Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001479.1 Hibiscus syriacus cultivar Beakdansim tig00002870_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: 67358
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:51 original size:33 final size:33
Alignment explanation
Indices: 9--75 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
1 ATCTAGGT
9 AGATAGGATTTGATTTCTCTGATTGGGTGAATA
1 AGATAGGATTTGATTTCTCTGATTGGGTGAATA
42 AGATAGGATTTGATTTCTCTGATTGGGTGAATA
1 AGATAGGATTTGATTTCTCTGATTGGGTGAATA
75 A
1 A
76 AATCCAGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.28, C:0.06, G:0.27, T:0.39
Consensus pattern (33 bp):
AGATAGGATTTGATTTCTCTGATTGGGTGAATA
Found at i:371 original size:25 final size:25
Alignment explanation
Indices: 340--414 Score: 141
Period size: 25 Copynumber: 3.0 Consensus size: 25
330 AGTTAGGGGA
340 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
365 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
*
390 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
415 GGGTTGTTGG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAACTGAT
Found at i:512 original size:3 final size:3
Alignment explanation
Indices: 491--532 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
481 TAATTAATTT
* **
491 ATA ATA AAA ATA ACG ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
533 CGGTAAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (3 bp):
ATA
Found at i:768 original size:43 final size:43
Alignment explanation
Indices: 720--949 Score: 149
Period size: 43 Copynumber: 5.1 Consensus size: 43
710 AATGAAGAGG
* *
720 TCTGGTCGTCTAAGGGTGACACGGCTCCTACGTGATGAGGAAA
1 TCTGGTCATCTAAGGGTGACACGGCTCCTACGTGATGAGGACA
* * *
763 TCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACG
1 TCTGGTCATC--T---AAGGGTG---ACACGGCTCCTACGTGATGAGGACA
* * * * * *
814 GCTGGTTATC--AGGTTGACACGGCTCTTACGTGATGAAGAGA
1 TCTGGTCATCTAAGGGTGACACGGCTCCTACGTGATGAGGACA
* * * *
855 TCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACG
1 TCTGGTCATCT-AAGG-G-TGACACGGCTCCTACGTGATGAGGACA
* * * * * * *
901 GCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGA
1 TCTGGTCATCTAAGGGTGACACGGCTCCTACGTGATGAGGACA
944 TCTGGT
1 TCTGGT
950 GGGATGACAC
Statistics
Matches: 138, Mismatches: 36, Indels: 26
0.69 0.18 0.13
Matches are distributed among these distances:
41 26 0.19
43 35 0.25
44 8 0.06
45 4 0.03
46 29 0.21
48 7 0.05
51 29 0.21
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (43 bp):
TCTGGTCATCTAAGGGTGACACGGCTCCTACGTGATGAGGACA
Found at i:901 original size:87 final size:92
Alignment explanation
Indices: 736--948 Score: 319
Period size: 87 Copynumber: 2.3 Consensus size: 92
726 CGTCTAAGGG
* * * * *
736 TGACACGGCTCCTACGTGATGAGGAAATCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGCCATC-TTA-GAAGGGTGATAACACGGTTCCTA
801 CGTGATGAGGACGGCTGGTTATC-A-GGT
64 CGTGATGAGGACGGCTGGTTATCTATGGT
*
828 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATC-TA-AA-GGTGATAACACGGTTCCTACG
1 TGACACGGCTCATACGTGATGAAGAGATCTGGCCATCTTAGAAGGGTGATAACACGGTTCCTACG
890 TGATGAGGACGGCTGGTTATCTATGGT
66 TGATGAGGACGGCTGGTTATCTATGGT
917 TGACACGGCTCATACGTGATGAAGAGATCTGG
1 TGACACGGCTCATACGTGATGAAGAGATCTGG
949 TGGGATGACA
Statistics
Matches: 113, Mismatches: 6, Indels: 7
0.90 0.05 0.06
Matches are distributed among these distances:
87 41 0.36
88 3 0.03
89 34 0.30
90 2 0.02
92 33 0.29
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (92 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGCCATCTTAGAAGGGTGATAACACGGTTCCTACG
TGATGAGGACGGCTGGTTATCTATGGT
Found at i:912 original size:46 final size:45
Alignment explanation
Indices: 782--938 Score: 139
Period size: 46 Copynumber: 3.6 Consensus size: 45
772 CTTTAGGAAG
*
782 GGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATC--A
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAA
* * * * * **
825 GGT--TGACACGGCTCTTACGTGATGAAGA-GATCTGGCCATCTAAA
1 GGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCT-AA
*
869 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAT
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAA
* * *
914 GGT--TGACACGGCTCATACGTGATGA
1 GGTGATAACACGGTTCCTACGTGATGA
939 AGAGATCTGG
Statistics
Matches: 88, Mismatches: 19, Indels: 14
0.73 0.16 0.12
Matches are distributed among these distances:
40 1 0.01
41 27 0.31
43 22 0.25
44 4 0.05
45 4 0.05
46 29 0.33
47 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.27
