: 13, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
63 4 0.05
64 71 0.89
65 5 0.06
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACTTGTGCATCGATGCACCAAATACATTCGATGTTTGTTTATTAAAGA
Found at i:521427 original size:144 final size:144
Alignment explanation
Indices: 521114--521694 Score: 837
Period size: 144 Copynumber: 4.0 Consensus size: 144
521104 TAGAAAAGTC
* * * *
521114 AACTTTTTAGTGGCCAATTAATTATCTTCACCAGATTTTGAGTGATATATCAACTCATTTCAACA
1 AACTTTTCAGTGGCCAATTAATTATCTTCAACAGCTTTTCAGTGATATATCAACTCATTTCAACA
* * *
521179 AATTTTTCAATGCTGATATATCAC-TCATATCACAAAAAATGTACATTTCTCATAGGCAAAATAA
66 AACTTTTCAGTGCTGATATATCACTTCATATCACAAAAAATGTGCATTTCTCATAGGCAAAATAA
521243 TGCACCATGGCAAG-
131 TGCACCATGG-AAGA
* * * *
521257 AACTTTTTAGTGGCCAATTAATTATCTTTAGCAGCTTTTCAGGGATATATCAACTCATTTCAACA
1 AACTTTTCAGTGGCCAATTAATTATCTTCAACAGCTTTTCAGTGATATATCAACTCATTTCAACA
* * *
521322 AACTTTTCAGTGCTGATACATCACTTCATATCACAAAAAATGTGTATTTCTCATAAGCAAAATAA
66 AACTTTTCAGTGCTGATATATCACTTCATATCACAAAAAATGTGCATTTCTCATAGGCAAAATAA
521387 TGCACCATGGAAGA
131 TGCACCATGGAAGA
* * *
521401 AACTTTTCAGTGGCCAATTAATTATCTTCAACAGCTTTTCAATGATAAATCAACTCATTTCAGCA
1 AACTTTTCAGTGGCCAATTAATTATCTTCAACAGCTTTTCAGTGATATATCAACTCATTTCAACA
*
521466 AACTTTTCAGTGCTGATATATCACTTCATATCACAAAAAATGTGCATTTCTCATAGGTAAAATAA
66 AACTTTTCAGTGCTGATATATCACTTCATATCACAAAAAATGTGCATTTCTCATAGGCAAAATAA
**
521531 TGCAGTAT-GACAGA
131 TGCACCATGGA-AGA
* * * *
521545 AACTTTTCAGTGGACAATTAATTATCTTCAACAACTTTTCAGTGATATATCAACTCATTTTAGCA
1 AACTTTTCAGTGGCCAATTAATTATCTTCAACAGCTTTTCAGTGATATATCAACTCATTTCAACA
* * * *
521610 AACTTTTCAGTGTTGATATATCACTTCATATCAC-AAAAACGTCCATTTCTCATATGCAAAATAA
66 AACTTTTCAGTGCTGATATATCACTTCATATCACAAAAAATGTGCATTTCTCATAGGCAAAATAA
* * *
521674 TGCATCATGGCATA
131 TGCACCATGGAAGA
521688 AACTTTT
1 AACTTTT
521695 TAGTTCACAA
Statistics
Matches: 396, Mismatches: 38, Indels: 8
0.90 0.09 0.02
Matches are distributed among these distances:
143 127 0.32
144 269 0.68
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (144 bp):
AACTTTTCAGTGGCCAATTAATTATCTTCAACAGCTTTTCAGTGATATATCAACTCATTTCAACA
AACTTTTCAGTGCTGATATATCACTTCATATCACAAAAAATGTGCATTTCTCATAGGCAAAATAA
TGCACCATGGAAGA
Found at i:528936 original size:20 final size:21
Alignment explanation
Indices: 528911--528950 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
528901 CTCAACATAG
528911 TAGTATCGATACCAT-AGGCT
1 TAGTATCGATACCATCAGGCT
528931 TAGTATCGATACCATCAGGC
1 TAGTATCGATACCATCAGGC
528951 CCAACGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.28
Consensus pattern (21 bp):
TAGTATCGATACCATCAGGCT
Found at i:540724 original size:15 final size:16
Alignment explanation
Indices: 540704--540746 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
540694 GTTTACTTCA
*
