Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008336.1 Hibiscus syriacus cultivar Beakdansim tig00111053_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: 846240
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 2 of 4
Found at i:266541 original size:6 final size:6
Alignment explanation
Indices: 266530--266562 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
266520 ATTGGCTGAA
*
266530 CAAGGC CAAGGC CAAGGC CAAGGC CAAGCC CAA
1 CAAGGC CAAGGC CAAGGC CAAGGC CAAGGC CAA
266563 AGAAATAGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.36, C:0.36, G:0.27, T:0.00
Consensus pattern (6 bp):
CAAGGC
Found at i:267930 original size:20 final size:19
Alignment explanation
Indices: 267877--267933 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
267867 GAAAGTCAGA
267877 TTAAATATCAAATTTTAA-T
1 TTAAATAT-AAATTTTAATT
* * *
267896 TTAAAAATATTATTTTTATT
1 TTAAATATA-AATTTTAATT
267916 TTAAATTATAAATTTTAA
1 TTAAA-TATAAATTTTAA
267934 AAATCAAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
18 1 0.03
19 13 0.45
20 12 0.41
21 3 0.10
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TTAAATATAAATTTTAATT
Found at i:282417 original size:18 final size:19
Alignment explanation
Indices: 282394--282437 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
282384 ATCTGAAATT
282394 TTATTTTA-TAATTATATA
1 TTATTTTATTAATTATATA
*
282412 TTATTTAAATTAATTATATA
1 TTATTT-TATTAATTATATA
282432 TT-TTTT
1 TTATTTT
282438 TGAATTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 6 0.27
19 4 0.18
20 12 0.55
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATTTTATTAATTATATA
Found at i:283905 original size:45 final size:45
Alignment explanation
Indices: 283855--283940 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
283845 TACATCCAAC
* *
283855 TAGATGGTGACATGTGTCACCACCTTATTTGATAAGAAAAAAGCT
1 TAGATGGTGACACGTATCACCACCTTATTTGATAAGAAAAAAGCT
*
283900 TAGATGGTGACACGTATCACCACCTTATTTGATAATAAAAA
1 TAGATGGTGACACGTATCACCACCTTATTTGATAAGAAAAA
283941 GGCATGAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.29
Consensus pattern (45 bp):
TAGATGGTGACACGTATCACCACCTTATTTGATAAGAAAAAAGCT
Found at i:284215 original size:22 final size:24
Alignment explanation
Indices: 284166--284218 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
284156 ACTATATATT
*
284166 TTTTTATATAATCGTTAAATTAAC
1 TTTTTATATAATCATTAAATTAAC
*
284190 TTTTTATATAAT-ATTAAATTTA-
1 TTTTTATATAATCATTAAATTAAC
284212 TTTTTAT
1 TTTTTAT
284219 TTTAATCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 7 0.26
23 8 0.30
24 12 0.44
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (24 bp):
TTTTTATATAATCATTAAATTAAC
Found at i:284233 original size:23 final size:22
Alignment explanation
Indices: 284137--284233 Score: 74
Period size: 23 Copynumber: 4.3 Consensus size: 22
284127 ACTAAAATTA
*
284137 TATATTTATTTTTAAATTAA-C-
1 TATATTTATTTTTATA-TAATCT
284158 TATATATT-TTTTTATATAATCGT
1 TATAT-TTATTTTTATATAATC-T
* * *
284181 TAAATTAACTTTTTATATAATAT
1 TATATTTA-TTTTTATATAATCT
* *
284204 TAAATTTATTTTTATTTTAATCT
1 TATATTTATTTTTA-TATAATCT
284227 TATATTT
1 TATATTT
284234 TAAATTAATT
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
20 3 0.05
21 13 0.21
22 9 0.15
23 24 0.39
24 12 0.20
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (22 bp):
TATATTTATTTTTATATAATCT
Found at i:284746 original size:2 final size:2
Alignment explanation
Indices: 284735--284789 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
284725 AAAAATTAAC
284735 AT AT -T 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
284776 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
284790 TGTAAAATTT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:285435 original size:23 final size:23
Alignment explanation
Indices: 285375--285436 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
285365 AGAGCTTTGC
* * *
285375 AGAGAGTTTTACCATGAGATTGG
1 AGAGAGCTTTACCGTGAGACTGG
285398 AGAGAGCTTTACCGTGAGACTGG
1 AGAGAGCTTTACCGTGAGACTGG
*
285421 AGAGAGCTTTGCCGTG
1 AGAGAGCTTTACCGTG
285437 GGAGGGGGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.26, C:0.15, G:0.34, T:0.26
Consensus pattern (23 bp):
AGAGAGCTTTACCGTGAGACTGG
Found at i:285863 original size:15 final size:15
Alignment explanation
Indices: 285845--285882 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
285835 TCAATTTTAC
*
285845 ATATTTATTTTAATT
1 ATATTTAATTTAATT
*
285860 ATATTTAATTTAGTT
1 ATATTTAATTTAATT
285875 AT-TTTAAT
1 ATATTTAAT
285883 CTTTAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (15 bp):
ATATTTAATTTAATT
Found at i:288554 original size:19 final size:20
Alignment explanation
Indices: 288518--288559 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
288508 TCAAATTTAA
* **
288518 TTTAATTTTATCTTTTAT-T
1 TTTAATTATATCAATTATGT
288537 TTTAATTATATCAATTATGT
1 TTTAATTATATCAATTATGT
288557 TTT
1 TTT
288560 CGGACTCATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTAATTATATCAATTATGT
Found at i:292276 original size:21 final size:21
Alignment explanation
Indices: 292250--292289 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
292240 TCTGCTGAAA
*
292250 CTCCACCTGTTTTGGAGTATG
1 CTCCACCTGTTATGGAGTATG
292271 CTCCACCTGTTATGGAGTA
1 CTCCACCTGTTATGGAGTA
292290 CTACTTGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (21 bp):
CTCCACCTGTTATGGAGTATG
Found at i:294559 original size:21 final size:21
Alignment explanation
Indices: 294535--294579 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
294525 GAACCACCAG
294535 GATAACCTCAACTGAAGCTCT
1 GATAACCTCAACTGAAGCTCT
294556 GATAACCTCAACTGAAGCTCT
1 GATAACCTCAACTGAAGCTCT
294577 GAT
1 GAT
294580 GCCAAAGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (21 bp):
GATAACCTCAACTGAAGCTCT
Found at i:296685 original size:23 final size:25
Alignment explanation
Indices: 296650--296695 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
296640 TATATTTTAA
296650 TTAATTAATAA-TTT-AAATATAAT
1 TTAATTAATAATTTTAAAATATAAT
296673 TTAACTTAA-AATTTTAAAATATA
1 TTAA-TTAATAATTTTAAAATATA
296696 TAGATCAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TTAATTAATAATTTTAAAATATAAT
Found at i:296757 original size:2 final size:2
Alignment explanation
Indices: 296752--296804 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
296742 AAAAAACTTT
296752 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
296794 TA TA TA TA TA T
1 TA TA TA TA TA T
296805 TCACATGAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:296975 original size:32 final size:33
Alignment explanation
Indices: 296914--296976 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
296904 TTCTGACAAA
*
296914 TTGATTTTTTGTCAAAATTTAGAAGAGGAAAAAT
1 TTGATTTTTTG-CAAAATTTAGAAAAGGAAAAAT
*
296948 TTGATTTTTTG-AGAATTTAGAAAAGGAAA
1 TTGATTTTTTGCAAAATTTAGAAAAGGAAA
296977 GACAATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 16 0.59
34 11 0.41
ACGTcount: A:0.41, C:0.02, G:0.19, T:0.38
Consensus pattern (33 bp):
TTGATTTTTTGCAAAATTTAGAAAAGGAAAAAT
Found at i:297283 original size:2 final size:2
Alignment explanation
Indices: 297276--297444 Score: 66
Period size: 2 Copynumber: 85.5 Consensus size: 2
297266 ATTTTTAATG
*
297276 AT AT AT AT AT AT AT AT ACT -T AT AT AT AC AT AT ACT -T AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT
* * * * * * * *
297318 AT TT AT AT AC AT AC CT AT AT AT AG AT ACT -T TT AT AT AT GT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* * * * * * * *
297360 GT AT GT AT GT GT A- AT -T AT AC AT AT AG GT AT AGT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
*
297401 GT AT A- AGT AT AT AT AT AT AT AT AT AT AT AT A- AGT AT AT AT -T
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
297442 AT A
1 AT A
297445 ATGTATGCAT
Statistics
Matches: 124, Mismatches: 29, Indels: 28
0.69 0.16 0.15
Matches are distributed among these distances:
1 8 0.06
2 109 0.88
3 7 0.06
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (2 bp):
AT
Found at i:297300 original size:16 final size:16
Alignment explanation
Indices: 297279--297355 Score: 82
Period size: 16 Copynumber: 4.6 Consensus size: 16
297269 TTTAATGATA
297279 TATATATATATATACT
1 TATATATATATATACT
*
297295 TATATATACATATACT
1 TATATATATATATACT
*
297311 TATATATATTTATATACA
1 TATATATA--TATATACT
*
297329 TACCTATATATAGATACT
1 TA--TATATATATATACT
*
297347 TTTATATAT
1 TATATATAT
297356 GTGTGTATGT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
16 30 0.59
18 15 0.29
20 6 0.12
ACGTcount: A:0.42, C:0.09, G:0.01, T:0.48
Consensus pattern (16 bp):
TATATATATATATACT
Found at i:297417 original size:12 final size:13
Alignment explanation
Indices: 297397--297450 Score: 58
Period size: 12 Copynumber: 4.2 Consensus size: 13
297387 TATAGTATAC
*
297397 ATATGTATAA-GT
1 ATATATATAATGT
*
297409 ATATATATATATAT
1 ATATATATA-ATGT
297423 ATATATATAA-GT
1 ATATATATAATGT
297435 ATATATTATAATGT
1 ATATA-TATAATGT
297449 AT
1 AT
297451 GCATAACATT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
12 14 0.40
13 7 0.20
14 14 0.40
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (13 bp):
ATATATATAATGT
Found at i:297493 original size:23 final size:22
Alignment explanation
Indices: 297380--297510 Score: 86
Period size: 20 Copynumber: 6.2 Consensus size: 22