Consensus pattern (45 bp):
GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAA
Found at i:2051 original size:17 final size:17
Alignment explanation
Indices: 2021--2053 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2011 TCCTTTATTT
2021 ATTTTTCTTCTTTTTTC
1 ATTTTTCTTCTTTTTTC
2038 ATTTTTCATT-TTTTTT
1 ATTTTTC-TTCTTTTTT
2054 TTTTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (17 bp):
ATTTTTCTTCTTTTTTC
Found at i:15245 original size:10 final size:10
Alignment explanation
Indices: 15230--15254 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
15220 TTTCTCTCCT
15230 TTTTTTTCTG
1 TTTTTTTCTG
15240 TTTTTTTCTG
1 TTTTTTTCTG
15250 TTTTT
1 TTTTT
15255 AATCCCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.84
Consensus pattern (10 bp):
TTTTTTTCTG
Found at i:15679 original size:25 final size:25
Alignment explanation
Indices: 15648--15722 Score: 141
Period size: 25 Copynumber: 3.0 Consensus size: 25
15638 AGTTAGGGGA
15648 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
15673 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
*
15698 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
15723 GGGTTGTTGG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAACTGAT
Found at i:15822 original size:3 final size:3
Alignment explanation
Indices: 15801--15842 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
15791 TAATTAATTT
* **
15801 ATA ATA AAA ATA ACG ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
15843 CGGTAAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (3 bp):
ATA
Found at i:17074 original size:4 final size:4
Alignment explanation
Indices: 17065--17112 Score: 55
Period size: 4 Copynumber: 12.0 Consensus size: 4
17055 AAGACATGCA
*
17065 AAAT AAAT AAAT ATAAT AAA- ATAA- AAAT TAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT A-AAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT
17113 GTAAAAAAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
3 3 0.08
4 32 0.82
5 4 0.10
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:17085 original size:18 final size:18
Alignment explanation
Indices: 17064--17109 Score: 64
Period size: 16 Copynumber: 2.8 Consensus size: 18
17054 AAAGACATGC
17064 AAAATAAATAAATATAAT
1 AAAATAAATAAATATAAT
17082 AAAAT-AA-AAAT-TAAT
1 AAAATAAATAAATATAAT
17097 -AAATAAATAAATA
1 AAAATAAATAAATA
17110 AATGTAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 4 0.16
15 6 0.24
16 8 0.32
17 2 0.08
18 5 0.20
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATAAATAAATATAAT
Found at i:17098 original size:15 final size:13
Alignment explanation
Indices: 17066--17112 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
17056 AGACATGCAA
*
17066 AATAAATAAATAT
1 AATAAATAAAAAT
17079 AATAAAATAAAAATT
1 AAT-AAATAAAAA-T
*
17094 AATAAATAAATA-
1 AATAAATAAAAAT
17106 AATAAAT
1 AATAAAT
17113 GTAAAAAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 7 0.23
13 3 0.10
14 16 0.53
15 4 0.13
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AATAAATAAAAAT
Found at i:20080 original size:21 final size:19
Alignment explanation
Indices: 20054--20093 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
20044 ATATTAGTCA
20054 TTTTATTTATTGTATATATTT
1 TTTTATTTATT-TAT-TATTT
20075 TTTTATTTATTTATTATTT
1 TTTTATTTATTTATTATTT
20094 ACATTATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 3 0.16
21 11 0.58
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (19 bp):
TTTTATTTATTTATTATTT
Found at i:20192 original size:63 final size:65
Alignment explanation
Indices: 20115--20269 Score: 172
Period size: 67 Copynumber: 2.4 Consensus size: 65
20105 ATTATATAAA
* * *
20115 TATATATACGTATATATTTTTTAAATGATTTTCA-A-TTGATTTTTTTACACTATATATTATTA-
1 TATATATACATATATATTTTTTAAATGATATTCATAGTTGATTTTTTAACACTATATATT-TTAT
20177 T
65 T
* * * * *
20178 TATATATACATATATATTTTATTTATTTATATTCATTAGTTTATTTTTTAATACTATATATTTTA
1 TATATATACATATATATTTT-TTAAATGATATTCA-TAGTTGATTTTTTAACACTATATATTTTA
20243 TT
64 TT
* *
20245 TATATATATATATACATTTTTTAAA
1 TATATATACATATATATTTTTTAAA
20270 ATATTTTACT
Statistics
Matches: 75, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
63 19 0.25
64 10 0.13
66 7 0.09
67 39 0.52
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (65 bp):
TATATATACATATATATTTTTTAAATGATATTCATAGTTGATTTTTTAACACTATATATTTTATT
Found at i:20220 original size:22 final size:24
Alignment explanation