540704 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
540719 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
540735 GAATGATTCAAA
1 GAATGATTCAAA
540747 GGTAGCTCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.28
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:540737 original size:16 final size:16
Alignment explanation
Indices: 540716--540746 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
540706 ATGATTAAGC
540716 GCTGAATGATTCAAAT
1 GCTGAATGATTCAAAT
540732 GCTGAATGATTCAAA
1 GCTGAATGATTCAAA
540747 GGTAGCTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (16 bp):
GCTGAATGATTCAAAT
Found at i:546645 original size:46 final size:45
Alignment explanation
Indices: 546555--546651 Score: 113
Period size: 46 Copynumber: 2.1 Consensus size: 45
546545 GTGCTGTTGC
* * * * ***
546555 GAAAGTGAAATCGCAACGGGAATTTTAATTCTGTGTTTTTAAATT
1 GAAATTGAAATCGCAACGCGAAGTTTAATTATGTGTTGCGAAATT
546600 GAAATTGAAATTCGCAACGCGAAGTTTAATTATGTGTTGCGAAATT
1 GAAATTGAAA-TCGCAACGCGAAGTTTAATTATGTGTTGCGAAATT
*
546646 TAAATT
1 GAAATT
546652 CGCGTTGCGA
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
45 9 0.21
46 34 0.79
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.36
Consensus pattern (45 bp):
GAAATTGAAATCGCAACGCGAAGTTTAATTATGTGTTGCGAAATT
Found at i:546658 original size:20 final size:21
Alignment explanation
Indices: 546635--546722 Score: 69
Period size: 20 Copynumber: 4.4 Consensus size: 21
546625 TTAATTATGT
546635 GTTGCGAAATTTA-AATTCGC
1 GTTGCGAAATTTAGAATTCGC
* * *
546655 GTTGCG-AATTTGGAA-ACTGT
1 GTTGCGAAATTTAGAATTC-GC
* *
546675 GTTACGAAA-TTAGAGTTCGC
1 GTTGCGAAATTTAGAATTCGC
*
546695 GTTGCG-AATTTAGAGTTCGC
1 GTTGCGAAATTTAGAATTCGC
*
546715 GTTACGAA
1 GTTGCGAA
546723 TTTGTTGGTT
Statistics
Matches: 52, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
19 8 0.15
20 40 0.77
21 4 0.08
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (21 bp):
GTTGCGAAATTTAGAATTCGC
Found at i:546723 original size:20 final size:20
Alignment explanation
Indices: 546675--546725 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
546665 TGGAAACTGT
*
546675 GTTACGAAATTAGAGTTCGC
1 GTTACGAATTTAGAGTTCGC
*
546695 GTTGCGAATTTAGAGTTCGC
1 GTTACGAATTTAGAGTTCGC
546715 GTTACGAATTT
1 GTTACGAATTT
546726 GTTGGTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.35
Consensus pattern (20 bp):
GTTACGAATTTAGAGTTCGC
Found at i:555697 original size:13 final size:13
Alignment explanation
Indices: 555679--555703 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
555669 TAAAGTGAAC
555679 ATTTTTAACAAAT
1 ATTTTTAACAAAT
555692 ATTTTTAACAAA
1 ATTTTTAACAAA
555704 AATGTTATGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTTTTAACAAAT
Found at i:558629 original size:28 final size:28
Alignment explanation
