Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008086.1 Hibiscus syriacus cultivar Beakdansim tig00110596_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: 756749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:529567 original size:26 final size:25
Alignment explanation
Indices: 529526--529577 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 25
529516 AACCATACTT
529526 TTTTTTTTCTCATTTAGGTGTCTAA
1 TTTTTTTTCTCATTTAGGTGTCTAA
*
529551 TTTTTTTTGTCAGTTTAGGTGTCTAA
1 TTTTTTTTCTCA-TTTAGGTGTCTAA
529577 T
1 T
529578 GTTTCCAACG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.15, C:0.10, G:0.15, T:0.60
Consensus pattern (25 bp):
TTTTTTTTCTCATTTAGGTGTCTAA
Found at i:536696 original size:19 final size:19
Alignment explanation
Indices: 536672--536716 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
536662 ATATACACTT
*
536672 TTTAATTCATATCAATTTG
1 TTTAATTCATATCAATTTA
* *
536691 TTTAATTTATATCCATTTA
1 TTTAATTCATATCAATTTA
536710 TTTAATT
1 TTTAATT
536717 AGCCCACCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTAATTCATATCAATTTA
Found at i:536824 original size:24 final size:24
Alignment explanation
Indices: 536796--536842 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
536786 CCATTGCTCA
*
536796 TATAATTTACACCGAAGTGCCACG
1 TATAATATACACCGAAGTGCCACG
*
536820 TATAATATGCACCGAAGTGCCAC
1 TATAATATACACCGAAGTGCCAC
536843 ATAGATTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (24 bp):
TATAATATACACCGAAGTGCCACG
Found at i:536879 original size:24 final size:24
Alignment explanation
Indices: 536847--536919 Score: 112
Period size: 24 Copynumber: 3.0 Consensus size: 24
536837 TGCCACATAG
536847 ATTTGTCCCGAAGGTCCGCGTAGA
1 ATTTGTCCCGAAGGTCCGCGTAGA
*
536871 ATTTGTCCCGAAGGAT-CACGTAGA
1 ATTTGTCCCGAAGG-TCCGCGTAGA
*
536895 ATTTGTCCCGAAGGACCGCGTAGA
1 ATTTGTCCCGAAGGTCCGCGTAGA
536919 A
1 A
536920 CCCTCGATTC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
24 43 0.98
25 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.23
Consensus pattern (24 bp):
ATTTGTCCCGAAGGTCCGCGTAGA
Found at i:537735 original size:20 final size:20
Alignment explanation
Indices: 537694--537735 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
537684 TCAATTATAG
* *
537694 TATCGATGCCCTACTATTGA
1 TATCGATACCCTACTATCGA
*
537714 TATCGATACCCTAGTATCGA
1 TATCGATACCCTACTATCGA
537734 TA
1 TA
537736 CTACATGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (20 bp):
TATCGATACCCTACTATCGA
Found at i:538642 original size:23 final size:23
Alignment explanation
Indices: 538611--538679 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
538601 CACCATAGCT
* *
538611 CGTATAATTGCACCAAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
538634 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
* *
538657 CGTAGAATTACACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
538680 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.29, C:0.26, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:543771 original size:23 final size:23
Alignment explanation
Indices: 543740--543794 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
543730 CACCACAGCT
*
543740 CGTATAATTGCACCAAAGTGCCA
1 CGTAGAATTGCACCAAAGTGCCA
** *
543763 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCAAAGTGCCA
*
543786 CATAGAATT
1 CGTAGAATT
543795 ACACTGTAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCAAAGTGCCA
Found at i:543805 original size:23 final size:23
Alignment explanation
Indices: 543756--543808 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
543746 ATTGCACCAA
* *
543756 AGTGCCACGTAGAATTGCACCGG
1 AGTGCCACATAGAATTACACCGG
* * *
543779 AGTGCCGCATAGAATTACACTGT
1 AGTGCCACATAGAATTACACCGG
543802 AGTGCCA
1 AGTGCCA
543809 TATAATAATG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.21
Consensus pattern (23 bp):
AGTGCCACATAGAATTACACCGG
Found at i:546642 original size:45 final size:45
Alignment explanation
Indices: 546593--546680 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
546583 GAAAATCGAA
* * *
546593 TGCATTTTATGCATCGATGCACATACCATGTATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAACCATGCATCGATGCACTCAG
546638 TGCATTTGATGCATCGATGCACAAACCATGCATCGATGCACTC
1 TGCATTTGATGCATCGATGCACAAACCATGCATCGATGCACTC
546681 TGGCTATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.28
Consensus pattern (45 bp):
TGCATTTGATGCATCGATGCACAAACCATGCATCGATGCACTCAG
Found at i:546807 original size:20 final size:21
Alignment explanation
Indices: 546782--546836 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
546772 TTTACACTTG
546782 ATGCACCGATGCACC-TGGGT
1 ATGCACCGATGCACCATGGGT
*
546802 ATGCACCGATACACCATGGGT
1 ATGCACCGATGCACCATGGGT
*
546823 ATGCATCGATGCAC
1 ATGCACCGATGCAC
546837 TGACGCTCCC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.25, C:0.29, G:0.25, T:0.20
Consensus pattern (21 bp):
ATGCACCGATGCACCATGGGT
Found at i:546823 original size:21 final size:20
Alignment explanation
Indices: 546782--546832 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
546772 TTTACACTTG
*
546782 ATGCACCGATGCACCTGGGT
1 ATGCACCGATACACCTGGGT
546802 ATGCACCGATACACCATGGGT
1 ATGCACCGATACACC-TGGGT
*
546823 ATGCATCGAT
1 ATGCACCGAT
546833 GCACTGACGC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.22
Consensus pattern (20 bp):
ATGCACCGATACACCTGGGT
Found at i:548969 original size:22 final size:21
Alignment explanation
Indices: 548939--548999 Score: 54
Period size: 23 Copynumber: 2.8 Consensus size: 21
548929 CTTTTCTTTT
548939 TTTTCATGTAATATTTTTTTAC
1 TTTT-ATGTAATATTTTTTTAC
* *
548961 ATTTTATGTATTTTCTTTTTTAC
1 -TTTTATGTAATAT-TTTTTTAC
548984 -TTTA-GTATATATTTTT
1 TTTTATGTA-ATATTTTT
549000 ATTTTTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
20 7 0.22
21 6 0.19
22 7 0.22
23 12 0.38
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (21 bp):
TTTTATGTAATATTTTTTTAC
Found at i:548996 original size:24 final size:23
Alignment explanation
Indices: 548953--548998 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
548943 CATGTAATAT
*
548953 TTTTTTACATTTTATGTATTTTC
1 TTTTTTACATTTTATATATTTTC
548976 TTTTTTAC-TTTAGTATATATTTT
1 TTTTTTACATTT--TATATATTTT
548999 TATTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 8 0.40
24 9 0.45
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTTTTACATTTTATATATTTTC
Found at i:549065 original size:44 final size:41
Alignment explanation
Indices: 549012--549141 Score: 122
Period size: 44 Copynumber: 3.0 Consensus size: 41
549002 TTTTTTTAGA
549012 TTATATATATAAATATATTATTTTTTATTATCAGTTTTATTAAT
1 TTATATATATAAATATATTATTTTTTATTAT-A-TTTTATT-AT
* *
549056 TTATATATATATATATATTTACTTTTT-TTAT-TTTTATTAT
1 TTATATATATAAATATA-TTATTTTTTATTATATTTTATTAT
* * *
549096 ATATATATAT-ATTATTTTTACTTTTTTATTATTATTTTATTTAT
1 TTATATATATAAATA-TATTA-TTTTTTATTA-TATTTTA-TTAT
549140 TT
1 TT
549142 GTTTTATTTC
Statistics
Matches: 71, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
39 5 0.07
40 17 0.24
41 10 0.14
42 1 0.01
43 5 0.07
44 25 0.35
45 8 0.11
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (41 bp):
TTATATATATAAATATATTATTTTTTATTATATTTTATTAT
Found at i:549101 original size:32 final size:31
Alignment explanation
Indices: 549046--549150 Score: 108
Period size: 32 Copynumber: 3.3 Consensus size: 31
549036 TTATTATCAG
549046 TTTTATTAATTTATATATATATATATATTTACTTT
1 TTTTATT--TTTAT-TATATATATATATTTA-TTT
549081 TTTTATTTTTATTATATATATATATATTATTT
1 TTTTATTTTTATTATATATATATAT-TTATTT
* *
549113 TTACT-TTTTTATTAT-TAT-TTTATTTATTT
1 TT-TTATTTTTATTATATATATATATTTATTT
549142 GTTTTATTT
1 -TTTTATTT
549151 CTATATTTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
29 7 0.11
30 9 0.14
31 3 0.05
32 28 0.44
33 9 0.14
35 7 0.11
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.70
Consensus pattern (31 bp):
TTTTATTTTTATTATATATATATATTTATTT
Found at i:549150 original size:38 final size:39
Alignment explanation
Indices: 548989--549131 Score: 133
Period size: 38 Copynumber: 3.8 Consensus size: 39
548979 TTTACTTTAG
* * *
548989 TATA-TATTTTTATTTTTTTTA-GATTA-TATATATAAA
1 TATATTATTTTTACTTTTTTTATTATTATTATATATATA