297370 GTAATTATAC
*
297380 ATATAGGTATAGTATACA-TAT
1 ATATAAGTATAGTATACATTAT
* *
297401 GTATAAGTATA-TATATA-TAT
1 ATATAAGTATAGTATACATTAT
*
297421 ATATATA-TATAAGTATATATTAT
1 ATATA-AGTAT-AGTATACATTAT
*
297444 A-AT--GTAT-GCATAACATTAT
1 ATATAAGTATAGTAT-ACATTAT
297463 ATAT--GTATA-TATACACTTAT
1 ATATAAGTATAGTATACA-TTAT
*
297483 GATATAAGTATAGTGTACATTAT
1 -ATATAAGTATAGTATACATTAT
297506 ATATA
1 ATATA
297511 CATGCATTAT
Statistics
Matches: 89, Mismatches: 8, Indels: 25
0.73 0.07 0.20
Matches are distributed among these distances:
18 3 0.03
19 10 0.11
20 30 0.34
21 15 0.17
22 13 0.15
23 13 0.15
24 5 0.06
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.42
Consensus pattern (22 bp):
ATATAAGTATAGTATACATTAT
Found at i:297803 original size:70 final size:69
Alignment explanation
Indices: 297711--297845 Score: 207
Period size: 70 Copynumber: 1.9 Consensus size: 69
297701 GTAATTTCAC
* * * *
297711 ATTTATTCAATTTAGTCCTTAAAATTATATTTGTATTTGAAATCGACTCATACTTATTTATATTT
1 ATTTATTCAATCTAGTCATTAAAATTATATTTGTATATGAAATCGACACATACTTATTTATATTT
297776 TGTA
66 TGTA
* *
297780 ATTTACTTCAATCTAGTCATTAAAATTATATTTGTATATGAAATTGGCACATACTTATTTATATT
1 ATTTA-TTCAATCTAGTCATTAAAATTATATTTGTATATGAAATCGACACATACTTATTTATATT
297845 T
65 T
297846 CGATTCGATG
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
69 5 0.08
70 54 0.92
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.49
Consensus pattern (69 bp):
ATTTATTCAATCTAGTCATTAAAATTATATTTGTATATGAAATCGACACATACTTATTTATATTT
TGTA
Found at i:301757 original size:2 final size:2
Alignment explanation
Indices: 301752--301785 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
301742 ATAATAACAC
301752 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
301786 CACATTAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:303592 original size:2 final size:2
Alignment explanation
Indices: 303585--303626 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
303575 ATTCTTAAGG
303585 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
303627 GTAACCATTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:310160 original size:23 final size:25
Alignment explanation
Indices: 310125--310170 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
310115 TATATTTTAA
310125 TTAATTAATAA-TTT-AAATATAAT
1 TTAATTAATAATTTTAAAATATAAT
310148 TTAACTTAA-AATTTTAAAATATA
1 TTAA-TTAATAATTTTAAAATATA
310171 TAGATCAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TTAATTAATAATTTTAAAATATAAT
Found at i:310741 original size:16 final size:16
Alignment explanation
Indices: 310722--310818 Score: 86
Period size: 16 Copynumber: 5.6 Consensus size: 16
310712 ATGATATATA
310722 TATATATATATATACT
1 TATATATATATATACT
*
310738 TATATATACATATACT
1 TATATATATATATACT
310754 TATATATTATACTTTATACT
1 TATATA-TATA---TATACT
*
310774 TATATATATTTATATACA
1 TATATATA--TATATACT
*
310792 TACCTATATATAGATACT
1 TA--TATATATATATACT
*
310810 TTTATATAT
1 TATATATAT
310819 GTGTGTATGT
Statistics
Matches: 67, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
16 28 0.42
17 3 0.04
18 14 0.21
19 2 0.03
20 18 0.27
21 2 0.03
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.49
Consensus pattern (16 bp):
TATATATATATATACT
Found at i:310903 original size:2 final size:2
Alignment explanation
Indices: 310715--310892 Score: 66
Period size: 2 Copynumber: 89.5 Consensus size: 2
310705 ATTTTTAATG
*
310715 AT AT AT AT AT AT AT AT AT AT ACT -T AT AT AT AC AT AT ACT -T AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT
* * * * *
310757 AT AT -T AT ACT TT AT ACT -T AT AT AT AT TT AT AT AC AT AC CT AT
1 AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * * *
310799 AT AT AG AT ACT -T TT AT AT AT GT GT GT AT GT AT GT GT A- AT -T
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
310839 AT AC AT AT AG GT AT AGT AT AC AT AT GT AT A- AGT AT AT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT
310882 AT AT AT AT AT A
1 AT AT AT AT AT A
310893 AAAGTATATA
Statistics
Matches: 130, Mismatches: 31, Indels: 30
0.68 0.16 0.16
Matches are distributed among these distances:
1 8 0.06
2 114 0.88
3 8 0.06
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.47
Consensus pattern (2 bp):
AT
Found at i:310957 original size:23 final size:22
Alignment explanation
Indices: 310843--310974 Score: 77
Period size: 20 Copynumber: 6.2 Consensus size: 22
310833 GTAATTATAC
*
310843 ATATAGGTATAGTATACA-TAT
1 ATATAAGTATAGTATACATTAT
* *
310864 GTATAAGTATA-TATATA-TAT
1 ATATAAGTATAGTATACATTAT
* *
310884 ATATATA-TAAAAGTATATATT-T
1 ATATA-AGT-ATAGTATACATTAT
* *
310906 ATA-ATGTAT-GCATAACATTAT
1 ATATAAGTATAGTAT-ACATTAT
310927 ATAT--GTATA-TATACACTTAT
1 ATATAAGTATAGTATACA-TTAT
*
310947 GATATAAGTATAGTGTACATTAT
1 -ATATAAGTATAGTATACATTAT
310970 ATATA
1 ATATA
310975 CATTCATTAT
Statistics
Matches: 86, Mismatches: 11, Indels: 27
0.69 0.09 0.22
Matches are distributed among these distances:
19 6 0.07
20 28 0.33
21 22 0.26
22 15 0.17
23 10 0.12
24 5 0.06
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.42
Consensus pattern (22 bp):
ATATAAGTATAGTATACATTAT
Found at i:310991 original size:23 final size:25
Alignment explanation
Indices: 310965--311022 Score: 68
Period size: 23 Copynumber: 2.4 Consensus size: 25
310955 TATAGTGTAC
*
310965 ATTAT-ATATACATTCATTAT-CAT
1 ATTATAATATACATTCATCATACAT
* *
310988 ATTATCATA-ACATTCATCATACGT
1 ATTATAATATACATTCATCATACAT
311012 ATTATAATATA
1 ATTATAATATA
311023 TATATATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 15 0.52
24 13 0.45
25 1 0.03
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (25 bp):
ATTATAATATACATTCATCATACAT
Found at i:311025 original size:2 final size:2
Alignment explanation
Indices: 311014--311048 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
311004 TCATACGTAT
311014 TA TA -A 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
311049 AAAATTGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:311718 original size:27 final size:27
Alignment explanation
Indices: 311688--311746 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
311678 TTGACCTGAG
311688 CTGAAATTAACCTTATCTGAACCCGAA
1 CTGAAATTAACCTTATCTGAACCCGAA
311715 CTGAAATTAACCTTATCTGAACCCGAA
1 CTGAAATTAACCTTATCTGAACCCGAA
311742 CTGAA
1 CTGAA
311747 TCTGATGGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.25
Consensus pattern (27 bp):
CTGAAATTAACCTTATCTGAACCCGAA
Found at i:315973 original size:23 final size:22
Alignment explanation
Indices: 315922--315973 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
315912 AATTTTTTTT
*
315922 TTCTTTGTGGCACGATTTTCTC
1 TTCTTTGTGACACGATTTTCTC
*
315944 TACCTTTGTGACAC-ATTTTCCGTC
1 T-TCTTTGTGACACGATTTT-C-TC
315968 TTCTTT
1 TTCTTT
315974 TTCAGTCGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
22 6 0.25
23 15 0.62
24 3 0.12
ACGTcount: A:0.12, C:0.25, G:0.13, T:0.50
Consensus pattern (22 bp):
TTCTTTGTGACACGATTTTCTC
Found at i:316684 original size:41 final size:41
Alignment explanation
Indices: 316639--316954 Score: 219
Period size: 41 Copynumber: 7.7 Consensus size: 41
316629 CAAATGCCAG
* * *
316639 TAAATACGCGTACTTTAGTAGCGTTTTTATATAAACGCCGC
1 TAAATACTCGTACTTTAGTGGCATTTTTATATAAACGCCGC
* * * **
316680 TAAATA-TTGTACTTTAGTGGCATTTTTGTACAAACGCATC
1 TAAATACTCGTACTTTAGTGGCATTTTTATATAAACGCCGC
* * * * ** *
316720 TAAAGACTCGTATTTTAGTGACATTTTT-TGAATAAATGTTGG
1 TAAATACTCGTACTTTAGTGGCATTTTTAT--ATAAACGCCGC
* *
316762 TAAATACTCGTACTTTAGTGGCATTTTTGTATAAACGCCGT
1 TAAATACTCGTACTTTAGTGGCATTTTTATATAAACGCCGC
* * * * *
316803 TAAAAACTCGTACTTTAGTGGCGTTTGTATATAAATGCCAC
1 TAAATACTCGTACTTTAGTGGCATTTTTATATAAACGCCGC
* * * * * * *
316844 TAAATACTCGTTCTTTAGTGGCGTTTTAAGCACAAATGCAGC
1 TAAATACTCGTACTTTAGTGGCATTTTTA-TATAAACGCCGC
** * * * * *
316886 TAAATA-TTATACTTTAATGGCATTTTT-TGAACAAATGTCGG
1 TAAATACTCGTACTTTAGTGGCATTTTTAT--ATAAACGCCGC
*
316927 TAAATACTCGTACTTTATTGGC-TTTTTA
1 TAAATACTCGTACTTTAGTGGCATTTTTA
316955 AGAACAAACG
Statistics
Matches: 213, Mismatches: 53, Indels: 17
0.75 0.19 0.06
Matches are distributed among these distances:
40 32 0.15
41 124 0.58
42 56 0.26
43 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (41 bp):
TAAATACTCGTACTTTAGTGGCATTTTTATATAAACGCCGC
Found at i:316786 original size:83 final size:83
Alignment explanation
Indices: 316680--316953 Score: 263
Period size: 83 Copynumber: 3.3 Consensus size: 83
316670 TAAACGCCGC
* * * *
316680 TAAATA-TTGTACTTTAGTGGCATTTTTGTACAAACGCATCTAAAGACTCGTATTTTAGTGACAT
1 TAAATACTCGTACTTTAGTGGCATTTTTGTACAAACGCATCTAAAAACTCGTACTTTAGTGGCAT
*
316744 TTTTTGAATAAATGTTGG
66 TTTTTGAATAAATGTCGG
* *
316762 TAAATACTCGTACTTTAGTGGCATTTTTGTATAAACGCCGT-TAAAAACTCGTACTTTAGTGGC-
1 TAAATACTCGTACTTTAGTGGCATTTTTGTACAAACG-CATCTAAAAACTCGTACTTTAGTGGCA
* * * **
316825 GTTTGT-ATATAAATGCCAC
65 TTTTTTGA-ATAAATGTCGG
* * * * * * * ** *
316844 TAAATACTCGTTCTTTAGTGGCGTTTTAAGCACAAATGCAGCTAAATA-TTATACTTTAATGGCA
1 TAAATACTCGTACTTTAGTGGCATTTT-TGTACAAACGCATCTAAAAACTCGTACTTTAGTGGCA
*
316908 TTTTTTGAACAAATGTCGG
65 TTTTTTGAATAAATGTCGG
*
316927 TAAATACTCGTACTTTATTGGC-TTTTT
1 TAAATACTCGTACTTTAGTGGCATTTTT
316954 AAGAACAAAC
Statistics
Matches: 152, Mismatches: 33, Indels: 15
0.76 0.17 0.08
Matches are distributed among these distances:
81 1 0.01
82 59 0.39
83 89 0.59
84 3 0.02