Indices: 558596--558662 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
558586 AATGTATTGA
*
558596 TTGTAAAAATAT-GAGTTGTTATTG-CAT
1 TTGTAAAAATATGGA-TTGTTATTGTAAT
558623 TGTGTAAAAATATGGATTGTTATTGTAAT
1 T-TGTAAAAATATGGATTGTTATTGTAAT
558652 TTGTAAAAATA
1 TTGTAAAAATA
558663 ATATGCCATT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
27 1 0.03
28 30 0.83
29 5 0.14
ACGTcount: A:0.37, C:0.01, G:0.18, T:0.43
Consensus pattern (28 bp):
TTGTAAAAATATGGATTGTTATTGTAAT
Found at i:558675 original size:29 final size:29
Alignment explanation
Indices: 558642--558833 Score: 126
Period size: 29 Copynumber: 6.7 Consensus size: 29
558632 ATATGGATTG
* *
558642 TTATTGTAATTTGTAAAAATAATATGCCA
1 TTATTGTAATTTATAAAAATAATATGTCA
*
558671 TTATTGTAATTTATAATAAGAT-TTAT-TC-
1 TTATTGTAATTTATAA-AA-ATAATATGTCA
** * *
558699 TCTATTCCAATTTATAAAAAT-ATTTGTCT
1 T-TATTGTAATTTATAAAAATAATATGTCA
* * * *
558728 TCTATTGTACTTTGTAAAAAGAATATGACA
1 T-TATTGTAATTTATAAAAATAATATGTCA
* *
558758 TTATTGTAATTTATAAAAAAAATAT-TCT
1 TTATTGTAATTTATAAAAATAATATGTCA
** * * *
558786 TTATTCCAATTTATAAAAGT-ATTTGTCT
1 TTATTGTAATTTATAAAAATAATATGTCA
*
558814 TCTATTGTATTTTATAAAAA
1 T-TATTGTAATTTATAAAAA
558834 AAATTATCCT
Statistics
Matches: 126, Mismatches: 29, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
27 7 0.06
28 26 0.21
29 80 0.63
30 11 0.09
31 2 0.02
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (29 bp):
TTATTGTAATTTATAAAAATAATATGTCA
Found at i:558803 original size:86 final size:87
Alignment explanation
Indices: 558643--558833 Score: 285
Period size: 86 Copynumber: 2.2 Consensus size: 87
558633 TATGGATTGT
* * * **
558643 TATTGTAATTTGTAAAAATAATATGCCATTATTGTAATTTATAATAAGATTTATTCTCTATTCCA
1 TATTGTAATTTGTAAAAAGAATATGACATTATTGTAATTTATAATAAAAAATATTCTCTATTCCA
558708 ATTTATAAAAATATTTGTCTTC
66 ATTTATAAAAATATTTGTCTTC
* *
558730 TATTGTACTTTGTAAAAAGAATATGACATTATTGTAATTTATAA-AAAAAATATTCTTTATTCCA
1 TATTGTAATTTGTAAAAAGAATATGACATTATTGTAATTTATAATAAAAAATATTCTCTATTCCA
*
558794 ATTTATAAAAGTATTTGTCTTC
66 ATTTATAAAAATATTTGTCTTC
* *
558816 TATTGTATTTTATAAAAA
1 TATTGTAATTTGTAAAAA
558834 AAATTATCCT
Statistics
Matches: 94, Mismatches: 10, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
86 53 0.56
87 41 0.44
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (87 bp):
TATTGTAATTTGTAAAAAGAATATGACATTATTGTAATTTATAATAAAAAATATTCTCTATTCCA
ATTTATAAAAATATTTGTCTTC
Found at i:558876 original size:86 final size:85
Alignment explanation
Indices: 558643--558861 Score: 233
Period size: 86 Copynumber: 2.5 Consensus size: 85
558633 TATGGATTGT
* * * ** * ** *
558643 TATTGTAATTTGTAAAAATAATATGCCATTATTGTAATTTATAATAAGATTTATTCTCTATTCCA
1 TATTGTAATTTATAAAAAAAATAT-ACATTATTGTAATAAATAA-AAAAAATATTCTTTATTCCA
*
558708 ATTTATAAAAATATTTGTCTTC