549025 TATATTATTTTTTA-TTATCAGTTTTATTA--ATT-TATATATA
1 TATATTA-TTTTTACTT-T---TTTTATTATTATTATATATATA
* *
549065 TATA-TATATTTACTTTTTTTATTTTTATTATATATATA
1 TATATTATTTTTACTTTTTTTATTATTATTATATATATA
549103 TATATTATTTTTAC-TTTTTTATTATTATT
1 TATATTATTTTTACTTTTTTTATTATTATT
549132 TTATTTATTT
Statistics
Matches: 88, Mismatches: 6, Indels: 24
0.75 0.05 0.20
Matches are distributed among these distances:
35 7 0.08
36 4 0.05
37 7 0.08
38 39 0.44
39 12 0.14
40 12 0.14
41 6 0.07
42 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.65
Consensus pattern (39 bp):
TATATTATTTTTACTTTTTTTATTATTATTATATATATA
Found at i:549308 original size:15 final size:15
Alignment explanation
Indices: 549290--549319 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
549280 TATTTATTTC
549290 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
549305 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
549320 ACATGTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:550422 original size:19 final size:20
Alignment explanation
Indices: 550386--550423 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
550376 ACCTTACTAA
*
550386 CTCTTTTCATTTTTTTTCCT
1 CTCTTTTCATTTTATTTCCT
550406 CTCTTTT-ATTTTATTTCC
1 CTCTTTTCATTTTATTTCC
550424 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (20 bp):
CTCTTTTCATTTTATTTCCT
Found at i:551475 original size:23 final size:23
Alignment explanation
Indices: 551449--551493 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
551439 CACCACAGCT
*
551449 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
551472 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
551494 ATATAATAAT
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:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:551739 original size:149 final size:149
Alignment explanation
Indices: 551469--551775 Score: 614
Period size: 149 Copynumber: 2.1 Consensus size: 149
551459 CACCGAAGTG
551469 CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAG
1 CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAG
551534 AATCATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGAT
66 AATCATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGAT
551599 ATACATATGTCCTAAAGAA
131 ATACATATGTCCTAAAGAA
551618 CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAG
1 CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAG
551683 AATCATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGAT
66 AATCATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGAT
551748 ATACATATGTCCTAAAGAA
131 ATACATATGTCCTAAAGAA
551767 CCGCGTAGA
1 CCGCGTAGA
551776 CCCTCTACCC
Statistics
Matches: 158, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 158 1.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAG
AATCATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGAT
ATACATATGTCCTAAAGAA
Found at i:551890 original size:24 final size:26
Alignment explanation
Indices: 551863--551923 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 26
551853 TATCGCGTAG
551863 ACATAGTAT-TTT-CATACCTTTATC
1 ACATAGTATATTTACATACCTTTATC
551887 ACATAGGCATATCATTTACATACCTTTATC
1 ACATA-G--TAT-ATTTACATACCTTTATC
551917 ACATAGT
1 ACATAGT
551924 TCATATAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
24 5 0.16
25 1 0.03
27 4 0.13
29 4 0.13
30 17 0.55
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (26 bp):
ACATAGTATATTTACATACCTTTATC
Found at i:552384 original size:67 final size:67
Alignment explanation
Indices: 552286--552437 Score: 232
Period size: 67 Copynumber: 2.3 Consensus size: 67
552276 TTTTTCTCAT
* *
552286 GGGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCACAAGCATTCTGGAATTTCATATACGA
1 GGGGGTATCGGTT-CCCCCCTGGGGGTATCGATTCCCCACAAGCATTCTGGAAATTCATATACGA
552351 TGA
65 TGA
* * * * *
552354 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGTATTCTGGAAATTCATATCCGTT
1 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCACAAGCATTCTGGAAATTCATATACGAT
552419 GA
66 GA
552421 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
552438 TTGAATGGGT
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
67 65 0.84
68 12 0.16
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.28
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCACAAGCATTCTGGAAATTCATATACGAT
GA
Found at i:558526 original size:23 final size:23
Alignment explanation
Indices: 558500--558544 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
558490 CACCACAGCT
*
558500 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
558523 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
558545 ATATAATAAT
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:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:558790 original size:149 final size:149
Alignment explanation
Indices: 558520--558826 Score: 614
Period size: 149 Copynumber: 2.1 Consensus size: 149
558510 CACCGAAGTG
558520 CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAG
1 CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAG
558585 AATCATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGAT
66 AATCATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGAT
558650 ATACATATGTCCTAAAGAA
131 ATACATATGTCCTAAAGAA
558669 CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAG
1 CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAG
558734 AATCATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGAT
66 AATCATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGAT
558799 ATACATATGTCCTAAAGAA
131 ATACATATGTCCTAAAGAA
558818 CCGCGTAGA
1 CCGCGTAGA
558827 CCCTCTACCC
Statistics
Matches: 158, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 158 1.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAG
AATCATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGAT
ATACATATGTCCTAAAGAA
Found at i:558941 original size:24 final size:26
Alignment explanation
Indices: 558914--558974 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 26
558904 TATCGCGTAG
558914 ACATAGTAT-TTT-CATACCTTTATC
1 ACATAGTATATTTACATACCTTTATC
558938 ACATAGGCATATCATTTACATACCTTTATC
1 ACATA-G--TAT-ATTTACATACCTTTATC
558968 ACATAGT
1 ACATAGT
558975 TCATATAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
24 5 0.16
25 1 0.03
27 4 0.13
29 4 0.13
30 17 0.55
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (26 bp):
ACATAGTATATTTACATACCTTTATC
Found at i:559435 original size:67 final size:67
Alignment explanation
Indices: 559337--559488 Score: 232
Period size: 67 Copynumber: 2.3 Consensus size: 67
559327 TTTTTCTCAT
* *
559337 GGGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCACAAGCATTCTGGAATTTCATATACGA
1 GGGGGTATCGGTT-CCCCCCTGGGGGTATCGATTCCCCACAAGCATTCTGGAAATTCATATACGA
559402 TGA
65 TGA
* * * * *
559405 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGTATTCTGGAAATTCATATCCGTT
1 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCACAAGCATTCTGGAAATTCATATACGAT
559470 GA
66 GA
559472 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
559489 TTGAATGGGT
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
67 65 0.84
68 12 0.16
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.28
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCACAAGCATTCTGGAAATTCATATACGAT
GA
Found at i:561183 original size:8 final size:8
Alignment explanation
Indices: 561170--561208 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
561160 GAACATTTCA
*
561170 TGCATTCT
1 TGCATTTT
561178 TGCA-TTT
1 TGCATTTT
561185 TGCATTTT
1 TGCATTTT
*
561193 TGCCTTTT
1 TGCATTTT
561201 TGCATTTT
1 TGCATTTT
561209 CATCTACAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:562405 original size:9 final size:9
Alignment explanation
Indices: 562393--562442 Score: 64
Period size: 9 Copynumber: 5.3 Consensus size: 9
562383 TAAAAAGGGC
562393 AAAAAGAAAA
1 AAAAAG-AAA
562403 AAAAAGAAAA
1 AAAAAG-AAA
*
562413 AAAAAGCAA
1 AAAAAGAAA
*
562422 AAAAAGAAT
1 AAAAAGAAA
562431 AAAAAGAAA
1 AAAAAGAAA
562440 AAA
1 AAA
562443 GAAAAAGGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
9 20 0.56
10 16 0.44
ACGTcount: A:0.86, C:0.02, G:0.10, T:0.02