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (83 bp):
TAAATACTCGTACTTTAGTGGCATTTTTGTACAAACGCATCTAAAAACTCGTACTTTAGTGGCAT
TTTTTGAATAAATGTCGG
Found at i:316881 original size:124 final size:124
Alignment explanation
Indices: 316621--316948 Score: 299
Period size: 124 Copynumber: 2.7 Consensus size: 124
316611 TTTATCGGCG
* * * *
316621 TTTT-AGAACAAATGCCA-GTAAATACGCGTACTTTAGTAGCGTTTTTATATAAACGCCGCTAAA
1 TTTTAAGAACAAATG-CAGGTAAATACTCGTACTTTAGTGGCATTTTTGTATAAACGCCGCTAAA
* * *
316684 TA-TTGTACTTTAGTGGCATTTTTGTACAAACGCATCTAAAGACTCGTATTTTAGTGACA
65 TACTCGTACTTTAGTGGCATTTGTATACAAACGCATCTAAAGACTCGTATTTTAGTGACA
** * ** * *
316743 TTTTTTGAATAAATGTTGGTAAATACTCGTACTTTAGTGGCATTTTTGTATAAACGCCGTTAAAA
1 TTTTAAGAACAAATGCAGGTAAATACTCGTACTTTAGTGGCATTTTTGTATAAACGCCGCTAAAT
* * * * * *
316808 ACTCGTACTTTAGTGGCGTTTGTATATAAATGCCA-CTAAATACTCGT-TCTTTAGTGGCG
66 ACTCGTACTTTAGTGGCATTTGTATACAAACG-CATCTAAAGACTCGTAT-TTTAGTGACA
* * ** * * * * * *
316867 TTTTAAGCACAAATGCAGCTAAATA-TTATACTTTAATGGCATTTTTTGAACAAATGTCGGTAAA
1 TTTTAAGAACAAATGCAGGTAAATACTCGTACTTTAGTGGCA-TTTTTGTATAAACGCCGCTAAA
*
316931 TACTCGTACTTTATTGGC
65 TACTCGTACTTTAGTGGC
316949 TTTTTAAGAA
Statistics
Matches: 164, Mismatches: 36, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
122 4 0.02
123 64 0.39
124 94 0.57
125 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (124 bp):
TTTTAAGAACAAATGCAGGTAAATACTCGTACTTTAGTGGCATTTTTGTATAAACGCCGCTAAAT
ACTCGTACTTTAGTGGCATTTGTATACAAACGCATCTAAAGACTCGTATTTTAGTGACA
Found at i:316973 original size:42 final size:40
Alignment explanation
Indices: 316843--316983 Score: 122
Period size: 42 Copynumber: 3.4 Consensus size: 40
316833 ATAAATGCCA
* * * *
316843 CTAAATACTCGTTCTTTAGTGGCGTTTTAAGCACAAATGCAG
1 CTAAATA-TCGTACTTTAATGGCTTTTTAAGAACAAATGC-G
** *
316885 CTAAATATTATACTTTAATGGCATTTTT-TGAACAAATGTCG
1 CTAAATATCGTACTTTAATGGC-TTTTTAAGAACAAATG-CG
* * *
316926 GTAAATACTCGTACTTTATTGGCTTTTTAAGAACAAACGACG
1 CTAAATA-TCGTACTTTAATGGCTTTTTAAGAACAAATG-CG
*
316968 CTAAATATTGTACTTT
1 CTAAATATCGTACTTT
316984 GATGCTGAGG
Statistics
Matches: 79, Mismatches: 16, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
41 39 0.49
42 40 0.51
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.38
Consensus pattern (40 bp):
CTAAATATCGTACTTTAATGGCTTTTTAAGAACAAATGCG
Found at i:316981 original size:41 final size:40
Alignment explanation
Indices: 316856--316983 Score: 123
Period size: 41 Copynumber: 3.1 Consensus size: 40
316846 AATACTCGTT
* * * *
316856 CTTTAGTGGCGTTTTAAGCACAAATGCAGCTAAATATTATA
1 CTTTAATGGCTTTTTAAGAACAAATGC-GCTAAATATTGTA
* * *
316897 CTTTAATGGCATTTTT-TGAACAAATGTCGGTAAATACTCGTA
1 CTTTAATGGC-TTTTTAAGAACAAATG-CGCTAAATA-TTGTA
* *
316939 CTTTATTGGCTTTTTAAGAACAAACGACGCTAAATATTGTA
1 CTTTAATGGCTTTTTAAGAACAAATG-CGCTAAATATTGTA
316980 CTTT
1 CTTT
316984 GATGCTGAGG
Statistics
Matches: 70, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
41 37 0.53
42 33 0.47
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.38
Consensus pattern (40 bp):
CTTTAATGGCTTTTTAAGAACAAATGCGCTAAATATTGTA
Found at i:322065 original size:24 final size:24
Alignment explanation
Indices: 322038--322152 Score: 142
Period size: 24 Copynumber: 4.8 Consensus size: 24
322028 TTCGATTTGA
*
322038 ATTCTGATCTGATACTTAACATGG
1 ATTCTGATCTGATACTTGACATGG
* *
322062 ATTCTGATATGATATTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
322086 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
322110 ATTATGATCTGATACTTGATC-TAG
1 ATTCTGATCTGATACTTGA-CATGG
* *
322134 ATTTTGATATGATACTTGA
1 ATTCTGATCTGATACTTGA
322153 TCTGATTTAT
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
24 79 0.99
25 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:322131 original size:12 final size:12
Alignment explanation
Indices: 322114--322158 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
322104 ACTTGGATTA
322114 TGATCTGATACT
1 TGATCTGATACT
*
322126 TGATCTAGAT-TT
1 TGATCT-GATACT
*
322138 TGATATGATACT
1 TGATCTGATACT
322150 TGATCTGAT
1 TGATCTGAT
322159 TTATGTTTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
11 3 0.11
12 21 0.78
13 3 0.11
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.44
Consensus pattern (12 bp):
TGATCTGATACT
Found at i:323123 original size:65 final size:65
Alignment explanation
Indices: 323019--323143 Score: 250
Period size: 65 Copynumber: 1.9 Consensus size: 65
323009 AGTATGGGTT
323019 TTAACTTAGGAGTACAAATGTCACATTTACATCCCTACATACCATACAACACTCTCTCACGACTA
1 TTAACTTAGGAGTACAAATGTCACATTTACATCCCTACATACCATACAACACTCTCTCACGACTA
323084 TTAACTTAGGAGTACAAATGTCACATTTACATCCCTACATACCATACAACACTCTCTCAC
1 TTAACTTAGGAGTACAAATGTCACATTTACATCCCTACATACCATACAACACTCTCTCAC
323144 TGCTACAAGG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 60 1.00
ACGTcount: A:0.35, C:0.30, G:0.07, T:0.28
Consensus pattern (65 bp):
TTAACTTAGGAGTACAAATGTCACATTTACATCCCTACATACCATACAACACTCTCTCACGACTA
Found at i:323950 original size:45 final size:45
Alignment explanation
Indices: 323894--323979 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
323884 AAGGTTTATA
323894 AATAAATTATAGATAATATCTATACCAATATACAACTATAATGAT
1 AATAAATTATAGATAATATCTATACCAATATACAACTATAATGAT
* * *
323939 AATAAATTATAGATCATATTTATACCAATATGCAACTATAA
1 AATAAATTATAGATAATATCTATACCAATATACAACTATAA
323980 AAAATAGATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.34
Consensus pattern (45 bp):
AATAAATTATAGATAATATCTATACCAATATACAACTATAATGAT
Found at i:328088 original size:42 final size:41
Alignment explanation
Indices: 328042--328179 Score: 108
Period size: 42 Copynumber: 3.3 Consensus size: 41
328032 CGTTTTACAA
328042 AAAAACACCACTAAAGTTTTAGATAATTTGCGTCGTTTATAC
1 AAAAA-ACCACTAAAGTTTTAGATAATTTGCGTCGTTTATAC
* * * *
328084 AAAAAACCATTATA-TAATT-G-TCAA-TAGCGGT-GTTT-TAC
1 AAAAAACCACTAAAGT-TTTAGAT-AATTTGC-GTCGTTTATAC
*
328122 TATAAAAACGCCACTAAAGTTTTAGATAATTTGCGACGTTTATAC
1 -A-AAAAA--CCACTAAAGTTTTAGATAATTTGCGTCGTTTATAC
328167 AAAAAAGCCACTA
1 AAAAAA-CCACTA
328180 TAGAATTGTC
Statistics
Matches: 74, Mismatches: 9, Indels: 26
0.68 0.08 0.24
Matches are distributed among these distances:
38 3 0.04
39 9 0.12
40 11 0.15
41 9 0.12
42 20 0.27
43 10 0.14
44 9 0.12
45 3 0.04
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (41 bp):
AAAAAACCACTAAAGTTTTAGATAATTTGCGTCGTTTATAC
Found at i:328089 original size:43 final size:43
Alignment explanation
Indices: 328032--328172 Score: 109
Period size: 44 Copynumber: 3.3 Consensus size: 43
328022 TCAATACCGG
328032 CGTTTTACAAAAAAACACCACTAAAGTTTTAGATAATTTGCGT
1 CGTTTTACAAAAAAACACCACTAAAGTTTTAGATAATTTGCGT
* * * *
328075 CGTTTATAC--AAAAA-ACCATTATA-TAATT-G-TCAA-TAGCGGT
1 CGTTT-TACAAAAAAACACCACTAAAGT-TTTAGAT-AATTTGC-GT
* * *
328115 -GTTTTACTATAAAAACGCCACTAAAGTTTTAGATAATTTGCGA
1 CGTTTTAC-AAAAAAACACCACTAAAGTTTTAGATAATTTGCGT
328158 CGTTTATACAAAAAA
1 CGTTT-TACAAAAAA
328173 GCCACTATAG
Statistics
Matches: 73, Mismatches: 11, Indels: 27
0.66 0.10 0.24
Matches are distributed among these distances:
38 3 0.04
39 8 0.11
40 6 0.08
41 14 0.19
42 13 0.18
43 10 0.14
44 16 0.22
45 3 0.04
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (43 bp):
CGTTTTACAAAAAAACACCACTAAAGTTTTAGATAATTTGCGT
Found at i:328145 original size:83 final size:84
Alignment explanation
Indices: 328022--328217 Score: 315
Period size: 83 Copynumber: 2.4 Consensus size: 84
328012 AAATACGTAA
* * *
328022 TCAATACCGGCGTTTTAC-AAAAAAACACCACTAAAGTTTTAGATAATTTGCGTCGTTTATACAA
1 TCAATAGCGGCGTTTTACTATAAAAACACCACTAAAGTTTTAGATAATTTGCGACGTTTATACAA
* *
328086 AAAA-CCATTATATAATTG
66 AAAAGCCACTATAGAATTG
* *
328104 TCAATAGCGGTGTTTTACTATAAAAACGCCACTAAAGTTTTAGATAATTTGCGACGTTTATACAA
1 TCAATAGCGGCGTTTTACTATAAAAACACCACTAAAGTTTTAGATAATTTGCGACGTTTATACAA
328169 AAAAGCCACTATAGAATTG
66 AAAAGCCACTATAGAATTG
328188 TCAATAGCGGCGTTTTACTATAAAAACACC
1 TCAATAGCGGCGTTTTACTATAAAAACACC
328218 GCTATGTGTC
Statistics
Matches: 103, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
82 16 0.16
83 47 0.46
84 40 0.39
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (84 bp):
TCAATAGCGGCGTTTTACTATAAAAACACCACTAAAGTTTTAGATAATTTGCGACGTTTATACAA
AAAAGCCACTATAGAATTG
Found at i:328213 original size:42 final size:42
Alignment explanation
Indices: 328084--328213 Score: 115
Period size: 42 Copynumber: 3.1 Consensus size: 42
328074 TCGTTTATAC
* * *
328084 AAAAAA-CCATTATATAATTGTCAATAGCGGTGTTTTACTAT
1 AAAAAAGCCACTATAGAATTGTCAATAGCGGCGTTTTACTAT
* * ** * * *
328125 AAAAACGCCACTAAAGTTTTAGAT-AATTTGCGACG-TTTA-TAC
1 AAAAAAGCCACTATAGAATT-G-TCAA-TAGCGGCGTTTTACTAT
328167 AAAAAAGCCACTATAGAATTGTCAATAGCGGCGTTTTACTAT
1 AAAAAAGCCACTATAGAATTGTCAATAGCGGCGTTTTACTAT
328209 AAAAA
1 AAAAA
328214 CACCGCTATG
Statistics
Matches: 65, Mismatches: 17, Indels: 13
0.68 0.18 0.14
Matches are distributed among these distances:
40 7 0.11
41 12 0.18
42 33 0.51
43 7 0.11
44 6 0.09
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.31
Consensus pattern (42 bp):
AAAAAAGCCACTATAGAATTGTCAATAGCGGCGTTTTACTAT
Found at i:330273 original size:2 final size:2
Alignment explanation
Indices: 330266--330321 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
330256 CAGAACTGGC
330266 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
330308 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
330322 CACCTCTTCA