Indices: 20163--20258 Score: 82
Period size: 22 Copynumber: 4.2 Consensus size: 24
20153 ATTTTTTTAC
20163 ACTATATA--TTA-TTATTATATAT
1 ACTATATAGTTTATTTATT-TATAT
*
20185 ACATATATATTTTATTTATTTATAT
1 AC-TATATAGTTTATTTATTTATAT
*
20210 TC-AT-TAGTTTATTT-TTTA-AT
1 ACTATATAGTTTATTTATTTATAT
* *
20230 ACTATATATTTTATTTATATATAT
1 ACTATATAGTTTATTTATTTATAT
20254 A-TATA
1 ACTATA
20259 CATTTTTTAA
Statistics
Matches: 61, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
20 3 0.05
21 6 0.10
22 20 0.33
23 15 0.25
24 3 0.05
25 9 0.15
26 5 0.08
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.58
Consensus pattern (24 bp):
ACTATATAGTTTATTTATTTATAT
Found at i:20546 original size:2 final size:2
Alignment explanation
Indices: 20539--20571 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20529 TTTACTCATT
20539 TA TA TA TA 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 TA TA TA TA T
20572 TTTAATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20607 original size:16 final size:16
Alignment explanation
Indices: 20588--20629 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
20578 ATTTCATTTA
20588 TTTATTTATTTTTACT
1 TTTATTTATTTTTACT
*
20604 TTTATTTTTTTTTACT
1 TTTATTTATTTTTACT
20620 TATT-TTTATT
1 T-TTATTTATT
20630 CTTCATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTATTTATTTTTACT
Found at i:25105 original size:17 final size:17
Alignment explanation
Indices: 25083--25169 Score: 85
Period size: 17 Copynumber: 5.2 Consensus size: 17
25073 AATCAAGAAC
*
25083 AAAAAAGAAAAGAAGCA
1 AAAAAAGAAAAGAAACA
25100 AAAAAAGAAAA-AAACA
1 AAAAAAGAAAAGAAACA
*
25116 AAGAAAA-AAGAGAAACA
1 AA-AAAAGAAAAGAAACA
*
25133 AAAAAGAGAAACA-AAAGA
1 AAAAA-AGAAA-AGAAACA
25151 AAAAAAG-AAAG-AACA
1 AAAAAAGAAAAGAAACA
25166 AAAA
1 AAAA
25170 TAAAAAAGGG
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
15 8 0.14
16 14 0.24
17 25 0.42
18 11 0.19
19 1 0.02
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAGAAACA
Found at i:25107 original size:12 final size:12
Alignment explanation
Indices: 25090--25148 Score: 54
Period size: 12 Copynumber: 5.1 Consensus size: 12
25080 AACAAAAAAG
*
25090 AAAAGAAGCAAA
1 AAAAGAAACAAA
25102 AAAAGAAA-AAA
1 AAAAGAAACAAA
25113 ACAAAG--A-AAA
1 A-AAAGAAACAAA
*
25123 AAGAGAAACAAA
1 AAAAGAAACAAA
25135 AAAGAGAAACAAA
1 AAA-AGAAACAAA
25148 A
1 A
25149 GAAAAAAAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
9 3 0.08
10 5 0.13
11 5 0.13
12 16 0.41
13 10 0.26
ACGTcount: A:0.80, C:0.07, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAGAAACAAA
Found at i:25135 original size:13 final size:13
Alignment explanation
Indices: 25119--25148 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
25109 AAAAACAAAG
25119 AAAAAAGAGAAAC
1 AAAAAAGAGAAAC
25132 AAAAAAGAGAAAC
1 AAAAAAGAGAAAC
25145 AAAA
1 AAAA
25149 GAAAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (13 bp):
AAAAAAGAGAAAC
Found at i:25161 original size:12 final size:11
Alignment explanation
Indices: 25083--25169 Score: 70
Period size: 11 Copynumber: 7.6 Consensus size: 11
25073 AATCAAGAAC
25083 AAAAAAGAAAAG
1 AAAAAA-AAAAG
*
25095 AAGCAAAAAAAG
1 AA-AAAAAAAAG
25107 AAAAAAACAAAG
1 AAAAAAA-AAAG
*
25119 --AAAAAAGAG
1 AAAAAAAAAAG
*
25128 AAACAAAAAAG
1 AAAAAAAAAAG
* *
25139 AGAAACAAAAG
1 AAAAAAAAAAG
25150 AAAAAAAGAAAG
1 AAAAAAA-AAAG
25162 AACAAAAA
1 AA-AAAAA
25170 TAAAAAAGGG
Statistics
Matches: 59, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
9 3 0.05
10 5 0.08
11 24 0.41
12 19 0.32
13 8 0.14
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:25177 original size:20 final size:19
Alignment explanation
Indices: 25085--25177 Score: 59
Period size: 20 Copynumber: 4.7 Consensus size: 19
25075 TCAAGAACAA
*
25085 AAAAGAAAAGAAGCAAAAA-
1 AAAAGAAAAAAAG-AAAAAC
*
25104 AAGAAAAAAACAAAGAAAAA-
1 AA-AAGAAAA-AAAGAAAAAC
*
25124 AGAGAA-ACAAAAAAGAGAAAC
1 A-A-AAGA-AAAAAAGAAAAAC
25145 AAAAGAAAAAAAGAAAGAAC
1 AAAAGAAAAAAAGAAA-AAC
25165 AAAA-ATAAAAAAG
1 AAAAGA-AAAAAAG
25178 GGACAAAAAG
Statistics
Matches: 62, Mismatches: 4, Indels: 15
0.77 0.05 0.19
Matches are distributed among these distances:
19 14 0.23
20 37 0.60
21 11 0.18
ACGTcount: A:0.80, C:0.05, G:0.14, T:0.01
Consensus pattern (19 bp):
AAAAGAAAAAAAGAAAAAC
Found at i:26872 original size:106 final size:106
Alignment explanation
Indices: 26745--27694 Score: 1276
Period size: 106 Copynumber: 9.0 Consensus size: 106
26735 ATATCTTGCC
* * * * *