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:562406 original size:10 final size:10
Alignment explanation
Indices: 562393--562442 Score: 68
Period size: 10 Copynumber: 5.2 Consensus size: 10
562383 TAAAAAGGGC
562393 AAAAAGAAAA
1 AAAAAGAAAA
562403 AAAAAGAAAA
1 AAAAAGAAAA
*
562413 AAAAAG-CAA
1 AAAAAGAAAA
*
562422 AAAAAG-AAT
1 AAAAAGAAAA
562431 AAAAAGAAAA
1 AAAAAGAAAA
562441 AA
1 AA
562443 GAAAAAGGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
9 15 0.43
10 20 0.57
ACGTcount: A:0.86, C:0.02, G:0.10, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:563075 original size:22 final size:22
Alignment explanation
Indices: 563047--563090 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
563037 AGCTACTCCA
563047 TCAAACC-TTTGAGCATCAAATG
1 TCAAACCATTT-AGCATCAAATG
563069 TCAAACCATTTAGCATCAAATG
1 TCAAACCATTTAGCATCAAATG
563091 AACAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (22 bp):
TCAAACCATTTAGCATCAAATG
Found at i:564163 original size:36 final size:36
Alignment explanation
Indices: 564055--564178 Score: 160
Period size: 36 Copynumber: 3.4 Consensus size: 36
564045 ATTGAAAACA
* * *
564055 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
* *
564091 TTTCCCTTGGAACTAAGTTTT-GTCTCTCTTAAGACAG
1 TTTCCCTTGAAAC-AA-TTTTCGTCTCTCTTGAGACAG
* *
564128 TTTCTCTTGAAACAATTTTCGTCTATCTTGAGACAG
1 TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
564164 TTTCCCTTGAAACAA
1 TTTCCCTTGAAACAA
564179 AACCTTTGAA
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
35 4 0.05
36 41 0.55
37 27 0.36
38 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
Found at i:564272 original size:67 final size:68
Alignment explanation
Indices: 564154--564310 Score: 205
Period size: 68 Copynumber: 2.4 Consensus size: 68
564144 TTTCGTCTAT
* **
564154 CTTGAGACAGTTTCCCTTG-AA-ACAAAACCTTTGAATTTATTTCCCCTAAAACA-AATTTT-TT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT
564215 CTCC
66 -TCC
* * *
564219 CTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACATAATTTTGTT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT
564284 TCC
66 TCC
* *
564287 CTTGAGACCGTTTCTCATGAAACA
1 CTTGAGACAGTTTCTCTTGAAACA
564311 ACAGATATCT
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 17 0.22
66 2 0.03
67 28 0.35
68 30 0.38
69 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (68 bp):
CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT
TCC
Found at i:565138 original size:105 final size:105
Alignment explanation
Indices: 564954--565677 Score: 1131
Period size: 105 Copynumber: 7.0 Consensus size: 105
564944 GCACTCGAGG
* * ** *
564954 CAACACAAGTTCAACTTCACAACGAAGGGACAACTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
*
565019 AGCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
565060 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
565125 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
565165 CAACGCAAGTGCAACTTCACGACGAAGGGACCGCTGCCTGT---CAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* * *
565227 ACCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
565267 CAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
565332 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * **
565372 CAACGCAAGTTCAACTTCACGACGAAGAGACCGCTACTTGTCAACAACAACTTCCCAATCGCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
565437 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
565477 CAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
565542 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
565582 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** * *
565642 TTCAATTTCAACTTCACGACGGAGGATATTGGACTC
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTC
565678 TGAACAATGC
Statistics
Matches: 581, Mismatches: 34, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
100 37 0.06
101 1 0.00
102 99 0.17
103 2 0.00
104 2 0.00
105 401 0.69
106 39 0.07
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:565324 original size:207 final size:207
Alignment explanation
Indices: 564954--565677 Score: 1103
Period size: 207 Copynumber: 3.5 Consensus size: 207
564944 GCACTCGAGG
* * ** *
564954 CAACACAAGTTCAACTTCACAACGAAGGGACAACTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGT---C-AACAACTTCTCAATTTCAG
*
565019 AGCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
62 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
565084 AAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAG
127 AAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAG
565149 GATATTGGACTTCAGA
192 GATATTGGACTTCAGA
* * *
565165 CAACGCAAGTGCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACTTCTCAATTTCAGAACC
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACTTCTCAATTTCAGAGCC
* *
565230 AATTTCAACTTCACAATGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGG
66 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
565295 GACTGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATA
131 GACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATA
565360 TTGGACTTCAGA
196 TTGGACTTCAGA
* * * **
565372 CAACGCAAGTTCAACTTCACGACGAAGAGACCGCTACTTGTCAACAACAACTTCCCAATCGCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGT---CAACAACTTCTCAATTTCAGA
*
565437 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGA
63 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* *
565502 AGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGG
128 AGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
*
565567 ATATTGGACTCCAGA
193 ATATTGGACTTCAGA
* **
565582 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATT-TC-A-TTCAGATT
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACTTCTCAATTTCAGAGC
* *
565644 CAATTTCAACTTCACGACGGAGGATATTGGACTC
65 CAATTTCAACTTCACAACGAAGGATATTGGACTC
565678 TGAACAATGC
Statistics
Matches: 470, Mismatches: 39, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
205 36 0.08
206 1 0.00
207 200 0.43
208 5 0.01
210 194 0.41
211 34 0.07
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (207 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACTTCTCAATTTCAGAGCC
AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
GACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATA
TTGGACTTCAGA
Found at i:566772 original size:22 final size:21
Alignment explanation
Indices: 566742--566802 Score: 54
Period size: 23 Copynumber: 2.8 Consensus size: 21
566732 CTTTTCTTTT
566742 TTTTCATGTAATATTTTTTTAC
1 TTTT-ATGTAATATTTTTTTAC
* *
566764 ATTTTATGTATTTTCTTTTTTAC
1 -TTTTATGTAATAT-TTTTTTAC
566787 -TTTA-GTATATATTTTT
1 TTTTATGTA-ATATTTTT
566803 ATTTTTTTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
20 7 0.22
21 6 0.19
22 7 0.22
23 12 0.38
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (21 bp):
TTTTATGTAATATTTTTTTAC
Found at i:566799 original size:24 final size:23
Alignment explanation
Indices: 566756--566801 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
566746 CATGTAATAT
*
566756 TTTTTTACATTTTATGTATTTTC
1 TTTTTTACATTTTATATATTTTC
566779 TTTTTTAC-TTTAGTATATATTTT
1 TTTTTTACATTT--TATATATTTT
566802 TATTTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 8 0.40
24 9 0.45
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTTTTACATTTTATATATTTTC
Found at i:566887 original size:37 final size:36
Alignment explanation
Indices: 566798--566926 Score: 129
Period size: 41 Copynumber: 3.4 Consensus size: 36
566788 TTAGTATATA
* *
566798 TTTTTATTTTTTTA-GATTATATATAAATATATTA-T
1 TTTTTATTTTTTTATTATTATATATATATAT-TTACT
566833 TTTTTATTATCAGTTTTATTAATTATATATATATATTTACT
1 TTTTTATT-T---TTTTATT-ATTATATATATATATTTACT
*
566874 TTTTTATTTTTTTATTA-TATATATATTTATTTTACT
1 TTTTTATTTTTTTATTATTATATATATATA-TTTACT
*
566910 TTTATTATTATTTTATT
1 TTT-TTATTTTTTTATT
566927 TATTTGTTTT
Statistics
Matches: 81, Mismatches: 4, Indels: 16
0.80 0.04 0.16
Matches are distributed among these distances:
35 19 0.23
36 11 0.14
37 19 0.23
39 5 0.06
40 4 0.05
41 23 0.28
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (36 bp):
TTTTTATTTTTTTATTATTATATATATATATTTACT