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:334275 original size:57 final size:56
Alignment explanation
Indices: 334050--334276 Score: 319
Period size: 57 Copynumber: 4.0 Consensus size: 56
334040 AAAACCATAC
* * * * * *
334050 AACCCCGTCACGAACAGTAAAGCCCTGAGCACAAAGCCAAGGAACCTTCAAGTAATC
1 AACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGT-ATT
*
334107 AACCCCGTCACGAACAATAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
1 AACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
* * *
334163 CAACCCTGTCACGAATAGTAAGGCTCTCAGCACAAAGTCGAGGAACCTGCAAGTATT
1 -AACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
* *
334220 ATTCCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGGAAGTATT
1 A-ACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
334277 CTTCCTCCAA
Statistics
Matches: 152, Mismatches: 16, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
56 3 0.02
57 149 0.98
ACGTcount: A:0.35, C:0.29, G:0.20, T:0.16
Consensus pattern (56 bp):
AACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
Found at i:334362 original size:24 final size:24
Alignment explanation
Indices: 334335--334395 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
334325 TATATCAAAA
* *
334335 ATCAAATCATAGTCCAGGTCAAGT
1 ATCAAATCAGAATCCAGGTCAAGT
* * *
334359 ATCATATCAGAATCCATGTCAGGT
1 ATCAAATCAGAATCCAGGTCAAGT
334383 ATCATAA-CAGAAT
1 ATCA-AATCAGAAT
334396 TCAAATCATA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
24 29 0.97
25 1 0.03
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAATCAGAATCCAGGTCAAGT
Found at i:336174 original size:18 final size:19
Alignment explanation
Indices: 336145--336180 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
336135 AAATATATAT
336145 ATATTAAAAATTTTAAATA
1 ATATTAAAAATTTTAAATA
336164 ATATT-AAAATTTTAAAT
1 ATATTAAAAATTTTAAAT
336181 TTTACTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATTAAAAATTTTAAATA
Found at i:336413 original size:11 final size:11
Alignment explanation
Indices: 336397--336421 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
336387 AGGAAAGGCG
336397 GGTTAATATAC
1 GGTTAATATAC
336408 GGTTAATATAC
1 GGTTAATATAC
336419 GGT
1 GGT
336422 GTTACCAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (11 bp):
GGTTAATATAC
Found at i:336810 original size:20 final size:19
Alignment explanation
Indices: 336787--336833 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
336777 CGATATACCA
336787 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
336807 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
336827 GGTAAAA
1 GGTAAAA
336834 CGTTACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:336910 original size:181 final size:183
Alignment explanation
Indices: 336575--337048 Score: 729
Period size: 182 Copynumber: 2.6 Consensus size: 183
336565 GATCCAAATT
* * * **
336575 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATTGAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATAAAAATGATA
* * * * *
336640 AAACCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
*
336705 GTGAATTTAAAAGAGAAGCAGTTTTAAAT-CCTATAAAGTGTCGATACTTT-TA
131 GTGAATTTAAAAGAGAAGCAGTTTT-AATGCCTATAAAGTGTCGATACTTTAAA
* *
336757 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATAAAAATGATA
* *
336822 AAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* *
336886 GTGAATTTAAAAGAGAAGCAGTTTTAGTGCCTATAATGTGTCGATACTTTAAA
131 GTGAATTTAAAAGAGAAGCAGTTTTAATGCCTATAAAGTGTCGATACTTTAAA
* * * *
336939 AAAAATATATCGATCCACAATGATATAACAGGTAAAAATATGATAAAACCGATATAAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATAAAAATGATA
337004 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
337049 CGTAAGTACG
Statistics
Matches: 268, Mismatches: 22, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
180 2 0.01
181 63 0.24
182 203 0.76
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (183 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATAAAAATGATA
AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTTTAATGCCTATAAAGTGTCGATACTTTAAA
Found at i:336983 original size:20 final size:19
Alignment explanation
Indices: 336957--337015 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 19
336947 ATCGATCCAC
* *
336957 AATGATATAACAGGTAAAA
1 AATGATAAAACCGGTAAAA
*
336976 ATATGATAAAACCGATATAAA
1 A-ATGATAAAACCGGTA-AAA
336997 AATGATAAAACCGGTAAAA
1 AATGATAAAACCGGTAAAA
337016 CGATACCGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 4 0.12
20 26 0.76
21 4 0.12
ACGTcount: A:0.58, C:0.08, G:0.14, T:0.20
Consensus pattern (19 bp):
AATGATAAAACCGGTAAAA
Found at i:339262 original size:21 final size:21
Alignment explanation
Indices: 339238--339297 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
339228 GACAATCAAT
*
339238 AGTCGAAGAGAAACTTGATAG
1 AGTCGAAGAGAAACTTGAGAG
339259 AGTCGAAGAGAAACTTGAGAG
1 AGTCGAAGAGAAACTTGAGAG
* *
339280 AGTCGAAGATACACTTGA
1 AGTCGAAGAGAAACTTGA
339298 AAGGCATAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.42, C:0.12, G:0.28, T:0.18
Consensus pattern (21 bp):
AGTCGAAGAGAAACTTGAGAG
Found at i:339376 original size:33 final size:33
Alignment explanation
Indices: 339334--339399 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
339324 AAATAGATGG
*
339334 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
339367 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
339400 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:341215 original size:19 final size:19
Alignment explanation
Indices: 341191--341239 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
341181 AATGTAGGGT
341191 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
341210 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
341229 TAATTTTGTAT
1 TAATTTTGTAT
341240 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:342255 original size:200 final size:200
Alignment explanation
Indices: 341473--342236 Score: 1350
Period size: 200 Copynumber: 3.8 Consensus size: 200
341463 AATTTACAAT
* *
341473 ATGGCAAACATGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
341538 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTACAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
341603 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
341668 AATGA
196 AATGA
*
341673 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
341738 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
341803 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
341868 AATGA
196 AATGA
341873 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* ** *
341938 CGAAACCCATAAGTATAATACAATAGGTAATTTTTCAATCTAACCGATACAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
342003 ATGATAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
342068 AATGA
196 AATGA
* *
342073 ATGGGAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
342138 CGAAACCCAAAAGTATAATGTATTAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * *
342203 ATGGGAGAATTGGTATATAAT-ATGTATCGACACT
131 ATGAGAGAATAGGTCTA-AATAATGTATCGACACT
342237 GTTTAATGTT
Statistics
Matches: 539, Mismatches: 24, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
200 536 0.99
201 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
AATGA
Found at i:343368 original size:183 final size:183
Alignment explanation
Indices: 343006--343576 Score: 989
Period size: 183 Copynumber: 3.1 Consensus size: 183
342996 CAAAGTTTTC
* *
343006 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCATAATGGAAGAAAAATGTGTCGATACCTTTT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
* *** * *
343071 CAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATA
66 CAAAAAGTGTCGA-CGTTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATA
* * *
343136 TAATCGGTCTAAATATATCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
130 TAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
343190 ACACTTTTTAATATTGTGTCGGTACTTTATGTTCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
*
343255 CAAAAAGTGTCGACGTTTACACATCGAAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACGTTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
343320 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
343373 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
* *
343438 CAAAAAGTGTCGCCATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACGTTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
343503 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
343556 ACACTTTTTAATACTGTGTCG
1 ACACTTTTTAATATTGTGTCG
343577 CTAATTTTAA
Statistics
Matches: 369, Mismatches: 18, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
183 294 0.80
184 75 0.20
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (183 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
CAAAAAGTGTCGACGTTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:347028 original size:87 final size:87
Alignment explanation
Indices: 346924--347086 Score: 292
Period size: 87 Copynumber: 1.9 Consensus size: 87
346914 AAATAGGTCA
346924 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
346989 CCT-GTTAAATACCTATTTTATT
66 -CTGGTTAAATACCTATTTTATT
* *
347011 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
347076 CTGGTTAAATA
66 CTGGTTAAATA
347087 ATATAACATA
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