64 ATTTATAAAAGTATTTGTCTTC
* * * **
558730 TATTGTACTTTGTAAAAAGAATATGACATTATTGTAATTTATAAAAAAAATATTCTTTATTCCAA
1 TATTGTAATTTATAAAAAAAATAT-ACATTATTGTAATAAATAAAAAAAATATTCTTTATTCCAA
558795 TTTATAAAAGTATTTGTCTTC
65 TTTATAAAAGTATTTGTCTTC
* *
558816 TATTGTATTTTATAAAAAAAAT-TATCCTCTATTGTAATAAATAAAA
1 TATTGTAATTTATAAAAAAAATATA-CAT-TATTGTAATAAATAAAA
558862 GGTTTATCTA
Statistics
Matches: 116, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
84 1 0.01
85 3 0.03
86 71 0.61
87 41 0.35
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (85 bp):
TATTGTAATTTATAAAAAAAATATACATTATTGTAATAAATAAAAAAAATATTCTTTATTCCAAT
TTATAAAAGTATTTGTCTTC
Found at i:558877 original size:57 final size:57
Alignment explanation
Indices: 558757--558886 Score: 138
Period size: 57 Copynumber: 2.3 Consensus size: 57
558747 AGAATATGAC
* * ** *
558757 ATTATTGTAATTTATAAAAAAAATATTCTTTATTCCAATTTATAAAAGTATTTGTCT
1 ATTATTGTAATTTATAAAAAAAATATCCTCTATTCCAATAAATAAAAGTATTTATCT
* ** *
558814 -TCTATTGTATTTTATAAAAAAAATTATCCTCTATTGTAATAAATAAAAG-GTTTATCT
1 AT-TATTGTAATTTATAAAAAAAA-TATCCTCTATTCCAATAAATAAAAGTATTTATCT
*
558871 ATTATTGTAACTTATA
1 ATTATTGTAATTTATA
558887 CAAAGTTTTG
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
56 1 0.02
57 38 0.64
58 20 0.34
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (57 bp):
ATTATTGTAATTTATAAAAAAAATATCCTCTATTCCAATAAATAAAAGTATTTATCT
Found at i:560359 original size:6 final size:5
Alignment explanation
Indices: 560351--560441 Score: 83
Period size: 6 Copynumber: 16.2 Consensus size: 5
560341 TTCCGGGTTA
560351 TTATT ATTATT ATTATT ATTATT TTCATT TTCATT TTCATT TTCATT TTCATT
1 TTATT -TTATT -TTATT -TTATT TT-ATT TT-ATT TT-ATT TT-ATT TT-ATT
*
560404 TTATT TTATT TTATT TTATTT TTATT ACTATT TTATT T
1 TTATT TTATT TTATT TTA-TT TTATT -TTATT TTATT T
560442 ACAAGCCTTA
Statistics
Matches: 80, Mismatches: 2, Indels: 7
0.90 0.02 0.08
Matches are distributed among these distances:
5 25 0.31
6 55 0.69
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (5 bp):
TTATT
Found at i:560896 original size:26 final size:28
Alignment explanation
Indices: 560867--560919 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
560857 ACCCAGAGGA
560867 GGATCT-AAAAAGA-AGAAGAAAAAAAG
1 GGATCTAAAAAAGAGAGAAGAAAAAAAG
560893 GGATCTGAAAAAAGAGAGAAGAAAAAA
1 GGATCT-AAAAAAGAGAGAAGAAAAAA
560920 GACCCAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 6 0.25
28 7 0.29
29 11 0.46
ACGTcount: A:0.64, C:0.04, G:0.25, T:0.08
Consensus pattern (28 bp):
GGATCTAAAAAAGAGAGAAGAAAAAAAG
Found at i:561859 original size:19 final size:19
Alignment explanation
Indices: 561835--561877 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
561825 TTAGCGTATG
561835 TTGTTTAGCTACCATGTTT
1 TTGTTTAGCTACCATGTTT
561854 TTGTTTAGCTACCATGTTT