Found at i:566912 original size:29 final size:28
Alignment explanation
Indices: 566846--566940 Score: 86
Period size: 30 Copynumber: 3.3 Consensus size: 28
566836 TTATTATCAG
*
566846 TTTTA-TTAATTA-TATATATATATTTA
1 TTTTATTTTATTATTATATATATATTTA
*
566872 CTTTTTTATTTTTTTATTATATATATATTTA
1 ---TTTTATTTTATTATTATATATATATTTA
* * *
566903 TTTTACTTTTATTATTATTTTATTTATTTG
1 TTTTA-TTTTATTATTA-TATATATATTTA
566933 TTTTATTT
1 TTTTATTT
566941 CTATATTTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
28 5 0.09
29 18 0.32
30 19 0.34
31 14 0.25
ACGTcount: A:0.26, C:0.02, G:0.01, T:0.71
Consensus pattern (28 bp):
TTTTATTTTATTATTATATATATATTTA
Found at i:566947 original size:21 final size:20
Alignment explanation
Indices: 566909--566982 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 20
566899 TTTATTTTAC
566909 TTTTATTATTATTT-TAT-TT
1 TTTTATT-TTATTTCTATATT
* *
566928 ATTTGTTTTATTTCTATATT
1 TTTTATTTTATTTCTATATT
* *
566948 TTTT-TCTTCTTTTTCTTTATT
1 TTTTAT-TT-TATTTCTATATT
566969 TTTTATATTTATTT
1 TTTTAT-TTTATTT
566983 TACTTACTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
18 6 0.14
19 9 0.21
20 7 0.16
21 18 0.42
22 3 0.07
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.77
Consensus pattern (20 bp):
TTTTATTTTATTTCTATATT
Found at i:566947 original size:29 final size:27
Alignment explanation
Indices: 566866--566984 Score: 73
Period size: 29 Copynumber: 4.1 Consensus size: 27
566856 TATATATATA
*
566866 TATTTACTTTTTTATTTT-T-TTATTAT
1 TATTTATTTTTTTATTTTATATTATT-T
*
566892 ATATATATTTATTTTACTTTTATTATTATTT
1 -TATTTATTT-TTTTA-TTTTA-TATTATTT
*
566923 TATTTATTTGTTTTATTTCTATATTTTTT
1 TATTTATTT-TTTTATTT-TATATTATTT
*
566952 TCTTCT-TTTTCTTTATTTTTTATATTTATTT
1 TATT-TATTTT-TTTA--TTTTATA-TTATTT
566983 TA
1 TA
566985 CTTACTATTT
Statistics
Matches: 73, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
27 7 0.10
28 6 0.08
29 24 0.33
30 20 0.27
31 11 0.15
32 5 0.07
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.74
Consensus pattern (27 bp):
TATTTATTTTTTTATTTTATATTATTT
Found at i:567089 original size:15 final size:15
Alignment explanation
Indices: 567071--567100 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
567061 TATTTATTTC
567071 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
567086 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
567101 ACATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:571648 original size:2 final size:2
Alignment explanation
Indices: 571641--571669 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
571631 TTCTTTACTT
571641 TG TG TG TG 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 T
571670 TCTGTGGGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:601307 original size:16 final size:16
Alignment explanation
Indices: 601264--601314 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
601254 ATGGTACTTT
601264 TGGACCAACTAAGTTA
1 TGGACCAACTAAGTTA
* * *
601280 TGTATCATCTAAGTTA
1 TGGACCAACTAAGTTA
*
601296 TGGACCAACTAAGATA
1 TGGACCAACTAAGTTA
601312 TGG
1 TGG
601315 TGTTTCTAGA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (16 bp):
TGGACCAACTAAGTTA
Found at i:602874 original size:32 final size:32
Alignment explanation
Indices: 602772--602894 Score: 119
Period size: 31 Copynumber: 3.9 Consensus size: 32
602762 CCTCGACAAC
* **
602772 TGTCCATAGGTCCCGAAGAAGC-TAGGTAA-GC
1 TGTCCATATGTCCCGAAGAA-CATAGGTAATAT
* **
602803 TGTCCATATGTTCCTTAGAACATAGGT-ATAT
1 TGTCCATATGTCCCGAAGAACATAGGTAATAT
*
602834 TGTCCATATGTCCCGAA-AGACATAGGTAATTT
1 TGTCCATATGTCCCGAAGA-ACATAGGTAATAT
* *
602866 TGTCCATATGTTCCGTAGAACATAGGTAA
1 TGTCCATATGTCCCGAAGAACATAGGTAA
602895 ACCCTCGACT
Statistics
Matches: 75, Mismatches: 12, Indels: 9
0.78 0.12 0.09
Matches are distributed among these distances:
30 3 0.04
31 43 0.57
32 28 0.37
33 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (32 bp):
TGTCCATATGTCCCGAAGAACATAGGTAATAT
Found at i:604751 original size:23 final size:23
Alignment explanation
Indices: 604725--604849 Score: 101
Period size: 23 Copynumber: 5.3 Consensus size: 23
604715 CACCACAACT
604725 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
604748 CATATAATTGCACC-AGAGTACCG
1 CATATAATTGCACCGA-AGTGCCA
* *
604771 CATAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* * *
604794 TATAATAATTGCATC-AGAGTGCCG
1 CAT-ATAATTGCACCGA-AGTGCCA
* * *
604818 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
604841 TATAATAAT
1 CAT-ATAAT
604850 GTCCATAAGA
Statistics
Matches: 76, Mismatches: 20, Indels: 11
0.71 0.19 0.10
Matches are distributed among these distances:
22 1 0.01
23 55 0.72
24 20 0.26
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:604824 original size:47 final size:47
Alignment explanation
Indices: 604725--604849 Score: 189
Period size: 47 Copynumber: 2.7 Consensus size: 47
604715 CACCACAACT
* * *
604725 CATATAATTGCACCGAAGTGCCACAT-ATAATTGCACCAGAGTACCG
1 CATAGAATTGCACCGTAGTGCCATATAATAATTGCACCAGAGTACCG
* *
604771 CATAGAATTGCACCGTAGTGCCATATAATAATTGCATCAGAGTGCCG
1 CATAGAATTGCACCGTAGTGCCATATAATAATTGCACCAGAGTACCG
*
604818 CGTAGAATTGCACCGTAGTGCCATATAATAAT
1 CATAGAATTGCACCGTAGTGCCATATAATAAT
604850 GTCCATAAGA
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
46 23 0.32
47 49 0.68
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (47 bp):
CATAGAATTGCACCGTAGTGCCATATAATAATTGCACCAGAGTACCG
Found at i:604990 original size:103 final size:103
Alignment explanation
Indices: 604860--605176 Score: 580
Period size: 103 Copynumber: 3.1 Consensus size: 103
604850 GTCCATAAGA
* * *
604860 ACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACT
604925 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
**
604963 ACCACATATCATTCCTTAAGAATCATATACATATGCCAATAATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACT
605028 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
*
605066 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCCCCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACT
605131 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
605169 ACCACATA
1 ACCACATA
605177 GACCCTCGAC
Statistics
Matches: 206, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 206 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (103 bp):
ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACT
TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
Found at i:605983 original size:22 final size:22
Alignment explanation
Indices: 605940--605983 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
605930 AATTCTGTCG
* *
605940 TTTGAAAGGGTATCGGTACCCC
1 TTTGAAAGGGTACCGATACCCC
* *
605962 TTTGAATGGGTACCGATTCCCC
1 TTTGAAAGGGTACCGATACCCC
605984 CTAACCCAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (22 bp):
TTTGAAAGGGTACCGATACCCC
Found at i:610686 original size:23 final size:23
Alignment explanation
Indices: 610660--610784 Score: 124
Period size: 23 Copynumber: 5.3 Consensus size: 23
610650 CACCACAGCT
*
610660 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGGAGTGCCA
*
610683 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGGAGTGCCA
* * *
610706 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGGAGTGCCA
* * *
610729 TATAATAATTACACCGGAGTGCCG
1 CAT-ATAATTGCACCGGAGTGCCA
* * *
610753 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGGAGTGCCA
*
610776 TATAATAAT
1 CAT-ATAAT
610785 GTCCATAAGG
Statistics
Matches: 79, Mismatches: 21, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
23 58 0.73
24 21 0.27
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGGAGTGCCA
Found at i:610750 original size:47 final size:47
Alignment explanation
Indices: 610665--610784 Score: 206
Period size: 47 Copynumber: 2.6 Consensus size: 47
610655 CAGCTCATAT
* * *
610665 AATTGCACCGAAGTGCCACAT-ATAATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGTAGTGCCATATAATAATTACACCGGAGTGCCGCGTAG
610711 AATTGCACCGTAGTGCCATATAATAATTACACCGGAGTGCCGCGTAG
1 AATTGCACCGTAGTGCCATATAATAATTACACCGGAGTGCCGCGTAG
610758 AATTGCACCGTAGTGCCATATAATAAT
1 AATTGCACCGTAGTGCCATATAATAAT
610785 GTCCATAAGG
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
46 19 0.27