26745 ACTCGAGACAACACAAGTTCAACTTCACGACAAAGGGACGGTTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
26810 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
26851 ACTCTAGACAACGCAAGTTCAACTTCACGAAGAAGGAACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
26916 AATTTCAAAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
26957 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
27022 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
27063 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
27128 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* ** * * *
27169 ACTCAAGACAATACAAGTTCAACTTCACAACGAATGGACGGCTGGTTGTCAAC-AACAA-TCTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACT-TCC
* * *
27232 CAATTTCAGAGCCAGTTTCAACTTCGCAACGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
27274 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
27339 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGTTATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
27380 ACTCCAGACAACGCAAGTTTAACTTCACGAC-ATAGGG-CCGCTGGTTGTAAATAAATAACTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGA-AGGGACCGCTGGTTGTCAACAAACAACTTCC
* * *
27443 CAATTTCAGAGCCAATTTTAACTTCTCAGCGAAGGATCTTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* ** * * * * * *
27485 AC-CCAAGACAACACAAGCCCAACTTCACGATGAAGGGGCGGCTGATTGTCAA-TAA-AA-TT-T
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCC
* *
27545 C-A-TTCAGAGTCAATTTCAACTTCACGGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
27585 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
** * *
27650 GGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
27691 ACTC
1 ACTC
27695 GAAACAATGC
Statistics
Matches: 749, Mismatches: 80, Indels: 30
0.87 0.09 0.03
Matches are distributed among these distances:
100 76 0.10
101 4 0.01
102 3 0.00
103 4 0.01
104 6 0.01
105 181 0.24
106 474 0.63
107 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:27133 original size:212 final size:212
Alignment explanation
Indices: 26745--27694 Score: 1330
Period size: 211 Copynumber: 4.5 Consensus size: 212
26735 ATATCTTGCC
* * *
26745 ACTCGAGACAACACAAGTTCAACTTCACGACAAAGGGACGGTTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
*
26810 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* * *
26875 TCACGAAGAAGGAACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAAAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
26940 ACAGCGAAGGATATTGG
196 ACAGCGAAGGATATTGG
* * *
26957 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
27022 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* * * *
27087 TCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTCAATTTCAGAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
*
27152 ACATCGAAGGATATTGG
196 ACAGCGAAGGATATTGG
* * * *
27169 ACTCAAGACAATACAAGTTCAACTTCACAACGAATGGACGGCTGGTTGTCAAC-AACAA-TCTCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAACAAACAACT-TCC
* * *
27232 CAATTTCAGAGCCAGTTTCAACTTCGCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
* *
27297 TTCACGACGAAGGGACTGCTGGTTGTCAATAAACAATTTCCCAATTTCGGAGCCAATTTCAACTT
130 TTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTT
*
27362 CACAGCGAAGGTTATTGG
195 CACAGCGAAGGATATTGG
* * * * * *
27380 ACTCCAGACAACGCAAGTTTAACTTCACGAC-ATAGGG-CCGCTGGTTGTAAATAAATAACTTCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGA-AGGGACGGCTGGTTGTCAACAAACAACTTCC
* * * * **
27443 CAATTTCAGAGCCAATTTTAACTTCTCAGCGAAGGATCTTGGAC-CCAAGACAACACAAGCCCAA
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC-AGACAACGCAAGTTCAA
* * * * *
27507 CTTCACGATGAAGGGGCGGCTGATTGTCAAT-AA-AATTT--C-A-TTCAGAGTCAATTTCAACT
129 CTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACT
*
27566 TCACGGCGAAGGATATTGG
194 TCACAGCGAAGGATATTGG
* * *
27585 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
** * *
27650 GGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGGACTC
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
27695 GAAACAATGC
Statistics
Matches: 654, Mismatches: 75, Indels: 23
0.87 0.10 0.03
Matches are distributed among these distances:
205 66 0.10
206 58 0.09
207 2 0.00
209 5 0.01
210 18 0.03
211 261 0.40
212 244 0.37
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (212 bp):
ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
TCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
ACAGCGAAGGATATTGG