1 TTGTTTAGCTACCATGTTT
561873 TTGTT
1 TTGTT
561878 GGTCATTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.14, C:0.14, G:0.16, T:0.56
Consensus pattern (19 bp):
TTGTTTAGCTACCATGTTT
Found at i:562205 original size:12 final size:11
Alignment explanation
Indices: 562188--562232 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
562178 TTTGCTTTCG
562188 ATAATTTATAAA
1 ATAATTTAT-AA
*
562200 ATAATTTATAT
1 ATAATTTATAA
*
562211 ATTATTT-TAA
1 ATAATTTATAA
562221 ATAATTTATAA
1 ATAATTTATAA
562232 A
1 A
562233 GTGTAACCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
10 8 0.29
11 11 0.39
12 9 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
ATAATTTATAA
Found at i:568612 original size:23 final size:22
Alignment explanation
Indices: 568582--568657 Score: 73
Period size: 23 Copynumber: 3.4 Consensus size: 22
568572 TGAAGTCCTA
568582 AAAAAAGAGAAAACAACAAAAAG
1 AAAAAAGAGAAAA-AACAAAAAG
* *
568605 AAAAAAGA-ACAGAAAATAAAAAC
1 AAAAAAGAGA-A-AAAACAAAAAG
**
568628 AAAAAAGAGAAAAAAGGAAAAG
1 AAAAAAGAGAAAAAACAAAAAG
*
568650 AAGAAAGA
1 AAAAAAGA
568658 AAATAAATCA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
22 16 0.36
23 25 0.57
24 3 0.07
ACGTcount: A:0.78, C:0.05, G:0.16, T:0.01
Consensus pattern (22 bp):
AAAAAAGAGAAAAAACAAAAAG
Found at i:568642 original size:16 final size:16
Alignment explanation
Indices: 568583--568640 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
568573 GAAGTCCTAA
568583 AAAAAGAGAAAACAAC
1 AAAAAGAGAAAACAAC
* *
568599 AAAAAGAAAAAAGAAC
1 AAAAAGAGAAAACAAC
*
568615 AGAAAATA-AAAAC-A-
1 A-AAAAGAGAAAACAAC
568629 AAAAAGAGAAAA
1 AAAAAGAGAAAA
568641 AAGGAAAAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 5 0.14
14 5 0.14
15 1 0.03
16 19 0.54
17 5 0.14
ACGTcount: A:0.79, C:0.07, G:0.12, T:0.02
Consensus pattern (16 bp):
AAAAAGAGAAAACAAC
Found at i:571137 original size:241 final size:237
Alignment explanation
Indices: 570761--571706 Score: 745
Period size: 241 Copynumber: 3.9 Consensus size: 237
570751 AGTAAGTTCT
* * * * ** *
570761 TCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTAATCTATAAGCCTTTAAAGTAAGAC
1 TCAGTAAGTCTTTCGAGCATAAGGCCTAAATCCTTCGGGTCATCTATAAGCCTTTCGAGTAAGAT
* * * *
570826 GATAAGTCCTTCGGGCCATCCATAATACCTTCAGGAAGGATGTATTCACATGATTTTTGAAAATC
66 GATAAGTCCTTCGGGCCATCCATAAGACCTTC-GGAAGGATGTTTTCACATGATATTTGAAAAAC
** *
570891 GAGAAAGCGATTTCCAAAGTTTCTCATTTA-AACCTTTTCTGAAAATTGATTTTTGTTGAAAAGT
130 GAGAAAGCGATTTCCAAAGTTTCTCATTTAGAA--TTTTCTGAAAA-TGAAATTT-TTGAAAAAT
* * *
570955 GAGAAAATGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTTGGGCCA
191 AAGAAAACGATTTCCAAAGTTTCTTACCTAGTAAGTCCTTTGGGCCA
* *
571002 TCAGTAAGTCTTTCGAGCATAATGCCTAAATCTTTCGGGTCATCTATAAGCCTTTCGAGTAAGAT
1 TCAGTAAGTCTTTCGAGCATAAGGCCTAAATCCTTCGGGTCATCTATAAGCCTTTCGAGTAAGAT