86 2 0.03
87 71 0.97
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CTGGTTAAATACCTATTTTATT
Found at i:347058 original size:23 final size:23
Alignment explanation
Indices: 347008--347052 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
346998 TACCTATTTT
* *
347008 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
347031 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGCTACCTAATA
347053 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:348022 original size:14 final size:14
Alignment explanation
Indices: 347999--348028 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
347989 GAACTCAACT
*
347999 TTTCCTGATTACCA
1 TTTCCAGATTACCA
348013 TTTCCAGATTACCA
1 TTTCCAGATTACCA
348027 TT
1 TT
348029 CGTCGGTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.27, G:0.07, T:0.43
Consensus pattern (14 bp):
TTTCCAGATTACCA
Found at i:349052 original size:34 final size:34
Alignment explanation
Indices: 349009--349091 Score: 159
Period size: 34 Copynumber: 2.5 Consensus size: 34
348999 TTTCGCAAAA
349009 ATTAATATTTCGTATTGTCAATTTGTTCTCATCG
1 ATTAATATTTCGTATTGTCAATTTGTTCTCATCG
349043 ATTAATATTTCGTATTGTCAATTTGTTCTCATCG
1 ATTAATATTTCGTATTGTCAATTTGTTCTCATCG
349077 ATTAATATTTC-TATT
1 ATTAATATTTCGTATT
349092 ATATGATGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 4 0.08
34 45 0.92
ACGTcount: A:0.25, C:0.13, G:0.10, T:0.52
Consensus pattern (34 bp):
ATTAATATTTCGTATTGTCAATTTGTTCTCATCG
Found at i:349354 original size:36 final size:36
Alignment explanation
Indices: 349301--349422 Score: 219
Period size: 36 Copynumber: 3.4 Consensus size: 36
349291 AATTACATCC
349301 ACTTTAGC-TTAGGTAAAAGCTTAAACGTAATATGA
1 ACTTTAGCTTTAGGTAAAAGCTTAAACGTAATATGA
*
349336 ACTTTAGCTTTAGGTAAAAGCTTAAACATAATATGA
1 ACTTTAGCTTTAGGTAAAAGCTTAAACGTAATATGA
*
349372 ACTTTAGCTTTAGGTAAAAGCTAAAACGTAATATGA
1 ACTTTAGCTTTAGGTAAAAGCTTAAACGTAATATGA
349408 ACTTTAGCTTTAGGT
1 ACTTTAGCTTTAGGT
349423 TAACTAAATT
Statistics
Matches: 83, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
35 8 0.10
36 75 0.90
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (36 bp):
ACTTTAGCTTTAGGTAAAAGCTTAAACGTAATATGA
Found at i:353309 original size:15 final size:15
Alignment explanation
Indices: 353291--353319 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
353281 TTCATTTCAA
353291 AATTTTATAAAATAC
1 AATTTTATAAAATAC
353306 AATTTTATAAAATA
1 AATTTTATAAAATA
353320 ACTTAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTTTATAAAATAC
Found at i:353480 original size:14 final size:14
Alignment explanation
Indices: 353461--353524 Score: 65
Period size: 14 Copynumber: 4.1 Consensus size: 14
353451 CAAACAGCGT
353461 AATTGGTTTTCTGG
1 AATTGGTTTTCTGG
*
353475 AATTGGTTTTCCAGAAATGT
1 AATTGGTTTT-C-----TGG
353495 AATTGGTTTTCTGG
1 AATTGGTTTTCTGG
353509 AATTGGTTTTCTGG
1 AATTGGTTTTCTGG
353523 AA
1 AA
353525 AACCAATTAC
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
14 28 0.67
15 1 0.02
19 1 0.02
20 12 0.29
ACGTcount: A:0.22, C:0.08, G:0.25, T:0.45
Consensus pattern (14 bp):
AATTGGTTTTCTGG
Found at i:356688 original size:22 final size:21
Alignment explanation
Indices: 356660--356712 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 21
356650 TACTCAGTTC
356660 AGTATCGATACCCCAGAGCCA-G
1 AGTATCGATACCCC--AGCCAGG
*
356682 AGTATCGATA-CTCAGCCAGG
1 AGTATCGATACCCCAGCCAGG
356702 AGTATCGATAC
1 AGTATCGATAC
356713 TACCTTACCC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 5 0.18
20 11 0.39
21 2 0.07
22 10 0.36
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.19
Consensus pattern (21 bp):
AGTATCGATACCCCAGCCAGG
Found at i:356700 original size:19 final size:20
Alignment explanation
Indices: 356676--356713 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
356666 GATACCCCAG
356676 AGCCA-GAGTATCGATACTC
1 AGCCAGGAGTATCGATACTC
356695 AGCCAGGAGTATCGATACT
1 AGCCAGGAGTATCGATACT
356714 ACCTTACCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.21
Consensus pattern (20 bp):
AGCCAGGAGTATCGATACTC
Found at i:357523 original size:16 final size:16
Alignment explanation
Indices: 357502--357532 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
357492 AGGTCCAACT
357502 CAGGTTCAGGTAAACA
1 CAGGTTCAGGTAAACA
357518 CAGGTTCAGGTAAAC
1 CAGGTTCAGGTAAAC
357533 GTAAGTTCAG
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:0.35, C:0.19, G:0.26, T:0.19
Consensus pattern (16 bp):
CAGGTTCAGGTAAACA
Found at i:361772 original size:106 final size:106
Alignment explanation
Indices: 361499--361925 Score: 603
Period size: 106 Copynumber: 4.0 Consensus size: 106
361489 CTTGTGTGAA
*
361499 CTCGAGTCTAATATCT-TTCGCTGTGAAGTTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTT
1 CTCGAGTCCAATATCTCTTCGCTGTGAAG-TTGAAATTGGCTCTGAAATTGGGAAATTATTTGTT
* * * *
361563 GACAGCCAGTCGTCACTTCGTTGTGAAGTTGAACTTGTGTTGC
65 GACA-CCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGT
* * * *
361606 CTCGAGTCCAATAT-TCATCG-TGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTC
1 CTCGAGTCCAATATCTCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTG
* *
361669 ACATCCAGCCATCCCTTCATTGTGAAGTTGAACTTGTGCTGT
66 ACA-CCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGT
* *
361711 CTCGAGTCCAAT-TCTCTTCGCTGTGAAGTTAAAATTGGCTCTAAAATTGGGAAATTATTTGTTG
1 CTCGAGTCCAATATCTCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTG
*
361775 ACGACCAGCCGTCCCTTCATTGTGAAGTTAAACTTGTGTTGT
66 AC-ACCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGT
* * * *
361817 CTTGAGTCCAATATC-CTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAGTTGTTTGTTG
1 CTCGAGTCCAATATCTCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTG
*
361881 ACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGT
66 AC-ACCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGT
361923 CTC
1 CTC
361926 AGGTGGCGCA
Statistics
Matches: 284, Mismatches: 31, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
104 1 0.00
105 85 0.30
106 179 0.63
107 19 0.07
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (106 bp):
CTCGAGTCCAATATCTCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTG
ACACCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGT
Found at i:362790 original size:36 final size:38
Alignment explanation
Indices: 362732--362808 Score: 122
Period size: 36 Copynumber: 2.1 Consensus size: 38
362722 GAAACAATTT
* *
362732 CAAAGGTTTTTTTCCAAGGGAAACTGTCTCAAGAGAGA
1 CAAAGGTTTGTTTCCAAAGGAAACTGTCTCAAGAGAGA
362770 CAAA-GTTTGTTT-CAAAGGAAACTGTCTCAAGAGAGA
1 CAAAGGTTTGTTTCCAAAGGAAACTGTCTCAAGAGAGA
362806 CAA
1 CAA
362809 TGGTGAGCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 26 0.70
37 7 0.19
38 4 0.11
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.25
Consensus pattern (38 bp):
CAAAGGTTTGTTTCCAAAGGAAACTGTCTCAAGAGAGA
Found at i:363293 original size:18 final size:18
Alignment explanation
Indices: 363266--363301 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
363256 TGTTGAATCC
* *
363266 CCAAAGATGCCCCAATAT
1 CCAAAAATGCACCAATAT
363284 CCAAAAATGCACCAATAT
1 CCAAAAATGCACCAATAT
363302 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.31, G:0.08, T:0.17
Consensus pattern (18 bp):
CCAAAAATGCACCAATAT
Found at i:364388 original size:10 final size:9
Alignment explanation
Indices: 364373--364427 Score: 58
Period size: 9 Copynumber: 5.8 Consensus size: 9
364363 TTTTTGCTTC
364373 TTTTCTTTT
1 TTTTCTTTT
364382 TTGTTCTTGTT
1 TT-TTCTT-TT
364393 TTTTCTTTT
1 TTTTCTTTT
*
364402 TTTT-TCTTC
1 TTTTCT-TTT
364411 TTTTCTTTT
1 TTTTCTTTT
364420 TTATTCTT
1 TT-TTCTT
364428 GATTGAATCT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
8 1 0.03
9 18 0.46
10 16 0.41
11 4 0.10
ACGTcount: A:0.02, C:0.13, G:0.04, T:0.82
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:364420 original size:18 final size:18
Alignment explanation
Indices: 364363--364427 Score: 76
Period size: 18 Copynumber: 3.5 Consensus size: 18
364353 TTCCTTTTGA
*
364363 TTTTTGCTTCTTTTCTTT
1 TTTTTTCTTCTTTTCTTT
* *
364381 TTTGTTCTTGTTTTTTCTTT
1 TTTTTTC-T-TCTTTTCTTT
364401 TTTTTTCTTCTTTTCTTT
1 TTTTTTCTTCTTTTCTTT
*
364419 TTTATTCTT
1 TTTTTTCTT
364428 GATTGAATCT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
18 22 0.56
19 2 0.05
20 15 0.38
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.80
Consensus pattern (18 bp):
TTTTTTCTTCTTTTCTTT
Found at i:376731 original size:4 final size:4
Alignment explanation
Indices: 376722--376750 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
376712 TTATCAAATT
376722 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
376751 CTGTATTCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:377842 original size:2 final size:2
Alignment explanation
Indices: 377835--377874 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
377825 AAGTATAATT
377835 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
377875 TATTAAATGA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:378921 original size:24 final size:24
Alignment explanation
Indices: 378894--378955 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
378884 CGTTCGTGAA
*
378894 CGTTCGGTTATGTTCGTTTATATG
1 CGTTCAGTTATGTTCGTTTATATG
* *
378918 CGTTTAGTTATGTTCGTTTATGTG
1 CGTTCAGTTATGTTCGTTTATATG
*
378942 CGTTCATTTATGTT
1 CGTTCAGTTATGTT