Found at i:28451 original size:37 final size:37
Alignment explanation
Indices: 28393--28489 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 37
28383 CCTTTTCGTC
*
28393 CTACTAGAATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
28430 TTTCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* *
28467 CTACTATGATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
28490 GATAAGATCC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:29052 original size:21 final size:21
Alignment explanation
Indices: 28960--29065 Score: 60
Period size: 22 Copynumber: 4.9 Consensus size: 21
28950 TTTCAATTGA
*
28960 TATTTTT-ACACTATATATTAT
1 TATTTTTAATACTATAT-TTAT
* *
28981 TA-TTATATATACATATATTTTT
1 TATTTTTA-ATAC-TATATTTAT
* *
29003 TATTTATTTATA-T-TCATTTGGT
1 TATTT-TTAATACTAT-ATTT-AT
29025 TATTTTTTAATACTATATTTAT
1 TA-TTTTTAATACTATATTTAT
29047 TATTTTTATATA-TATATTT
1 TATTTTTA-ATACTATATTT
29066 TTTTTAAATA
Statistics
Matches: 66, Mismatches: 8, Indels: 22
0.69 0.08 0.23
Matches are distributed among these distances:
20 4 0.06
21 20 0.30
22 22 0.33
23 18 0.27
24 2 0.03
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (21 bp):
TATTTTTAATACTATATTTAT
Found at i:29104 original size:2 final size:2
Alignment explanation
Indices: 29097--29143 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
29087 AGCGTATTAC
29097 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
29139 TA TA T
1 TA TA T
29144 GTAATTATCT
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:29310 original size:18 final size:19
Alignment explanation
Indices: 29284--29319 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
29274 GGTTTTGTTT
*
29284 TTTTTATATTA-TATTATA
1 TTTTCATATTACTATTATA
29302 TTTTCATATTACTATTAT
1 TTTTCATATTACTATTAT
29320 TATTGTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTCATATTACTATTATA
Found at i:29363 original size:2 final size:2
Alignment explanation
Indices: 29356--29386 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29346 TTTACTCATT
29356 TA TA TA 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 TA TA TA T
29387 TTCATTTATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29454 original size:16 final size:17
Alignment explanation
Indices: 29433--29468 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
29423 TTTTTACTTA
*
29433 TTTTTA-TTCTTCATTT
1 TTTTTATTTATTCATTT
29449 TTTTTATTTATTCATTT
1 TTTTTATTTATTCATTT
29466 TTT
1 TTT
29469 CCCTCTAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTATTTATTCATTT
Found at i:31159 original size:2 final size:2
Alignment explanation
Indices: 31152--31179 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31142 TAATGATTTC
31152 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
31180 CATTAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34038 original size:12 final size:12
Alignment explanation
Indices: 34007--34099 Score: 69
Period size: 12 Copynumber: 7.8 Consensus size: 12
33997 AATCAACATT
*
34007 TCCAGGCATCCC
1 TCCAGGCATACC
* * *
34019 ACCTGGCATGCC
1 TCCAGGCATACC
34031 TCCAGGCATACC
1 TCCAGGCATACC
* *
34043 TGCAGGCATTCC
1 TCCAGGCATACC
* *
34055 TCCAGGAAAACC
1 TCCAGGCATACC
* *
34067 TCCGGGCATCCC
1 TCCAGGCATACC
* * *
34079 ACCAGGAAAACC
1 TCCAGGCATACC
34091 TCCAGGCAT
1 TCCAGGCAT
34100 CCCACCCGGG
Statistics
Matches: 57, Mismatches: 24, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
12 57 1.00
ACGTcount: A:0.25, C:0.40, G:0.20, T:0.15
Consensus pattern (12 bp):
TCCAGGCATACC
Found at i:34067 original size:24 final size:24
Alignment explanation
Indices: 34023--34102 Score: 97
Period size: 24 Copynumber: 3.3 Consensus size: 24
34013 CATCCCACCT
* * * *
34023 GGCATGCCTCCAGGCATACCTGCA
1 GGCATCCCTCCAGGAAAACCTCCA
* *
34047 GGCATTCCTCCAGGAAAACCTCCG
1 GGCATCCCTCCAGGAAAACCTCCA
*
34071 GGCATCCCACCAGGAAAACCTCCA
1 GGCATCCCTCCAGGAAAACCTCCA
34095 GGCATCCC
1 GGCATCCC
34103 ACCCGGGAAC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.25, C:0.40, G:0.21, T:0.14
Consensus pattern (24 bp):
GGCATCCCTCCAGGAAAACCTCCA
Found at i:34103 original size:24 final size:24
Alignment explanation
Indices: 34040--34123 Score: 96
Period size: 24 Copynumber: 3.5 Consensus size: 24
34030 CTCCAGGCAT
* * *
34040 ACCTGCAGGCATTCCTCCAGGAAA
1 ACCTCCAGGCATCCCACCAGGAAA
*
34064 ACCTCCGGGCATCCCACCAGGAAA
1 ACCTCCAGGCATCCCACCAGGAAA
* *
34088 ACCTCCAGGCATCCCACCCGGGAA
1 ACCTCCAGGCATCCCACCAGGAAA
* *
34112 CCCACCAGGCAT
1 ACCTCCAGGCAT