* * * * *
571067 GATAAGTCCTTTGGGCCATCTATAAGACCTTCGGACATGATGCTTTCATATGATAATTTG-AAAA
66 GATAAGTCCTTCGGGCCATCCATAAGACCTTCGGA-AGGATGTTTTCACATGAT-ATTTGAAAAA
* * * *
571131 CGAGAAAGTGATTTTCAAAGTTTCTCTTTTAGTATTTT-TGAAAATTGAAATTTTTGAAAAATAA
129 CGAGAAAGCGATTTCCAAAGTTTCTCATTTAGAATTTTCTGAAAA-TGAAATTTTTGAAAAATAA
* * * **
571195 GTAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTACAAAATTGGTAATTCATTCAAGCCA
193 GAAAACGATTTCCAAAGTTTCTTACCTAGT--A--A-GT-C--CTTTGG------------GCCA
** * * *
571260 TCAGTAAGTCTTTCGAGCAT--GGATTAAA-CCATTCAGGTCATCTATTAGCCTTTCGAGTAAGG
1 TCAGTAAGTCTTTCGAGCATAAGGCCTAAATCC-TTCGGGTCATCTATAAGCCTTTCGAGTAAGA
* * * **
571322 TGATAAGTCCTTCGGGACATCTATAAGACCTTCGAGTAA-GATATTTTCATGTGATAATTTGAAA
65 TGATAAGTCCTTCGGGCCATCCATAAGACCTTCG-G-AAGGATGTTTTCACATGAT-ATTTGAAA
* * * **
571386 AATGAGAAGGCGATTTCTAAAGTTTCTCATTTA-AA---TC-----------TTTTCCAAAAAGT
127 AACGAGAAAGCGATTTCCAAAGTTTCTCATTTAGAATTTTCTGAAAATGAAATTTTTGAAAAA-T
* * * * * *
571436 GAGAAAACAATTGCCAAAGTTTCTTACTTAGTAAGTCCTTCT-AGCAA
191 AAGAAAACGATTTCCAAAGTTTCTTACCTAGTAAGTCCTT-TGGGCCA
* * * * *
571483 TCAATAAGTCTTTTGAGCATAAGGCCTAAATCCTTCGGGTCATCTATAAGCCTTTTGAGCATGAT
1 TCAGTAAGTCTTTCGAGCATAAGGCCTAAATCCTTCGGGTCATCTATAAGCCTTTCGAGTAAGAT
* * * * * *
571548 GATTAAGTCCTTCGAGCTATCCGTAAGACTTTTGGGCAGGATGTTTTCACATG--ATTTGAAAAA
66 GA-TAAGTCCTTCGGGCCATCCATAAGAC-CTTCGGAAGGATGTTTTCACATGATATTTGAAAAA
* ** * * *
571611 TGAGAAAGCGATTTTGAAAGTTTCTTATTTAGTATTTTCAGAAAATGAAATTTTTGAAAAATAAG
129 CGAGAAAGCGATTTCCAAAGTTTCTCATTTAGAATTTTCTGAAAATGAAATTTTTGAAAAATAAG
*
571676 AAAGCGATTTCCAAAGTTTCTTACCTAGTAA
194 AAAACGATTTCCAAAGTTTCTTACCTAGTAA
571707 ACTATTTACA
Statistics
Matches: 558, Mismatches: 96, Indels: 106
0.73 0.13 0.14
Matches are distributed among these distances:
223 58 0.10
224 1 0.00
225 35 0.06
226 35 0.06
227 5 0.01
235 1 0.00
236 1 0.00
237 31 0.06
238 45 0.08
239 14 0.03
240 8 0.01
241 133 0.24
242 15 0.03
243 28 0.05
244 1 0.00
246 4 0.01
253 1 0.00
255 1 0.00
256 85 0.15
257 31 0.06
258 25 0.04
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Consensus pattern (237 bp):
TCAGTAAGTCTTTCGAGCATAAGGCCTAAATCCTTCGGGTCATCTATAAGCCTTTCGAGTAAGAT
GATAAGTCCTTCGGGCCATCCATAAGACCTTCGGAAGGATGTTTTCACATGATATTTGAAAAACG
AGAAAGCGATTTCCAAAGTTTCTCATTTAGAATTTTCTGAAAATGAAATTTTTGAAAAATAAGAA
AACGATTTCCAAAGTTTCTTACCTAGTAAGTCCTTTGGGCCA
Found at i:571939 original size:3 final size:3
Alignment explanation
Indices: 571933--571957 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
571923 ATAATAAAAA
571933 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
571958 GTTTTCATTT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:572495 original size:27 final size:25
Alignment explanation
Indices: 572464--572530 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 25