47 51 0.73
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (47 bp):
AATTGCACCGTAGTGCCATATAATAATTACACCGGAGTGCCGCGTAG
Found at i:610962 original size:103 final size:103
Alignment explanation
Indices: 610791--611111 Score: 570
Period size: 103 Copynumber: 3.1 Consensus size: 103
610781 TAATGTCCAT
* * *
610791 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
610856 GACTTCACACATGTTCTAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
**
610894 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAATAATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
610959 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
610997 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCCCCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
611062 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
611100 AAAGACCACATA
1 AAGGACCACATA
611112 GACCCTCGAC
Statistics
Matches: 208, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 208 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:615041 original size:31 final size:31
Alignment explanation
Indices: 615006--615101 Score: 102
Period size: 31 Copynumber: 3.1 Consensus size: 31
614996 TACATGTTGC
* *
615006 TGATGTGATACATATCACGTGTCGAAAGTGA
1 TGATGTGATACATATCACATGTTGAAAGTGA
* * * * *
615037 TGATGTAATAAATGTCACTTGTTAAAAGTGA
1 TGATGTGATACATATCACATGTTGAAAGTGA
* * *
615068 TGATGTGTTACATATCCCATGTTGAAAATGA
1 TGATGTGATACATATCACATGTTGAAAGTGA
615099 TGA
1 TGA
615102 CAATGTACAT
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.33
Consensus pattern (31 bp):
TGATGTGATACATATCACATGTTGAAAGTGA
Found at i:615127 original size:31 final size:32
Alignment explanation
Indices: 615092--615166 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 32
615082 TCCCATGTTG
* *
615092 AAAATGATGACAATG-TACATATCGTA-TGTCA
1 AAAATGATGACAATGACACATATC-AAGTGTCA
*
615123 AAAATAATGAC-ATGACACATATCAAGTGTCA
1 AAAATGATGACAATGACACATATCAAGTGTCA
615154 AAAAGTGATGACA
1 AAAA-TGATGACA
615167 TGAAATATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
30 4 0.11
31 26 0.72
32 6 0.17
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (32 bp):
AAAATGATGACAATGACACATATCAAGTGTCA
Found at i:619178 original size:19 final size:19
Alignment explanation
Indices: 619139--619176 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
619129 AATATATATA
619139 TATATATATATGCTAAAAT
1 TATATATATATGCTAAAAT
619158 TATATATA-AT-CT-AAAT
1 TATATATATATGCTAAAAT
619174 TAT
1 TAT
619177 TAACGTGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 2 0.11
18 2 0.11
19 8 0.42
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (19 bp):
TATATATATATGCTAAAAT
Found at i:622368 original size:59 final size:59
Alignment explanation
Indices: 622300--622425 Score: 141
Period size: 59 Copynumber: 2.1 Consensus size: 59
622290 TAGGGTAAGC
* *
622300 TACACAAATGATC-CATGACTAT-AGAATGTTATTTTGTTGAGTC-CTCTAATTATTAAAAGT
1 TACA-AAATGATCTCACGACTATAAG-ATGTT-TTTTGTTGAGTCTCT-TAACTATTAAAAGT
* * *
622360 TACAAAATGATCTCCCGCCTATAAGATGTTTTTTGTTGAGTCTCTTGACTATTAAAAGT
1 TACAAAATGATCTCACGACTATAAGATGTTTTTTGTTGAGTCTCTTAACTATTAAAAGT
*
622419 TAGAAAA
1 TACAAAA
622426 ATTGTCATTT
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
59 38 0.67
60 17 0.30
61 2 0.04
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (59 bp):
TACAAAATGATCTCACGACTATAAGATGTTTTTTGTTGAGTCTCTTAACTATTAAAAGT
Found at i:623604 original size:26 final size:26
Alignment explanation
Indices: 623553--623628 Score: 68
Period size: 25 Copynumber: 3.0 Consensus size: 26
623543 TTTAAACATT
* *
623553 TTGATTTATTTTGATGTT-AAAA-AAA
1 TTGATTAAATTTGAT-TTAAAAATAAA
*
623578 TTGATTCAATTTGATTTAAAAATAAA
1 TTGATTAAATTTGATTTAAAAATAAA
* *
623604 -TGAATAAATTTGAGTTATAAAATAA
1 TTGATTAAATTTGATTTA-AAAATAA
623629 GACTTAAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
24 2 0.05
25 31 0.72
26 10 0.23
ACGTcount: A:0.46, C:0.01, G:0.11, T:0.42
Consensus pattern (26 bp):
TTGATTAAATTTGATTTAAAAATAAA
Found at i:623613 original size:25 final size:25
Alignment explanation
Indices: 623562--623628 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
623552 TTTGATTTAT
* * *
623562 TTTGATGTTAAAAA-AATTGATTCAA
1 TTTGAT-TTAAAAATAAATGAATAAA
623587 TTTGATTTAAAAATAAATGAATAAA
1 TTTGATTTAAAAATAAATGAATAAA
*
623612 TTTGAGTTATAAAATAA
1 TTTGATTTA-AAAATAA
623629 GACTTAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 7 0.19
25 22 0.61
26 7 0.19
ACGTcount: A:0.49, C:0.01, G:0.10, T:0.39
Consensus pattern (25 bp):
TTTGATTTAAAAATAAATGAATAAA
Found at i:630829 original size:14 final size:14
Alignment explanation
Indices: 630810--630836 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
630800 TCTATTGGAG
630810 AAAAAGAAAAAGAA
1 AAAAAGAAAAAGAA
630824 AAAAAGAAAAAGA
1 AAAAAGAAAAAGA
630837 GAACTAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAGAA
Found at i:632590 original size:20 final size:20
Alignment explanation
Indices: 632565--632616 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
632555 ACTGTAGACT
632565 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
632585 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
*
632605 ATCACAACGCGA
1 ATCGCAACGCGA
632617 TTTCAACTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.48, C:0.23, G:0.19, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:634639 original size:18 final size:17
Alignment explanation
Indices: 634604--634636 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
634594 GGAAACATTA
634604 TTATTTCTACGATTTTG
1 TTATTTCTACGATTTTG
634621 TTATTTCTACGATTTT
1 TTATTTCTACGATTTT
634637 TGTATATTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.12, G:0.09, T:0.61
Consensus pattern (17 bp):
TTATTTCTACGATTTTG
Found at i:638799 original size:36 final size:36
Alignment explanation
Indices: 638752--638826 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 36
638742 AAATCAAACA
*
638752 AACCGATAATGTAAGGGATTAAAATATTTTTCTTTG
1 AACCGATAATGTAAGGGATTAAAACATTTTTCTTTG
* *
638788 AACCGATAATGTAATGGATTAAAACCTTTTTCTTTG
1 AACCGATAATGTAAGGGATTAAAACATTTTTCTTTG
638824 AAC
1 AAC
638827 TGGTGACAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (36 bp):
AACCGATAATGTAAGGGATTAAAACATTTTTCTTTG
Found at i:640421 original size:28 final size:30
Alignment explanation
Indices: 640361--640422 Score: 76
Period size: 28 Copynumber: 2.1 Consensus size: 30
640351 AATAAAACAG
*
640361 AAGATGCCGAATGATCCAAACATCTATCTA
1 AAGATGCCGAATGATCCAAACATCTATCGA
*
640391 AAGAT-CCG-ATGATCC-AACATCTTTCCGA
1 AAGATGCCGAATGATCCAAACATCTAT-CGA
640419 AAGA
1 AAGA
640423 AGTCGATGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 8 0.28
28 13 0.45
29 3 0.10
30 5 0.17
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.23
Consensus pattern (30 bp):
AAGATGCCGAATGATCCAAACATCTATCGA
Found at i:641399 original size:29 final size:29
Alignment explanation
Indices: 641342--641426 Score: 129
Period size: 30 Copynumber: 2.9 Consensus size: 29
641332 CTCACCTAAC
641342 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
641372 TAAATGATGGTAAGCAATGACATC-TTAAT
1 TAAATGAT-GTAAGCAATGACATCATTAAT
*
641401 TAAATGATGTAAGTAAT-ACATCATTA
1 TAAATGATGTAAGCAATGACATCATTA
641427 GTTTGGGTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
27 5 0.10
28 11 0.21
29 17 0.33
30 19 0.37
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:646073 original size:29 final size:29
Alignment explanation
Indices: 646035--646109 Score: 123
Period size: 29 Copynumber: 2.6 Consensus size: 29
646025 CTAACTAAAT
*
646035 TGTAAACAATGACATCATTAATTAAATGA
1 TGTAAGCAATGACATCATTAATTAAATGA
*
646064 TGTAAGCAATGACATCTTTAATTAAATGA
1 TGTAAGCAATGACATCATTAATTAAATGA
*
646093 TGTAAGTAATGACATCA
1 TGTAAGCAATGACATCA
646110 ATTTAGTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (29 bp):
TGTAAGCAATGACATCATTAATTAAATGA
Found at i:650760 original size:15 final size:16
Alignment explanation
Indices: 650740--650771 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
650730 TATCGTTAAC
650740 CCCTTCCTC-CCTCCT
1 CCCTTCCTCTCCTCCT
650755 CCCTTCCTCTCCTCCT
1 CCCTTCCTCTCCTCCT
650771 C
1 C