378956 TAACCTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.13, C:0.11, G:0.23, T:0.53
Consensus pattern (24 bp):
CGTTCAGTTATGTTCGTTTATATG
Found at i:380490 original size:16 final size:16
Alignment explanation
Indices: 380467--380521 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
380457 GGGTCTCCAA
380467 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
380483 CATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
380499 CGTTTATGTTTGTGTT
1 CGTTTATGTTCGTGTT
380515 CGTTTAT
1 CGTTTAT
380522 TTATTAAATG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.09, C:0.11, G:0.22, T:0.58
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:382006 original size:32 final size:33
Alignment explanation
Indices: 381942--382008 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 33
381932 GTACCCTACC
* *
381942 GTTAAAAATTTAGGCACTAAAATAAAATAAGAA
1 GTTAAAAATTAAGGCACTAAAATAAAACAAGAA
* *
381975 GTTAAAAA-TAAGGTACTAAAATGAAACAAGAA
1 GTTAAAAATTAAGGCACTAAAATAAAACAAGAA
382007 GT
1 GT
382009 AAACGATGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 22 0.73
33 8 0.27
ACGTcount: A:0.57, C:0.06, G:0.15, T:0.22
Consensus pattern (33 bp):
GTTAAAAATTAAGGCACTAAAATAAAACAAGAA
Found at i:385643 original size:3 final size:3
Alignment explanation
Indices: 385637--385677 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
385627 CAATTTTAAA
* *
385637 TAT TAT TAT TAT TAT TAT TAT TA- TAT AAT GAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
385678 GATAACATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:392277 original size:209 final size:213
Alignment explanation
Indices: 391910--392337 Score: 702
Period size: 209 Copynumber: 2.0 Consensus size: 213
391900 ACAAAATAAA
*
391910 ATATCCGAAGATCATAGTACCCGAAACTTCGGATACCCGGATACCAAGTACTCAGATTTAAACAC
1 ATATCCGAAGATCATAGTACCCGAAACTTCGGATACCCAGATACCAAGTACTCAGATTTAAACAC
*
391975 CCCTATATATATATATATAACATTTTGGGGCATTGGTGGGCCATGATCTAGGTAGGCCCACACCT
66 CCC---ATATATATATATAACATTTTGGGGCATGGGTGGGCCATGATCTAGGTAGGCCCACACCT
*
392040 AGATATGCCCCTGATGAATGGTGATAAGAGATTTTAGAGCACATAATTTTATTGGTGAGTTACCA
128 AGATATGCCCCTGATGAATGGTGATAAGAGACTTTAGAGCACATAATTTTATTGGTGAGTTACCA
*
392105 CATTTTCATTTTTTATAATAG
193 CATTTTCATTTTTGATAATAG
* * *
392126 ATATCCGAAGATTATAGTACCCGAAGCTTC-GA-A-CCAGATACCAAGTACTCAGATTTGAACAC
1 ATATCCGAAGATCATAGTACCCGAAACTTCGGATACCCAGATACCAAGTACTCAGATTTAAACAC
* *
392188 CCC-TATATATATATAACATTTTGGGGCATGGGTGGGCCATGATTTAGGTAGGCCCACCCCTAGA
66 CCCATATATATATATAACATTTTGGGGCATGGGTGGGCCATGATCTAGGTAGGCCCACACCTAGA
*
392252 TATGCCCCTGGTGAATGGTGATAAGAGACTTTAGAGCACATAATTTTATTGGTGAGTTACCACAT
131 TATGCCCCTGATGAATGGTGATAAGAGACTTTAGAGCACATAATTTTATTGGTGAGTTACCACAT
*
392317 TTTCGTTTTTGATAATAG
196 TTTCATTTTTGATAATAG
392335 ATA
1 ATA
392338 ACAGTTCACT
Statistics
Matches: 201, Mismatches: 11, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
209 140 0.70
213 30 0.15
214 1 0.00
215 2 0.01
216 28 0.14
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (213 bp):
ATATCCGAAGATCATAGTACCCGAAACTTCGGATACCCAGATACCAAGTACTCAGATTTAAACAC
CCCATATATATATATAACATTTTGGGGCATGGGTGGGCCATGATCTAGGTAGGCCCACACCTAGA
TATGCCCCTGATGAATGGTGATAAGAGACTTTAGAGCACATAATTTTATTGGTGAGTTACCACAT
TTTCATTTTTGATAATAG
Found at i:395775 original size:110 final size:110
Alignment explanation
Indices: 395624--395838 Score: 376
Period size: 110 Copynumber: 2.0 Consensus size: 110
395614 GCCCAATGTT
395624 TCCAAGGTAGACCTATATAATGTTTTCCGATAATGTCGTAGTCTTATCCCAACTGCTCATCTTTT
1 TCCAAGGTAGACCTATATAATGTTTTCCGATAATGTCGTAGTCTTATCCCAACTGCTCATCTTTT
* * *
395689 TCGATTGATTGTATTGACTGGTTTTTTATTGTTGATTTGTCAATA
66 TCGAATGATTGTATTGACTGGTTTTTGATTATTGATTTGTCAATA
* * *
395734 TCCAAGGTAGACCTATATAATGTTTTCTGATACTGTTGTAGTCTTATCCCAACTGCTCATCTTTT
1 TCCAAGGTAGACCTATATAATGTTTTCCGATAATGTCGTAGTCTTATCCCAACTGCTCATCTTTT
395799 TCGAATGATTGTATTGACTGGTTTTTGATTATTGATTTGT
66 TCGAATGATTGTATTGACTGGTTTTTGATTATTGATTTGT
395839 TAACCTTAGG
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
110 99 1.00
ACGTcount: A:0.22, C:0.16, G:0.17, T:0.45
Consensus pattern (110 bp):
TCCAAGGTAGACCTATATAATGTTTTCCGATAATGTCGTAGTCTTATCCCAACTGCTCATCTTTT
TCGAATGATTGTATTGACTGGTTTTTGATTATTGATTTGTCAATA
Found at i:404873 original size:24 final size:25
Alignment explanation
Indices: 404817--404875 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 25
404807 ACATGAAAGT
*
404817 AGATTTATTTGTAAAAAGTGAAAAAA
1 AGATTTATTTGTAAAAACTG-AAAAA
*
404843 ATATTTATTTGTAAAAACTG-AAAA
1 AGATTTATTTGTAAAAACTGAAAAA
*
404867 AGGTTTATT
1 AGATTTATT
404876 AAAGATTAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 11 0.38
26 18 0.62
ACGTcount: A:0.47, C:0.02, G:0.14, T:0.37
Consensus pattern (25 bp):
AGATTTATTTGTAAAAACTGAAAAA
Found at i:409800 original size:20 final size:21
Alignment explanation
Indices: 409760--409804 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
409750 TTAATAATTT
409760 TTTTTGATTATTTTAATAAAA
1 TTTTTGATTATTTTAATAAAA
409781 TTTTTGATTATTTTAA-AAAA
1 TTTTTGATTATTTTAATAAAA
409801 TTTT
1 TTTT
409805 ACCCGGCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (21 bp):
TTTTTGATTATTTTAATAAAA
Found at i:412184 original size:41 final size:42
Alignment explanation
Indices: 412134--412217 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
412124 ATATTTGATT
412134 ATTTGACTATAATAATATCAA-GTTTGAAGTTTATTTCTATA
1 ATTTGACTATAATAATATCAACGTTTGAAGTTTATTTCTATA
*
412175 ATTTTACTATAATAATATCAACGTTTGAAGTTTATTTCTATA
1 ATTTGACTATAATAATATCAACGTTTGAAGTTTATTTCTATA
412217 A
1 A
412218 CTTAAAAATG
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 20 0.49
42 21 0.51
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.46
Consensus pattern (42 bp):
ATTTGACTATAATAATATCAACGTTTGAAGTTTATTTCTATA
Found at i:416757 original size:31 final size:31
Alignment explanation
Indices: 416719--416784 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
416709 AGTTACATCG
*
416719 GGGACCATATTACAAAT-GTACTAAATGTTGA
1 GGGACCATATTACAAATAG-ACTAAATATTGA
* *
416750 GGGACCATATTGCAAATAGACTAAATATTGG
1 GGGACCATATTACAAATAGACTAAATATTGA
416781 GGGA
1 GGGA
416785 TCCGGTAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (31 bp):
GGGACCATATTACAAATAGACTAAATATTGA
Found at i:417258 original size:29 final size:29
Alignment explanation
Indices: 417215--417272 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
417205 AATATGATCC
417215 TTTGACCAACATTTTCTGTCATTGACCAA
1 TTTGACCAACATTTTCTGTCATTGACCAA
*
417244 TTTGACCAACGTTTTCTGTCATTGACCAA
1 TTTGACCAACATTTTCTGTCATTGACCAA
417273 AATTTCGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (29 bp):
TTTGACCAACATTTTCTGTCATTGACCAA
Found at i:426552 original size:22 final size:21
Alignment explanation
Indices: 426527--426568 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
426517 GGATTCTACC
426527 TAAAAATCAC-AAAATATATATA
1 TAAAAAT-ACTAAAATA-ATATA
426549 TAAAAATACTAAAATAATAT
1 TAAAAATACTAAAATAATAT
426569 CATTTGATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAAATACTAAAATAATATA
Found at i:437909 original size:20 final size:22
Alignment explanation
Indices: 437884--437928 Score: 76
Period size: 20 Copynumber: 2.1 Consensus size: 22
437874 CGGTAAAAAA
437884 TTACCTAAAATATT-AT-TTTT
1 TTACCTAAAATATTAATGTTTT
437904 TTACCTAAAATATTAATGTTTT
1 TTACCTAAAATATTAATGTTTT
437926 TTA
1 TTA
437929 ATATTTTCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 14 0.61
21 2 0.09
22 7 0.30
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (22 bp):
TTACCTAAAATATTAATGTTTT
Found at i:439418 original size:2 final size:2
Alignment explanation
Indices: 439411--439457 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
439401 GGGGTATCCT
439411 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
439453 TA TA T
1 TA TA T
439458 CGTTATTCTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:439748 original size:3 final size:3
Alignment explanation
Indices: 439740--439778 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
439730 GTTCATGCAG
439740 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
439779 AAGGGAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:443943 original size:24 final size:23
Alignment explanation
Indices: 443907--443954 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
443897 TCTCAAGTCT
*
443907 TGCTTCGCCGATCTTCACCTTCCC
1 TGCTCCGCCGATCTTC-CCTTCCC
* *
443931 TGCTCCGCTGATCTTCCTTTCCC
1 TGCTCCGCCGATCTTCCCTTCCC
443954 T
1 T
443955 TGCCACTTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.06, C:0.44, G:0.12, T:0.38
Consensus pattern (23 bp):
TGCTCCGCCGATCTTCCCTTCCC
Found at i:444197 original size:18 final size:18
Alignment explanation
Indices: 444174--444216 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
444164 TAATGGTCTT
444174 GCATCTTTATGTTTACTA
1 GCATCTTTATGTTTACTA
444192 GCATCTTTATGTTTACTA
1 GCATCTTTATGTTTACTA
444210 GCATCTT
1 GCATCTT
444217 CTTCTTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.49
Consensus pattern (18 bp):
GCATCTTTATGTTTACTA
Found at i:444751 original size:21 final size:21
Alignment explanation
Indices: 444725--444910 Score: 136
Period size: 21 Copynumber: 9.0 Consensus size: 21
444715 CATATTCACA
444725 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
** *
444746 TTGCGATTTTCCAAATT--CG
1 TTGCGATAGTCCAAGTTCGCG