572454 AAAGGGATCC
*
572464 GAAAAAAAGAGAAAAGAAAAAACCTA
1 GAAAAAAAGAGAAAAGAAAAAA-ATA
*
572490 GTAAAAAAAGAGTAGAACGAAAAAAATA
1 G-AAAAAAAGAG-A-AAAGAAAAAAATA
572518 GAAAAAAAGAGAA
1 GAAAAAAAGAGAA
572531 GCTTATTGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
25 1 0.03
26 2 0.06
27 20 0.56
28 4 0.11
29 9 0.25
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (25 bp):
GAAAAAAAGAGAAAAGAAAAAAATA
Found at i:575664 original size:33 final size:32
Alignment explanation
Indices: 575621--575687 Score: 98
Period size: 33 Copynumber: 2.1 Consensus size: 32
575611 TTTACAACTC
* *
575621 CCTAGTTTTTCACGGGCTAAACTAGAACCTTTT
1 CCTAGCTTTTCACGGGATAAACTAGAA-CTTTT
*
575654 CCTAGCTTTTCACGGGATCAACTAGAACTTTT
1 CCTAGCTTTTCACGGGATAAACTAGAACTTTT
575686 CC
1 CC
575688 CCTTTACAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 7 0.23
33 24 0.77
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.34
Consensus pattern (32 bp):
CCTAGCTTTTCACGGGATAAACTAGAACTTTT
Found at i:576116 original size:21 final size:22
Alignment explanation
Indices: 576092--576133 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
576082 AATTTGAACC
*
576092 TTCAT-GGGGTATTGATACCCT
1 TTCATAGGGGTATCGATACCCT
576113 TTCATAGGGGTATCGATACCC
1 TTCATAGGGGTATCGATACCC
576134 ATTAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.33
Consensus pattern (22 bp):
TTCATAGGGGTATCGATACCCT
Found at i:576153 original size:23 final size:22
Alignment explanation
Indices: 576099--576153 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
576089 ACCTTCATGG
* * *
576099 GGTATTGATACCCTTTCATAGG
1 GGTATTGATACCCATTAATAGA
* *
576121 GGTATCGATACCCATTAATAATA
1 GGTATTGATACCCATTAAT-AGA
576144 GGTATTGATA
1 GGTATTGATA
576154 GGGGTATTGG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.35
Consensus pattern (22 bp):
GGTATTGATACCCATTAATAGA
Found at i:576179 original size:22 final size:22
Alignment explanation
Indices: 576151--576204 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
576141 ATAGGTATTG
*
576151 ATAGGGGTATTGGTACCCATTC
1 ATAGGGGTATTGATACCCATTC
576173 ATAGGGGTATTGATACCCATTC
1 ATAGGGGTATTGATACCCATTC
576195 ATAGGGGTAT
1 ATAGGGGTAT
576205 CAGTACCTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (22 bp):
ATAGGGGTATTGATACCCATTC
Found at i:576211 original size:22 final size:21
Alignment explanation
Indices: 576151--576211 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 21
576141 ATAGGTATTG
*
576151 ATAGGGGTATTGGTACCCATTC
1 ATAGGGGTA-TAGTACCCATTC
*
576173 ATAGGGGTATTGATACCCATTC
1 ATAGGGGTATAG-TACCCATTC
576195 ATAGGGGTATCAGTACC
1 ATAGGGGTAT-AGTACC
576212 TCTTAATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 2 0.06
22 32 0.91
23 1 0.03
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (21 bp):