34124 GCCTGCAGGT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.27, C:0.42, G:0.20, T:0.11
Consensus pattern (24 bp):
ACCTCCAGGCATCCCACCAGGAAA
Found at i:37229 original size:39 final size:40
Alignment explanation
Indices: 37165--37240 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 40
37155 ATTTTAAATG
* * *
37165 ACCTAAATGATTAAACCTAAAAATATATGCTCTAATATTA
1 ACCTAAATAATTAAACCTAAAAATATAGGCCCTAATATTA
37205 ACCTAAATAATT-AACCTAAAAATATAGGCCCTAATA
1 ACCTAAATAATTAAACCTAAAAATATAGGCCCTAATA
37241 GAAAGGTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 22 0.67
40 11 0.33
ACGTcount: A:0.49, C:0.17, G:0.05, T:0.29
Consensus pattern (40 bp):
ACCTAAATAATTAAACCTAAAAATATAGGCCCTAATATTA
Found at i:38995 original size:2 final size:2
Alignment explanation
Indices: 38988--39012 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38978 AATACCCCTT
38988 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
39013 TCCAATTAAG
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:39000 original size:225 final size:218
Alignment explanation
Indices: 38580--39128 Score: 672
Period size: 225 Copynumber: 2.5 Consensus size: 218
38570 CTTATTCATA
38580 TATTG-ATAAAAAT-ATTTTTTATTATTTCGGGTCGGGTCGAGTTTCTAATTCATATATTCGGGT
1 TATTGAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGA-TTTCTAATTCATATATTCGGGT
38643 TGGGTCGGGTGAAACTTTATTTTTTTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCC
65 TGGGTCGGGTGAAACTTTA---TTTT--GGTC--G--G-G-TCGGGTTTAGGGTGAAAAATACCC
* * ** *
38708 GACTCGAAAATGTATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATA
119 GACCCAAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTATATA
38773 TATA-ACT-T-T-T-GT-CAATTAAGTCACTGTTTT
184 TATATA-TATATATAGTCCAATTAAGTCACTGTTTT
*
38803 TATTGAATAAAAATAATTTTTTACTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGT
1 TATTGAATAAAAATAATTTTTTATTATTTCGGGTCGGGTC-GATTTCTAATTCATATATTCGGGT
*
38868 TGGTTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTTTAGGGTGAAAAATACCCGACCCAACCCA
65 TGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTTTAGGGTGAAAAATACCCG-----ACCCA
38933 AAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTTTATATATATA
125 AAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCC------TATATA
* *
38998 TATATATATATATATTCCAATTAAGTTACTGTTTT
184 TATATATATATATAGTCCAATTAAGTCACTGTTTT
* *
39033 TATTGAATAAAAATAATTTTTTATTATTTCGGGTC--G-AG-TTTCTAATTCATATATTCGGGTC
1 TATTGAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGATTTCTAATTCATATATTCGGGTT
* *
39094 GGGTCGGGTGAAACTTTGTTTTGGTCGGGTTGGGT
66 GGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGT
39129 CTCGGATGAA
Statistics
Matches: 291, Mismatches: 15, Indels: 38
0.85 0.04 0.11
Matches are distributed among these distances:
214 25 0.09
215 1 0.00
216 1 0.00
218 1 0.00
219 54 0.19
220 4 0.01
222 4 0.01
223 5 0.02
224 8 0.03
225 128 0.44
226 5 0.02
227 1 0.00
228 2 0.01
229 1 0.00
230 51 0.18
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (218 bp):
TATTGAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGATTTCTAATTCATATATTCGGGTT
GGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTTTAGGGTGAAAAATACCCGACCCAAAAAAA
TATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTATATATATATATATATA
TAGTCCAATTAAGTCACTGTTTT
Found at i:39543 original size:18 final size:17
Alignment explanation
Indices: 39500--39546 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
39490 TATGGAATTG
*
39500 GATTCCAATTCCTGACA
1 GATTCCAATTCCTCACA
* *
39517 GATTTCAATTCCTTCATA
1 GATTCCAATTCC-TCACA
39535 GATTCCAATTCC
1 GATTCCAATTCC
39547 CTCAAAAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.36
Consensus pattern (17 bp):
GATTCCAATTCCTCACA
Found at i:40687 original size:21 final size:21
Alignment explanation
Indices: 40636--40688 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
40626 ATTATGACTA
40636 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
* **
40657 TCACGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
40678 TCGCAATGCGA
1 TCGCAATGCGA
40689 ATAAGTAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:40708 original size:41 final size:42
Alignment explanation
Indices: 40663--40771 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 42
40653 AATTTCACGT
* * * *
40663 TGCGATTTTCCCAATTCGCAATGCGAA-TAAGTAAATCGCAA
1 TGCGAATTTCCAAAATCGCAATGCGAATTAAGAAAATCGCAA
** **
40704 TGCGAATTTGGAAAATCGCAATGCGAATTTGGAAAATCGCAA