444765 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
* * * *
444786 TTACGATTTATTCCAAATT--TG
1 TTGCGA--TAGTCCAAGTTCGCG
444807 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
* *
444828 TTGCGATTTATTCCAAATT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
* *
444849 TTGCGATAATCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
* *
444870 TTGCGATTTATTCCAAATT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
*
444891 TTGCGATAGTCGAAGTTCGC
1 TTGCGATAGTCCAAGTTCGC
444911 AACGACTGGT
Statistics
Matches: 126, Mismatches: 25, Indels: 28
0.70 0.14 0.16
Matches are distributed among these distances:
19 41 0.33
21 59 0.47
23 26 0.21
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (21 bp):
TTGCGATAGTCCAAGTTCGCG
Found at i:444813 original size:42 final size:42
Alignment explanation
Indices: 444725--444910 Score: 313
Period size: 42 Copynumber: 4.5 Consensus size: 42
444715 CATATTCACA
444725 TTGCGATAGTCCAAGTTCGCGTTGCGA-TT-TTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
444765 TTGCGATAGTCCAAGTTCGCGTTACGATTTATTCCAAATTTG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
444807 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
444849 TTGCGATAATCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
444891 TTGCGATAGTCGAAGTTCGC
1 TTGCGATAGTCCAAGTTCGC
444911 AACGACTGGT
Statistics
Matches: 137, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
40 26 0.19
41 2 0.01
42 109 0.80
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:445005 original size:6 final size:6
Alignment explanation
Indices: 444994--445025 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
444984 GACACATATT
444994 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
445026 CCAGACGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:445806 original size:21 final size:19
Alignment explanation
Indices: 445773--446088 Score: 245
Period size: 21 Copynumber: 15.3 Consensus size: 19
445763 CGTTGCGATT
*
445773 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
*
445792 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
*
445815 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
* *
445838 TTCGACAATCGCAACGCGAAC
1 TTGGACTATCGCAA--CGAAC
*
445859 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
* *
445878 TTGAAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
*
445901 TTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
445920 TTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAA--CGAAC
*
445941 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
*
445960 TTGGAATAAATCGCAACGTGAAC
1 TTGGACT--ATCGCAAC--GAAC
*
445983 TTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
446002 TTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAA--CGAAC
*
446023 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
* *
446042 TTGGAATAAATTGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
* *
446065 TTGGACTATCGCAAAGAAT
1 TTGGACTATCGCAACGAAC
446084 TTGGA
1 TTGGA
446089 AAATCGCATT
Statistics
Matches: 248, Mismatches: 29, Indels: 40
0.78 0.09 0.13
Matches are distributed among these distances:
19 78 0.31
21 113 0.46
23 57 0.23
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (19 bp):
TTGGACTATCGCAACGAAC
Found at i:445890 original size:42 final size:42
Alignment explanation
Indices: 445773--446096 Score: 430
Period size: 42 Copynumber: 7.8 Consensus size: 42
445763 CGTTGCGATT
445773 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* * * *
445815 TTGGAATAAATCGCAACGCGAACTTCG-A-CAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAAC
*
445859 TTGGACTATCGCAACGAATTTGAAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* * *
445901 TTCGACTATCGCAACGAACTTGGACT--ATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
445941 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGTGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* * *
445983 TTCGACTATCGCAACGAACTTGGACT--ATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
446023 TTGGACTATCGCAACGAATTTGGAATAAATTGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
446065 TTGGACTATCGCAAAGAATTTGG-A-AAATCGCA
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCA
446097 TTGCGATAGT
Statistics
Matches: 245, Mismatches: 27, Indels: 22
0.83 0.09 0.07
Matches are distributed among these distances:
40 86 0.35
41 2 0.01
42 121 0.49
44 28 0.11
45 1 0.00
46 7 0.03
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
Found at i:445962 original size:82 final size:82
Alignment explanation
Indices: 445773--446088 Score: 506
Period size: 82 Copynumber: 3.8 Consensus size: 82
445763 CGTTGCGATT
* *
445773 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT--ATCGCAA--CGAAC
* *
445838 TTCGACAATCGCAACGCGAAC
62 TTGGACTATCGCAACGCGAAC
*
445859 TTGGACTATCGCAACGAATTTGAAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGG
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGG
445924 ACTATCGCAACGCGAAC
66 ACTATCGCAACGCGAAC
*
445941 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGTGAACTTCGACTATCGCAACGAACTTGG
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGG
446006 ACTATCGCAACGCGAAC
66 ACTATCGCAACGCGAAC
* * * *
446023 TTGGACTATCGCAACGAATTTGGAATAAATTGCAACGCGAACTTGGACTATCGCAAAGAATTTGG
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGG
446088 A
66 A
446089 AAATCGCATT
Statistics
Matches: 218, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
82 165 0.76
84 7 0.03
86 46 0.21
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (82 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGG
ACTATCGCAACGCGAAC
Found at i:446121 original size:21 final size:21
Alignment explanation
Indices: 446092--446144 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
446082 ATTTGGAAAA
*
446092 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
446113 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
446134 TCGCGTTGCGA
1 TCGCGTTGCGA
446145 ATATGGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:453314 original size:32 final size:32
Alignment explanation
Indices: 453228--453315 Score: 97
Period size: 32 Copynumber: 2.8 Consensus size: 32
453218 TAAGGTGACT
* * *
453228 CTTGGGTAGGCTCTGAGGCCCTAAGGTATTTC
1 CTTGGGTAGGCTCTAAGGCCCCAAGGTATTCC
* *
453260 CTTGGATAAGCT-TAAAGGCCCCAAGGTATTCC
1 CTTGGGTAGGCTCT-AAGGCCCCAAGGTATTCC
* *
453292 CTTGGGTAGGCTCTTAGACCCCAA
1 CTTGGGTAGGCTCTAAGGCCCCAA
453316 AGTACACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
31 1 0.02
32 43 0.96
33 1 0.02
ACGTcount: A:0.22, C:0.25, G:0.26, T:0.27
Consensus pattern (32 bp):
CTTGGGTAGGCTCTAAGGCCCCAAGGTATTCC
Found at i:455401 original size:64 final size:64
Alignment explanation
Indices: 455325--455444 Score: 186
Period size: 64 Copynumber: 1.9 Consensus size: 64
455315 GAAAGCAAGA
* * * *
455325 GACTACCGTCGATCTTAAAGTTTTATTTATAATTTTAAAACTATACAGTTTGTGAAAACTAAGG
1 GACTACCATCGATCCTAAAGCTTTATTTATAATTTTAAAACTATACAATTTGTGAAAACTAAGG
* *
455389 GACTACCATCGATCCTAAAGCTTTATTTATAGTTTTAAAACTATTCAATTTGTGAA
1 GACTACCATCGATCCTAAAGCTTTATTTATAATTTTAAAACTATACAATTTGTGAA
455445 GAAGAAGAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 50 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38
Consensus pattern (64 bp):
GACTACCATCGATCCTAAAGCTTTATTTATAATTTTAAAACTATACAATTTGTGAAAACTAAGG
Found at i:455938 original size:23 final size:23
Alignment explanation
Indices: 455903--455947 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
455893 TGAATGCTGA
* *
455903 AGTGCTGACTGATTCAGCAAAAC
1 AGTGCTAAATGATTCAGCAAAAC
455926 AGTGCTAAATGATTCAGCAAAA
1 AGTGCTAAATGATTCAGCAAAA
455948 AATACATTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (23 bp):
AGTGCTAAATGATTCAGCAAAAC
Found at i:458196 original size:27 final size:27
Alignment explanation
Indices: 458153--458205 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
458143 AATAATGATA
**
458153 CATATGTATTTTGCATGATTTGAGATT
1 CATATGTATTTCACATGATTTGAGATT
458180 CATATGTATTTCACATGATTTGAGAT
1 CATATGTATTTCACATGATTTGAGAT
458206 CTATTAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.28, C:0.09, G:0.17, T:0.45
Consensus pattern (27 bp):
CATATGTATTTCACATGATTTGAGATT
Found at i:462541 original size:30 final size:32
Alignment explanation
Indices: 462472--462556 Score: 102
Period size: 33 Copynumber: 2.7 Consensus size: 32
462462 AGCAAATACC
*
462472 AAAAGATAAAATTTTGAGTAAACCGATAAGAAA
1 AAAAGATAAAATTTTGAATAAACCGATAAG-AA
* *
462505 AAAAGATAAAATTTTGAATAAACC-ATTAG-G
1 AAAAGATAAAATTTTGAATAAACCGATAAGAA
* *
462535 AAAAGATAAACTTTTAAATAAA
1 AAAAGATAAAATTTTGAATAAA
462557 ACCCTTACAA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
30 20 0.43
32 4 0.09
33 23 0.49
ACGTcount: A:0.58, C:0.06, G:0.12, T:0.25
Consensus pattern (32 bp):
AAAAGATAAAATTTTGAATAAACCGATAAGAA
Found at i:463242 original size:40 final size:41
Alignment explanation
Indices: 463170--463249 Score: 117
Period size: 40 Copynumber: 1.9 Consensus size: 41
463160 AGGAAGTTCG
* *
463170 TTTATGTTCGTTTATTTATTAAATGAATGAACATGAACAAGAT
1 TTTATGTTCGTTTA--TATTAAATGAACGAACACGAACAAGAT
463213 TTTATGTTCGTTTA-ATTAAATGAACGAACACGAACAA
1 TTTATGTTCGTTTATATTAAATGAACGAACACGAACAA
463250 AGAGCTCATT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
40 21 0.60
43 14 0.40