ATAGGGGTATAGTACCCATTC
Found at i:576471 original size:18 final size:18
Alignment explanation
Indices: 576424--576481 Score: 89
Period size: 18 Copynumber: 3.1 Consensus size: 18
576414 ATGTTTAATG
576424 AAAAAGATACCAATTGTTT
1 AAAAAGATACCAATTG-TT
576443 ACAAAAGGATACCAATTGTT
1 A-AAAA-GATACCAATTGTT
576463 AAAAAGATACCAATTGTT
1 AAAAAGATACCAATTGTT
576481 A
1 A
576482 CTAATTGTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 14 0.38
19 5 0.14
20 7 0.19
21 11 0.30
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (18 bp):
AAAAAGATACCAATTGTT
Found at i:579191 original size:33 final size:33
Alignment explanation
Indices: 579154--579223 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
579144 CCTTTACAAC
* *
579154 TCCCTAGTTTTTCATGGGATAAACTAGAACCTT
1 TCCCTAGCTTTTCACGGGATAAACTAGAACCTT
* *
579187 TCCCTAGCTTTTCACGGGATCACCTAGAACCTT
1 TCCCTAGCTTTTCACGGGATAAACTAGAACCTT
579220 TCCC
1 TCCC
579224 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.33
Consensus pattern (33 bp):
TCCCTAGCTTTTCACGGGATAAACTAGAACCTT
Found at i:579721 original size:22 final size:22
Alignment explanation
Indices: 579689--579757 Score: 129
Period size: 22 Copynumber: 3.1 Consensus size: 22
579679 GTATTGATAT
*
579689 GGGTATCGATACCCATTCATAG
1 GGGTATTGATACCCATTCATAG
579711 GGGTATTGATACCCATTCATAG
1 GGGTATTGATACCCATTCATAG
579733 GGGTATTGATACCCATTCATAG
1 GGGTATTGATACCCATTCATAG
579755 GGG
1 GGG
579758 CATCGGTACC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (22 bp):
GGGTATTGATACCCATTCATAG
Found at i:579721 original size:34 final size:35
Alignment explanation
Indices: 579654--579721 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
579644 CCTTTCATAG
*
579654 GGGTATCGGTACCCATTCATAAGAGGTATTGATAT
1 GGGTATCGATACCCATTCATAAGAGGTATTGATAT
*
579689 GGGTATCGATACCCATTCAT-AGGGGTATTGATA
1 GGGTATCGATACCCATTCATAAGAGGTATTGATA
579722 CCCATTCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 12 0.39
35 19 0.61
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (35 bp):
GGGTATCGATACCCATTCATAAGAGGTATTGATAT
Found at i:579727 original size:57 final size:57
Alignment explanation
Indices: 579629--579743 Score: 169
Period size: 57 Copynumber: 2.0 Consensus size: 57
579619 TTGAGCCTTC
* * *
579629 ATGGTGTATTGATACCCTTTCATAGGGGTATCGGTACCCATTCATAAGAGGTATTGAT
1 ATGGTGTATCGATACCCATTCATAGGGGTATCGATACCCATTCAT-AGAGGTATTGAT
* *
579687 ATGG-GTATCGATACCCATTCATAGGGGTATTGATACCCATTCATAGGGGTATTGAT
1 ATGGTGTATCGATACCCATTCATAGGGGTATCGATACCCATTCATAGAGGTATTGAT
579743 A
1 A
579744 CCCATTCATA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
56 12 0.23
57 36 0.69
58 4 0.08
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (57 bp):
ATGGTGTATCGATACCCATTCATAGGGGTATCGATACCCATTCATAGAGGTATTGAT
Done.