1 TGCGAATTTCCAAAATCGCAATGCGAATTAAGAAAATCGCAA
** *
40746 TGCGAATTTGGAAAATCGCAACGCGA
1 TGCGAATTTCCAAAATCGCAATGCGA
40772 TACTGACTAT
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
41 22 0.38
42 36 0.62
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (42 bp):
TGCGAATTTCCAAAATCGCAATGCGAATTAAGAAAATCGCAA
Found at i:40721 original size:21 final size:21
Alignment explanation
Indices: 40678--40771 Score: 145
Period size: 21 Copynumber: 4.5 Consensus size: 21
40668 TTTTCCCAAT
** *
40678 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
40698 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
40719 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
40740 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
*
40761 TCGCAACGCGA
1 TCGCAATGCGA
40772 TACTGACTAT
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
20 12 0.17
21 57 0.83
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:40785 original size:20 final size:20
Alignment explanation
Indices: 40760--40874 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
40750 AATTTGGAAA
40760 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * **
40780 ATCGCAACGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
40801 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
40821 TTCGCAACGCGATACTTAAT
1 ATCGCAACGCGATACTGACT
* *
40841 TTCGCAACGCAATACTGACT
1 ATCGCAACGCGATACTGACT
* *
40861 TTCGCAACGAGATA
1 ATCGCAACGCGATA
40875 ATACATAATC
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
20 62 0.79
21 16 0.21
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:40802 original size:41 final size:41
Alignment explanation
Indices: 40757--40894 Score: 179
Period size: 41 Copynumber: 3.4 Consensus size: 41
40747 GCGAATTTGG
*
40757 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAA
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAA
* *
40798 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATACT-T
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAA
** * * *
40838 AATTTCGCAACGCAATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAA
* *
40879 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
40895 TTTCAAAGCG
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
40 34 0.41
41 48 0.59
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAA
Found at i:41406 original size:20 final size:20
Alignment explanation
Indices: 41367--41425 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
41357 TTTATTCTCT
* **
41367 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
41387 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* * *
41407 TGTTGTGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
41426 AGAAACTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:43353 original size:19 final size:20
Alignment explanation
Indices: 43299--43354 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
43289 TAGTTTACTT
* *
43299 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
43319 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
43339 TCGCAATGC-GAAATGA
1 TCGCAACGCGGAAATGA
43355 AAATCACAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:43392 original size:19 final size:19
Alignment explanation
Indices: 43338--43434 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 19
43328 GGAAATGGCT
43338 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
43357 ATCACAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
43371 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
43390 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
* *
43404 ATCGCAACGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
43423 ATCGCAATGCGA
1 ATCGCAATGCGA
43435 TTTGTGTTTC
Statistics
Matches: 59, Mismatches: 9, Indels: 20
0.67 0.10 0.23
Matches are distributed among these distances:
14 19 0.32
15 2 0.03
16 3 0.05
17 4 0.07
18 2 0.03
19 29 0.49
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:43406 original size:14 final size:14
Alignment explanation
Indices: 43354--43412 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
43344 ATGCGAAATG
*
43354 AAAATCACAACGAC
1 AAAATCGCAACGAC
*
43368 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
43387 AAAATCGCAACGAC
1 AAAATCGCAACGAC
43401 AAAATCGCAACG
1 AAAATCGCAACG
43413 TGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 21 0.57
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.27