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (41 bp):
TTTATGTTCGTTTATATTAAATGAACGAACACGAACAAGAT
Found at i:463309 original size:14 final size:16
Alignment explanation
Indices: 463280--463311 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
463270 CATTCGTGAA
463280 CGTTCGATTATATGTT
1 CGTTCGATTATATGTT
463296 CGTTC-ATT-TATGTT
1 CGTTCGATTATATGTT
463310 CG
1 CG
463312 AACAGAGGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.50
Consensus pattern (16 bp):
CGTTCGATTATATGTT
Found at i:463680 original size:16 final size:16
Alignment explanation
Indices: 463659--463691 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
463649 AAAAAAAAAT
463659 TGTTCGTTTATATTCG
1 TGTTCGTTTATATTCG
*
463675 TGTTCGTTTATGTTCG
1 TGTTCGTTTATATTCG
463691 T
1 T
463692 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATATTCG
Found at i:464258 original size:25 final size:25
Alignment explanation
Indices: 464206--464259 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
464196 TTTCGAAATT
****
464206 AAATAACTTTTCAAATACCGTTAAA
1 AAATAACTTTTCAAATACAAAGAAA
464231 AAATAACTTTTCAAATACAAAGACAA
1 AAATAACTTTTCAAATACAAAGA-AA
464257 AAA
1 AAA
464260 ATTTATAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.56, C:0.15, G:0.04, T:0.26
Consensus pattern (25 bp):
AAATAACTTTTCAAATACAAAGAAA
Found at i:465183 original size:7 final size:7
Alignment explanation
Indices: 465162--465205 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
465152 TTTTTATAAA
*
465162 AAAAATT
1 AAAATTT
465169 AAAA-TT
1 AAAATTT
465175 AAAATTT
1 AAAATTT
465182 AAAATTT
1 AAAATTT
465189 AAAATTT
1 AAAATTT
465196 AAAATTT
1 AAAATTT
465203 AAA
1 AAA
465206 GAAAAATAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 6 0.17
7 30 0.83
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (7 bp):
AAAATTT
Found at i:492624 original size:23 final size:22
Alignment explanation
Indices: 492582--492624 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
492572 TCATCATCAT
*
492582 CAAATTTGCATTATTTTTAATG
1 CAAATTTGCATTATTCTTAATG
492604 CAAACTTTGCATT-TTGCTTAA
1 CAAA-TTTGCATTATT-CTTAA
492625 ATGAATGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.47
Consensus pattern (22 bp):
CAAATTTGCATTATTCTTAATG
Found at i:499368 original size:19 final size:19
Alignment explanation
Indices: 499344--499391 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
499334 TTGAAGGTGT
499344 ATCGATGCACAGGTAGTGC
1 ATCGATGCACAGGTAGTGC
499363 ATCGATGCACAGGTAGTGC
1 ATCGATGCACAGGTAGTGC
499382 ATCGATGCAC
1 ATCGATGCAC
499392 TCTTTTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (19 bp):
ATCGATGCACAGGTAGTGC
Found at i:500486 original size:103 final size:103
Alignment explanation
Indices: 500307--500730 Score: 805
Period size: 103 Copynumber: 4.1 Consensus size: 103
500297 GTCGAGGGTC
*
500307 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
500372 TTGATCCTTGTCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGTCATATGTATATGATTCTTAAGGAATGA
500410 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
500475 TTGATCCTTGTCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGTCATATGTATATGATTCTTAAGGAATGA
500513 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
500578 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGTCATATGTATATGATTCTTAAGGAATGA
500616 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
500681 TTGATCCCTAGT-ATATGTATATGATTCTTAAGGAATGA
66 TTGAT-CCTTGTCATATGTATATGATTCTTAAGGAATGA
500719 TATGTGGTCCTT
1 TATGTGGTCCTT
500731 ATGAACATTA
Statistics
Matches: 316, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
103 312 0.99
104 4 0.01
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGTCATATGTATATGATTCTTAAGGAATGA
Found at i:500780 original size:23 final size:23
Alignment explanation
Indices: 500746--500835 Score: 117
Period size: 23 Copynumber: 3.9 Consensus size: 23
500736 CATTATTATA
* *
500746 TGGCACTACGGTACAATTCTACG
1 TGGCACTACGGTGCAATTATACG
* *
500769 CGGCACTCCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTATACG
*
500792 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTATACG
* *
500815 TGGCACTTCAGTGCAATTATA
1 TGGCACTACGGTGCAATTATA
500836 TGAGCTGTGG
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:506342 original size:102 final size:102
Alignment explanation
Indices: 506165--506482 Score: 550
Period size: 102 Copynumber: 3.1 Consensus size: 102
506155 GTCGAGGGTC
506165 TATGTGGAT-CTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
1 TATGTGG-TCCTTCGGGACATATATGTA-TCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
*
506229 ATTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
64 CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
506268 TATGTGGTCCTTCGGGACATATATGTATCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
1 TATGTGGTCCTTCGGGACATATATGTATCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
506333 TGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
506370 TATGTGGTCCTTCGGGACATATATAT-TCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
1 TATGTGGTCCTTCGGGACATATATGTATCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
* * * *
506434 TGATCCCTAGTATATGTATATGATTATTAAGGAATGA
66 TGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
506471 TATGTGGTCCTT
1 TATGTGGTCCTT
506483 ATGGACATTA
Statistics
Matches: 208, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
101 83 0.40
102 100 0.48
103 25 0.12
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (102 bp):
TATGTGGTCCTTCGGGACATATATGTATCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
TGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:506532 original size:23 final size:23
Alignment explanation
Indices: 506498--506587 Score: 153
Period size: 23 Copynumber: 3.9 Consensus size: 23
506488 CATTATTATA
* *
506498 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTATACG
*
506521 TGGCACTCCGGTGCAATTATACG
1 TGGCACTTCGGTGCAATTATACG
506544 TGGCACTTCGGTGCAATTATACG
1 TGGCACTTCGGTGCAATTATACG
506567 TGGCACTTCGGTGCAATTATA
1 TGGCACTTCGGTGCAATTATA
506588 TGAGCTGTGG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 64 1.00
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.29
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTATACG
Found at i:512225 original size:21 final size:21
Alignment explanation
Indices: 512179--512236 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
512169 CATGTGAAAC
*
512179 CTATGTCCCGAAGGACGTCAT
1 CTATGTCCCGAAGGACCTCAT
512200 CTATGTCCCGAAGGACCT-AT
1 CTATGTCCCGAAGGACCTCAT
* *
512220 CATATGTCTCAAAGGAC
1 C-TATGTCCCGAAGGAC
512237 ATATATAACC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 3 0.09
21 30 0.91
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (21 bp):
CTATGTCCCGAAGGACCTCAT
Found at i:516325 original size:30 final size:30
Alignment explanation
Indices: 516285--516356 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 30
516275 CGAAAACGAT
*
516285 TTGGTGCTTAACCAATTTTTTACTAAAAAA
1 TTGGTGCTTAACCAATTTTATACTAAAAAA
*
516315 TTGTTGCTTAACCAATTTTATACTAAAAAA
1 TTGGTGCTTAACCAATTTTATACTAAAAAA
516345 TTGGTGCTTAAC
1 TTGGTGCTTAAC
516357 GTTATGTGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (30 bp):
TTGGTGCTTAACCAATTTTATACTAAAAAA
Found at i:516869 original size:20 final size:19
Alignment explanation
Indices: 516819--516877 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
516809 ATCGGCGGTC
516819 GACATAATAGGGAGAAGTG
1 GACATAATAGGGAGAAGTG
516838 GACATAATAGGGAGAAGTG
1 GACATAATAGGGAGAAGTG
* * *
516857 GATGATAAAAGGGGGAAGTG
1 GA-CATAATAGGGAGAAGTG
516877 G
1 G
516878 GGGAAGGGGA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
19 21 0.58
20 15 0.42
ACGTcount: A:0.41, C:0.03, G:0.41, T:0.15
Consensus pattern (19 bp):
GACATAATAGGGAGAAGTG
Found at i:517517 original size:2 final size:2
Alignment explanation
Indices: 517510--517540 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
517500 ATTTATTACG
517510 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 A
517541 CTTTTTTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:525872 original size:15 final size:15
Alignment explanation
Indices: 525852--525894 Score: 86
Period size: 15 Copynumber: 2.9 Consensus size: 15
525842 ACCCATCCCG
525852 CATCCGCCCGCCCCA
1 CATCCGCCCGCCCCA
525867 CATCCGCCCGCCCCA
1 CATCCGCCCGCCCCA
525882 CATCCGCCCGCCC
1 CATCCGCCCGCCC
525895 ACTAAATACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.12, C:0.67, G:0.14, T:0.07
Consensus pattern (15 bp):
CATCCGCCCGCCCCA
Found at i:526606 original size:11 final size:11
Alignment explanation
Indices: 526590--526618 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
526580 CCCTATCGCT
526590 CGTTTGTTATA
1 CGTTTGTTATA
526601 CGTTTGTTATA
1 CGTTTGTTATA
526612 CGTTTGT
1 CGTTTGT
526619 GTGAGAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.14, C:0.10, G:0.21, T:0.55
Consensus pattern (11 bp):
CGTTTGTTATA
Found at i:527975 original size:3 final size:3
Alignment explanation
Indices: 527961--528007 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
527951 AATTTATCCA
* * * *
527961 TAT TAT TGT TAT TAT TAC TAT TAC TAT TAT TAT TAT TAT TAT AAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
528008 AAATACTCAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Done.