650772 TTTATCTGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (16 bp):
CCCTTCCTCTCCTCCT
Found at i:651826 original size:471 final size:474
Alignment explanation
Indices: 650922--651877 Score: 1467
Period size: 471 Copynumber: 2.0 Consensus size: 474
650912 ATTGATCAAA
*
650922 CAGAAAAGGATATATGGGATTTTCCGACGAGATTCGGGGGCCCTCTCCATGGCGAAAGGAGGTAA
1 CAGAAAAGGAGATATGGGATTTTCCGACGAGATTCGGGGGCCCTCTCCATGGCGAAAGGAGGTAA
* * * *
650987 GTCTCGGCGAGTGGCTAGTGAGGTTTTGGTCGGAATGAGGTGGCGCTCCTATTGGTATCGGCAGT
66 GTCTCGGCGAATGGCTAGTGAGGTTTTGGTCAGAATGAGGCGACGCTCCTATTGGTATCGGCAGT
* ** *
651052 GACGATCACTGATAACTGACGACAAAATCGAGGATGGGTGTTCAAATGATTTTTTGTGATTTGGG
131 GACGATCACCGATAACTGACGACAAAATCGAGGATGGGTGTTCAAACAATTTTTTGTGATTTGAG
* * *
651117 ATAACGGTGGATAATGAGTATGAATCAGGGTCGAGGTGTGGTCGAGGCCACATCGGTGACGATGG
196 AAAACGATGGACAATGAGTATGAATCAGGGTCGA------G--GAGGCCACATCGGTGACGATGG
* * *
651182 TGATGGTGGTGTGATCCACCGCTGACCAGAGGTGGGTGGTGGTGTGAGTGAGAGAAGAAGAAGAA
253 TGATGGCGGTGTAACCCACCGCTGACCAGA---GGGTGGTGGTGTGAGTGAGAGAAGAAGAAGAA
* * * *
651247 AACGAGGAATAAGAAGGGGGAGGGAGTTAATGGCGGTTAAGTGCCACGTCAGCAAATGGTTACAA
315 AACAAGGAATAAGAAGGGGGAGGAAGTTAACGGCAGTTAAGTGCCACGTCAGCAAATGGTTACAA
* *
651312 TAGGGACCTTATTGTAAACGATTAAAAGTCAGGTGACCAAAATGAAAGCGCCCCTAAAAGTTAGA
380 TAGGGACCTTATTGCAAACGATTAAAAGTCAGGTGACCAAAATGAAAGCACCCC-AAAAGTTAGA
* *
651377 TAC-TGTACTACAAGTTTTAAAAGTTAGGTG
444 TACTTGTACTACAACTTTCAAAAGTTAGGTG
651407 CAGAAAAGGAGATATGGGATTTTCCGACGAGATTC-GGGGCCCTCTCCATGGCGAAAGGAGGTAA
1 CAGAAAAGGAGATATGGGATTTTCCGACGAGATTCGGGGGCCCTCTCCATGGCGAAAGGAGGTAA
*
651471 GTCTCGGCGAATGGCTAGTGAGGTTTTGGTCAGAATGAGGCGACGCTCCTATTGGTATCGGCGGT
66 GTCTCGGCGAATGGCTAGTGAGGTTTTGGTCAGAATGAGGCGACGCTCCTATTGGTATCGGCAGT
*
651536 GACGATCACCGATAACTGACGACAAAGATCGAGGATGGGTGTTCGAACAATTTTTTGTGATTTGA
131 GACGATCACCGATAACTGACGACAAA-ATCGAGGATGGGTGTTCAAACAATTTTTTGTGATTTGA
*
651601 GACAAACGATGGACAATGAGTATGAATCAGGGGTCGA-GAGGCCACATCGGTGATGATGGTGATG
195 GA-AAACGATGGACAATGAGTATGAATCA-GGGTCGAGGAGGCCACATCGGTGACGATGGTGATG
651665 GCGGTGTAACCCACCGCTGACCAGA-GGT-G-GG-GTGAGTGAGAGAAGAAGAAGAAAACAAGGA
258 GCGGTGTAACCCACCGCTGACCAGAGGGTGGTGGTGTGAGTGAGAGAAGAAGAAGAAAACAAGGA
651726 ATAAGAAGGGGGAGGAAGTTAACGGCAGTTAAGTGCCACGTCAGCAAATGGTTACAATAGGGACC
323 ATAAGAAGGGGGAGGAAGTTAACGGCAGTTAAGTGCCACGTCAGCAAATGGTTACAATAGGGACC
* * *
651791 TTATTGCAAACGATTAAAAGTCAGGTGATCAAAATGCAAGCACCCCAAAAGTTAGATGCTTGTAC
388 TTATTGCAAACGATTAAAAGTCAGGTGACCAAAATGAAAGCACCCCAAAAGTTAGATACTTGTAC
651856 TACAACTTTCAAAAGTTAGGTG
453 TACAACTTTCAAAAGTTAGGTG
651878 ACCAAAATAC
Statistics
Matches: 438, Mismatches: 29, Indels: 22
0.90 0.06 0.04
Matches are distributed among these distances:
470 12 0.03
471 158 0.36
472 2 0.00
473 1 0.00
474 3 0.01
478 48 0.11
484 114 0.26
485 70 0.16
486 23 0.05
487 7 0.02
ACGTcount: A:0.30, C:0.15, G:0.32, T:0.22
Consensus pattern (474 bp):
CAGAAAAGGAGATATGGGATTTTCCGACGAGATTCGGGGGCCCTCTCCATGGCGAAAGGAGGTAA
GTCTCGGCGAATGGCTAGTGAGGTTTTGGTCAGAATGAGGCGACGCTCCTATTGGTATCGGCAGT
GACGATCACCGATAACTGACGACAAAATCGAGGATGGGTGTTCAAACAATTTTTTGTGATTTGAG
AAAACGATGGACAATGAGTATGAATCAGGGTCGAGGAGGCCACATCGGTGACGATGGTGATGGCG
GTGTAACCCACCGCTGACCAGAGGGTGGTGGTGTGAGTGAGAGAAGAAGAAGAAAACAAGGAATA
AGAAGGGGGAGGAAGTTAACGGCAGTTAAGTGCCACGTCAGCAAATGGTTACAATAGGGACCTTA
TTGCAAACGATTAAAAGTCAGGTGACCAAAATGAAAGCACCCCAAAAGTTAGATACTTGTACTAC
AACTTTCAAAAGTTAGGTG
Found at i:653825 original size:14 final size:14
Alignment explanation
Indices: 653806--653854 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
653796 TTTATGTTCT
653806 AAATTAAATATAAA
1 AAATTAAATATAAA
* *
653820 AAATTATCAACAT-CA
1 AAATTA--AATATAAA
653835 AAATTAAATATAAA
1 AAATTAAATATAAA
653849 AAATTA
1 AAATTA
653855 TGGATTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
13 4 0.14
14 13 0.46
15 7 0.25
16 4 0.14
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (14 bp):
AAATTAAATATAAA
Found at i:659928 original size:27 final size:25
Alignment explanation
Indices: 659874--659928 Score: 58
Period size: 25 Copynumber: 2.1 Consensus size: 25
659864 GTAACCATAA
*
659874 TTCATAAACCAGTAAATTCAATTAT
1 TTCATAAACCAGTAAATTCAACTAT
*
659899 TTCATAAATCATGTACAATTCATACT-T
1 TTCATAAACCA-GTA-AATTCA-ACTAT
659926 TTC
1 TTC
659929 GATGATAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 10 0.40
26 3 0.12
27 10 0.40
28 2 0.08
ACGTcount: A:0.38, C:0.18, G:0.04, T:0.40
Consensus pattern (25 bp):
TTCATAAACCAGTAAATTCAACTAT
Found at i:661995 original size:109 final size:109
Alignment explanation
Indices: 661804--662022 Score: 429
Period size: 109 Copynumber: 2.0 Consensus size: 109
661794 ATCACTAAGC
*
661804 ACATAACTTGTAATTTATTCTTTCAATCCTCAATTTTTTATAAAAGTTCTCTGAACCATAATCAA
1 ACATAACTTGTAATTTATTCTTTCAATCCTAAATTTTTTATAAAAGTTCTCTGAACCATAATCAA
661869 TTACTAAATTTCTACTGTATTCGGATTGAGTATAGAAATTCATT
66 TTACTAAATTTCTACTGTATTCGGATTGAGTATAGAAATTCATT
661913 ACATAACTTGTAATTTATTCTTTCAATCCTAAATTTTTTATAAAAGTTCTCTGAACCATAATCAA
1 ACATAACTTGTAATTTATTCTTTCAATCCTAAATTTTTTATAAAAGTTCTCTGAACCATAATCAA
661978 TTACTAAATTTCTACTGTATTCGGATTGAGTATAGAAATTCATT
66 TTACTAAATTTCTACTGTATTCGGATTGAGTATAGAAATTCATT
662022 A
1 A
662023 ACTACTCAAA
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 109 1.00
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (109 bp):
ACATAACTTGTAATTTATTCTTTCAATCCTAAATTTTTTATAAAAGTTCTCTGAACCATAATCAA
TTACTAAATTTCTACTGTATTCGGATTGAGTATAGAAATTCATT
Found at i:664118 original size:3 final size:3
Alignment explanation
Indices: 664110--664146 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
664100 CCCTTCCCTA
664110 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
664147 TTTCAATCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:669048 original size:16 final size:16
Alignment explanation
Indices: 669027--669079 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
669017 TTTCAGATTT
*
669027 AGATTCTAATTCCTTC
1 AGATTCCAATTCCTTC
*
669043 AGATTCCAATTCTTTCAC
1 AGATTCCAATTCCTT--C
*
669061 AGATTCCAATTCCCTC
1 AGATTCCAATTCCTTC
669077 AGA
1 AGA
669080 AACATTCTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
16 17 0.55
18 14 0.45
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.36
Consensus pattern (16 bp):
AGATTCCAATTCCTTC
Found at i:678541 original size:6 final size:6
Alignment explanation
Indices: 678532--678559 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
678522 TTCGTTGTCG
678532 TTGCCA TTGCCA TTGCCA TTGCCA TTGC
1 TTGCCA TTGCCA TTGCCA TTGCCA TTGC
678560 GTGGGATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.32, G:0.18, T:0.36
Consensus pattern (6 bp):
TTGCCA
Found at i:680387 original size:15 final size:15
Alignment explanation
Indices: 680367--680395 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
680357 ATTGCACATA
680367 GTTAATTTTCACGTG
1 GTTAATTTTCACGTG
680382 GTTAATTTTCACGT
1 GTTAATTTTCACGT
680396 ATTTATTTAT
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:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (15 bp):
GTTAATTTTCACGTG
Found at i:688139 original size:21 final size:22
Alignment explanation
Indices: 688115--688164 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
688105 TATCAATCTA
688115 TTATTTTTA-ATTCTGTAAAAG
1 TTATTTTTAGATTCTGTAAAAG
* *
688136 TTA-TTTTAGATTTTTTAAAAG
1 TTATTTTTAGATTCTGTAAAAG
688157 -TATTTTTA
1 TTATTTTTA
688165 CAGTAAATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (22 bp):
TTATTTTTAGATTCTGTAAAAG
Found at i:691702 original size:20 final size:20
Alignment explanation
Indices: 691674--691729 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
691664 AGCCATGGTT
*
691674 GTTATAAAAGAATATGGCAA
1 GTTACAAAAGAATATGGCAA
691694 GTTACAAAAGAATATGGCAA
1 GTTACAAAAGAATATGGCAA
* *
691714 ATTTCAAAAGCAATAT
1 GTTACAAAAG-AATAT
691730 ATATGTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 27 0.84
21 5 0.16
ACGTcount: A:0.50, C:0.09, G:0.16, T:0.25
Consensus pattern (20 bp):
GTTACAAAAGAATATGGCAA
Found at i:696412 original size:25 final size:25
Alignment explanation
Indices: 696379--696431 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
696369 TCTTAATTTA
696379 TTATAAGAAAAAAATAATCTCTAAC
1 TTATAAGAAAAAAATAATCTCTAAC
* * *
696404 TTATGAGAAAAATATAATCTTTAAC
1 TTATAAGAAAAAAATAATCTCTAAC
696429 TTA
1 TTA
696432 GAAAAACACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (25 bp):
TTATAAGAAAAAAATAATCTCTAAC
Found at i:696437 original size:23 final size:22
Alignment explanation
Indices: 696384--696437 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 22
696374 ATTTATTATA
696384 AGAAAAAAATAATCTCTAACTT
1 AGAAAAAAATAATCTCTAACTT
*
696406 ATGAGAAAAATATAATCTTTAACTT
1 A-GA-AAAAA-ATAATCTCTAACTT
696431 AGAAAAA
1 AGAAAAA
696438 CACTTTCATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 1 0.04
23 6 0.21
24 7 0.25
25 14 0.50
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.28
Consensus pattern (22 bp):
AGAAAAAAATAATCTCTAACTT
Found at i:697560 original size:18 final size:18
Alignment explanation
Indices: 697537--697609 Score: 83
Period size: 18 Copynumber: 3.9 Consensus size: 18
697527 ACTGAATATT
697537 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
697555 TGTCCCGAAGGACAACTGA
1 TGTCCCGAAGGACCACT-A
* * *
697574 TTGTTCCTAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
*
697593 TATCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
697610 CCTTAAGAAC
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
18 29 0.66
19 2 0.05
20 13 0.30
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:697862 original size:24 final size:21
Alignment explanation
Indices: 697806--697863 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 21
697796 ATATATTCTC
697806 ATCACTTTTCATATAAACATGT
1 ATCAC-TTTCATATAAACATGT
697828 ATTTCAC-TTCATATACACACATGT
1 A--TCACTTTCATATA-A-ACATGT
697852 GATCACTTTCAT
1 -ATCACTTTCAT
697864 TATTTCACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
22 9 0.30
23 5 0.17
24 15 0.50
25 1 0.03
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40
Consensus pattern (21 bp):
ATCACTTTCATATAAACATGT
Found at i:698397 original size:19 final size:19
Alignment explanation
Indices: 698350--698401 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
698340 TTTAAGTAGG
* *
698350 TGCATCAATGCACTCCTTA
1 TGCATCGATGCACTCCTCA
698369 TGCATCGATGCACTCCTCA
1 TGCATCGATGCACTCCTCA
*
698388 TGCATTGATGCACT
1 TGCATCGATGCACT
698402 AATTGCATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (19 bp):
TGCATCGATGCACTCCTCA
Found at i:699696 original size:65 final size:65
Alignment explanation
Indices: 699503--699756 Score: 384
Period size: 65 Copynumber: 3.9 Consensus size: 65
699493 TTTTGGGCCA
** * *
699503 AAATCACTCATATGACTTGTGTACCTTTGTGGTGCATGGGGTGGAGTGATAATTGAATAAAATAC
1 AAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACAATAC
* * * * *
699568 ACATCACTCATATGACTCGTGTACCTTT-TAGTACATGAGGTGGAGTGATAATTGGATACAATAC
1 AAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACAATAC
* *
699632 AGATCACTTATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACAATAC
1 AAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACAATAC
* *
699697 AAATCAGTCATATGACTCATGTACCTTTGTGGTGTATGAGGTGGAGTGATAATTGAATAC
1 AAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATAC
699757 TACAAAGATC
Statistics
Matches: 171, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
64 56 0.33
65 115 0.67
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (65 bp):
AAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACAATAC
Found at i:700020 original size:65 final size:65
Alignment explanation
Indices: 699919--700124 Score: 297
Period size: 65 Copynumber: 3.2 Consensus size: 65
699909 TACATATAAT
* * * * *
699919 TGATATGTACTATATTCAATTATTACTCCACTTCATGCACCACAAAGGTACATGATTCATATGAG
1 TGATATGTACTGTATTCAATTATCACTCCACCTCATGCATCACAAAGGTACATGAGTCATATGAG
* *
699984 TGATCTGTACTGTATTCAATTATCACTCCACCTCATGCATCACATAGGTACATGAGTCATATGAG
1 TGATATGTACTGTATTCAATTATCACTCCACCTCATGCATCACAAAGGTACATGAGTCATATGAG
* * *
700049 TGATATGTATTGTATTCAATTATCACTCTATCC-CATGCATCACAAAGGTACATGAGTCATATAA
1 TGATATGTACTGTATTCAATTATCACTCCA-CCTCATGCATCACAAAGGTACATGAGTCATATGA
700113 G
65 G
*
700114 TGATTTGTACT
1 TGATATGTACT
700125 TGTTCACTCT
Statistics
Matches: 126, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
65 124 0.98
66 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (65 bp):
TGATATGTACTGTATTCAATTATCACTCCACCTCATGCATCACAAAGGTACATGAGTCATATGAG
Found at i:706432 original size:2 final size:2
Alignment explanation
Indices: 706425--706449 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
706415 CAATTCCAGT
706425 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
706450 CCATTTCCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:716023 original size:24 final size:24
Alignment explanation
Indices: 715996--716071 Score: 127
Period size: 24 Copynumber: 3.2 Consensus size: 24
715986 GAGACTAATT
715996 TATAAATCTTAATATAT-TATAAGA
1 TATAAATCTTAATAT-TGTATAAGA
716020 TATAAATCTTAATATTGTATAAGA
1 TATAAATCTTAATATTGTATAAGA
*
716044 TATAAATTTTAATATTGTATAAGA
1 TATAAATCTTAATATTGTATAAGA
716068 TATA
1 TATA
716072 TGATGTCAGG
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
23 1 0.02
24 49 0.98
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (24 bp):
TATAAATCTTAATATTGTATAAGA
Found at i:723047 original size:23 final size:22
Alignment explanation
Indices: 723000--723051 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 22
722990 CTAATTTTTG
723000 AAAAAAAATCAACTCCATTCTAA
1 AAAAAAAATCAACTCCATTC-AA
* *
723023 AAAGAAAATCAACT-CTTTCAA
1 AAAAAAAATCAACTCCATTCAA
723044 AAAAAAAA
1 AAAAAAAA
723052 AACACGATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 9 0.35
22 4 0.15
23 13 0.50
ACGTcount: A:0.62, C:0.17, G:0.02, T:0.19
Consensus pattern (22 bp):
AAAAAAAATCAACTCCATTCAA
Found at i:723053 original size:23 final size:23
Alignment explanation
Indices: 723000--723052 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
722990 CTAATTTTTG
*
723000 AAAAAAAATCAACTCCATTCTAA
1 AAAAAAAATCAACTCCATTCAAA
* *
723023 AAAGAAAATCAACT-CTTTCAAA
1 AAAAAAAATCAACTCCATTCAAA
723045 AAAAAAAA
1 AAAAAAAA
723053 ACACGATCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 13 0.50
23 13 0.50
ACGTcount: A:0.62, C:0.17, G:0.02, T:0.19
Consensus pattern (23 bp):
AAAAAAAATCAACTCCATTCAAA
Found at i:724881 original size:27 final size:28
Alignment explanation
Indices: 724837--724892 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
724827 TCTGCCACGT
* *
724837 GTCAGTAAGGCG-AGCCCCCTACGGCGC
1 GTCAGTAAGGCGCACCCCCCTACGACGC
*
724864 GTCAGTAAGGCGCCCCCCCCTACGACGC
1 GTCAGTAAGGCGCACCCCCCTACGACGC
724892 G
1 G
724893 CCTTGGGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.18, C:0.41, G:0.30, T:0.11
Consensus pattern (28 bp):
GTCAGTAAGGCGCACCCCCCTACGACGC
Found at i:725078 original size:17 final size:17
Alignment explanation
Indices: 725056--725105 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 17
725046 TTAATATTCT
*
725056 GTATTTAATTTATTTAA
1 GTATTTAATTTAATTAA
*
725073 GTATTTTATTTAATTAA
1 GTATTTAATTTAATTAA
* *
725090 -TTTTTTATTTAATTAA
1 GTATTTAATTTAATTAA
725106 TTTTTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 15 0.50
17 15 0.50
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (17 bp):
GTATTTAATTTAATTAA
Found at i:725083 original size:38 final size:37
Alignment explanation
Indices: 725036--725108 Score: 85
Period size: 38 Copynumber: 1.9 Consensus size: 37
725026 ATGTATCTTT
*
725036 TATTATATTT-TTAATATTCTGTATTTAATTTATTTAAG
1 TATTATATTTATTAAT-TT-TGTATTTAATTAATTTAAG
* *
725074 TATTTTATTTAATTAATTTTTTATTTAATTAATTT
1 TATTATATTT-ATTAATTTTGTATTTAATTAATTT
725109 TTTTTTTGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
38 23 0.77
39 2 0.07
40 5 0.17
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (37 bp):
TATTATATTTATTAATTTTGTATTTAATTAATTTAAG
Found at i:725097 original size:16 final size:16
Alignment explanation
Indices: 725076--725111 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
725066 TATTTAAGTA
725076 TTTTATTTAATTAATT
1 TTTTATTTAATTAATT
725092 TTTTATTTAATTAATT
1 TTTTATTTAATTAATT
725108 TTTT
1 TTTT
725112 TTTTGCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTATTTAATTAATT
Found at i:726893 original size:29 final size:29
Alignment explanation
Indices: 726845--726902 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
726835 TTACCAGATA
* * *
726845 CCGCCGCCTTCACCGGGTTTTATGACCCC
1 CCGCCACCTTCACAGAGTTTTATGACCCC
726874 CCGCCACCTTCACAGAGTTTTATGACCCC
1 CCGCCACCTTCACAGAGTTTTATGACCCC
726903 TCCTGGAGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.16, C:0.43, G:0.17, T:0.24
Consensus pattern (29 bp):
CCGCCACCTTCACAGAGTTTTATGACCCC
Found at i:727228 original size:13 final size:12
Alignment explanation
Indices: 727206--727255 Score: 64
Period size: 13 Copynumber: 4.0 Consensus size: 12
727196 TTTGTATTTA
727206 GTATTTTTTATT
1 GTATTTTTTATT
*
727218 GTAGTTGTTTATT
1 GTA-TTTTTTATT
*
727231 GGATTTTTTTATT
1 GTA-TTTTTTATT
727244 GTATTTTTTATT
1 GTATTTTTTATT
727256 ATTTATCATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
12 12 0.38
13 20 0.62
ACGTcount: A:0.16, C:0.00, G:0.14, T:0.70
Consensus pattern (12 bp):
GTATTTTTTATT
Found at i:729585 original size:13 final size:13
Alignment explanation
Indices: 729567--729595 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
729557 TTCTAATCGA
729567 GAGGAGATGTGAG
1 GAGGAGATGTGAG
729580 GAGGAGATGTGAG
1 GAGGAGATGTGAG
729593 GAG
1 GAG
729596 TTACCCCGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.55, T:0.14
Consensus pattern (13 bp):
GAGGAGATGTGAG
Found at i:730319 original size:41 final size:41
Alignment explanation
Indices: 730274--730398 Score: 223
Period size: 41 Copynumber: 3.0 Consensus size: 41
730264 ATTCGCGTTG
*
730274 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
730315 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
730356 CATTTCGTGTTGCGATAGTTGAAAATAGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
730397 CA
1 CA
730399 ACGAATTTTC
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 81 1.00
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:730324 original size:20 final size:20
Alignment explanation
Indices: 730299--730371 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
730289 TAGTTGAAAA
*
730299 TCGCGTTGCGCTTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
730319 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
730340 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
730360 TCGTGTTGCGAT
1 TCGCGTTGCGAT
730372 AGTTGAAAAT
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 25 0.62
21 15 0.38
ACGTcount: A:0.14, C:0.22, G:0.25, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:730390 original size:21 final size:21
Alignment explanation
Indices: 730278--730392 Score: 99
Period size: 21 Copynumber: 5.6 Consensus size: 21
730268 GCGTTGCATT
730278 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
730299 TCGCGTTGCGCT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
730319 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
730340 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
730360 TCGTGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
730381 TAGCGTTGCGAT
1 TCGCGTTGCGAT
730393 TTTCCAACGA
Statistics
Matches: 67, Mismatches: 25, Indels: 4
0.70 0.26 0.04
Matches are distributed among these distances:
20 28 0.42
21 39 0.58
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:730451 original size:22 final size:22
Alignment explanation
Indices: 730425--730496 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 22
730415 AATTTGGAAA
*
730425 ATCGCAACGACAGCTGTAGACT
1 ATCGCAACGACAACTGTAGACT
** **
730447 ATCGCAACGA-ATTTG-A-AAA
1 ATCGCAACGACAACTGTAGACT
730466 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
730488 ATCGTAACG
1 ATCGCAACG
730497 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 11 0.29
20 4 0.11
21 4 0.11
22 19 0.50
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:730457 original size:41 final size:41
Alignment explanation
Indices: 730411--730516 Score: 151
Period size: 41 Copynumber: 2.6 Consensus size: 41
730401 GAATTTTCTT
* *
730411 AACGAATTTGGAAAATCGCAACGACAGCTGTAGACTATCGC
1 AACGAATTTGAAAAATCGCAACGACAACTGTAGACTATCGC
*
730452 AACGAATTTGAAAAATCGCAACGACAACTGTAGACTATCGT
1 AACGAATTTGAAAAATCGCAACGACAACTGTAGACTATCGC
*
730493 AACGCGAA-ATGAAAAATCGCAACG
1 AA--CGAATTTGAAAAATCGCAACG
730517 CGATTTTCAA
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
41 40 0.68
42 15 0.25
43 4 0.07
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.18
Consensus pattern (41 bp):
AACGAATTTGAAAAATCGCAACGACAACTGTAGACTATCGC
Found at i:730548 original size:21 final size:21
Alignment explanation
Indices: 730485--730548 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
730475 ACAACTGTAG
*
730485 ACTATCGTAACGCGAAATG-A
1 ACTATCGCAACGCGAAATGCA
** ** *
730505 AAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
730526 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
730547 AC
1 AC
730549 GCGAATTTGC
Statistics
Matches: 32, Mismatches: 11, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
20 13 0.41
21 19 0.59
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:738124 original size:21 final size:21
Alignment explanation
Indices: 738098--738142 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
738088 GATTTCTGGG
* *
738098 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
738119 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
738140 CAA
1 CAA
738143 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:739874 original size:23 final size:22
Alignment explanation
Indices: 739816--739881 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
739806 TATGGACATC
*
739816 ATTCTAC-GGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
739837 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
739859 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
739882 TTTATACGAG
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
21 7 0.17
22 20 0.48
23 15 0.36
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.26
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:744695 original size:22 final size:23
Alignment explanation
Indices: 744667--744711 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
744657 TATGGACATC
744667 ATTCTAC-GGGCACTACGGTGCA
1 ATTCTACGGGGCACTACGGTGCA
*
744689 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTACGGGGCACTACGGTGCA
744712 TTTATACGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.20, C:0.27, G:0.29, T:0.24
Consensus pattern (23 bp):
ATTCTACGGGGCACTACGGTGCA
Found at i:744719 original size:23 final size:23
Alignment explanation
Indices: 744674--744719 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
744664 ATCATTCTAC
*
744674 GGGCACTACGGTGCAATTCTACG
1 GGGCACTACGGTGCAATTATACG
* *
744697 GGGCACTTCGGTGCATTTATACG
1 GGGCACTACGGTGCAATTATACG
744720 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.24, G:0.30, T:0.26
Consensus pattern (23 bp):
GGGCACTACGGTGCAATTATACG
Found at i:749975 original size:17 final size:17
Alignment explanation
Indices: 749953--750027 Score: 80
Period size: 17 Copynumber: 4.3 Consensus size: 17
749943 GATTTTGATT
749953 ATTTTCCTTTGCTTTTA
1 ATTTTCCTTTGCTTTTA
*
749970 ATTTTCC-TTGATTTTGA
1 ATTTTCCTTTGCTTTT-A
* *
749987 TTCTTTTCCTTTGCTTTCA
1 --ATTTTCCTTTGCTTTTA
*
750006 ATTTTCCTTTGCTTTTG
1 ATTTTCCTTTGCTTTTA
750023 ATTTT
1 ATTTT
750028 TTCTAATAGT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
16 7 0.15
17 27 0.57
19 7 0.15
20 6 0.13
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (17 bp):
ATTTTCCTTTGCTTTTA
Found at i:749988 original size:36 final size:36
Alignment explanation
Indices: 749940--750030 Score: 139
Period size: 36 Copynumber: 2.5 Consensus size: 36
749930 TTACTTTACT
*
749940 TTTGATTTTGATTATTTTCCTTTGCTTTTAATTTTCC
1 TTTGATTTTGATT-TTTTCCTTTGCTTTCAATTTTCC
749977 -TTGATTTTGATTCTTTTCCTTTGCTTTCAATTTTCC
1 TTTGATTTTGATT-TTTTCCTTTGCTTTCAATTTTCC
*
750013 TTTGCTTTTGATTTTTTC
1 TTTGATTTTGATTTTTTC
750031 TAATAGTCTA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
36 39 0.78
37 11 0.22
ACGTcount: A:0.11, C:0.15, G:0.09, T:0.65
Consensus pattern (36 bp):
TTTGATTTTGATTTTTTCCTTTGCTTTCAATTTTCC
Done.