ACGTcount: A:0.51, C:0.24, G:0.15, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:43426 original size:33 final size:33
Alignment explanation
Indices: 43338--43429 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
43328 GGAAATGGCT
*
43338 ATCGCAATGCGAAATGAAAATCACAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
43371 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
43404 ATCGCAACGTGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
43430 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.49, C:0.21, G:0.17, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:43502 original size:20 final size:20
Alignment explanation
Indices: 43473--43546 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
43463 TGCGATTTTT
43473 ATTT-CGCATTGCGATAGCC
1 ATTTCCGCATTGCGATAGCC
*
43492 ATTTCCGCATTGCGATAACC
1 ATTTCCGCATTGCGATAGCC
* *
43512 ATTTCCGCGTTGCGATAGTC
1 ATTTCCGCATTGCGATAGCC
* *
43532 ATTTTCGCGTTGCGA
1 ATTTCCGCATTGCGA
43547 AAGTAAGTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 4 0.08
20 45 0.92
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.34
Consensus pattern (20 bp):
ATTTCCGCATTGCGATAGCC
Found at i:43557 original size:20 final size:20
Alignment explanation
Indices: 43517--43572 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
43507 TAACCATTTC
* * *
43517 CGCGTTGCGATAGTCATTTT
1 CGCGTTGCGAAAGTAAGTTT
43537 CGCGTTGCGAAAGTAAGTTT
1 CGCGTTGCGAAAGTAAGTTT
*
43557 CGTGTTGCGAAAGTAA
1 CGCGTTGCGAAAGTAA
43573 ACTATTCTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGAAAGTAAGTTT
Found at i:43986 original size:42 final size:42
Alignment explanation
Indices: 43913--44032 Score: 118
Period size: 42 Copynumber: 2.8 Consensus size: 42
43903 GACTCACCTG
*** *
43913 TCATCCCTCAAGAGT-CCCCTCCAATTGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCCTCC-ACCATTCAAGAGGCCACTA
*
43955 TCATCCCTCAAGAGTCCCCCTCCACCATTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCTCCACCATTCAAGAGGCCACTA
** * *
43997 TCATCGTTGAAGAGATCCCTCC-CCACCATTCCAGAG
1 TCATCCCTCAAGAG-TCCC-CCTCCACCATTCAAGAG
44033 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
42 40 0.61
43 24 0.36
44 2 0.03
ACGTcount: A:0.24, C:0.39, G:0.15, T:0.22
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCCTCCACCATTCAAGAGGCCACTA
Found at i:45447 original size:14 final size:14
Alignment explanation
Indices: 45413--45451 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
45403 TTGATTGTTT
45413 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
45427 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
45441 TGTTGATTTGT
1 AATTGATTTGT
45452 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:45699 original size:20 final size:20
Alignment explanation
Indices: 45674--45749 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
45664 TCGCATTGCG
* *
45674 ATTTTCTCGTTGTGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
45694 ATTTTCGTGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
**
45714 ATTTTCGCGTTGCGATAATC
1 ATTTTCGCGTTGCGATAGCC
45734 ATTTTCGCGTTGCGAT
1 ATTTTCGCGTTGCGAT
45750 TTCCCCGTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:45988 original size:20 final size:20
Alignment explanation
Indices: 45972--46048 Score: 127
Period size: 20 Copynumber: 3.9 Consensus size: 20
45962 ATTGCGATTT
*
45972 TCAGAATCTCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
45992 TCAGAATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
46012 TCAGAATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
* *
46032 TCAGTATCGCATTGCGA
1 TCAGAATCGCGTTGCGA
46049 TTTTCCAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (20 bp):
TCAGAATCGCGTTGCGAAAG
Found at i:46082 original size:20 final size:21
Alignment explanation
Indices: 46038--46089 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
46028 AAAGTCAGTA
*
46038 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
46059 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
46079 TCGCATTGCGA
1 TCGCATTGCGA
46090 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:46186 original size:20 final size:20
Alignment explanation
Indices: 46100--46178 Score: 131
Period size: 20 Copynumber: 4.0 Consensus size: 20
46090 ATTGGGAAAA
*
46100 TCGCAACGCGATACTTACTT
1 TCGCAACGCGATACTGACTT
46120 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
46140 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
*
46160 TCGCAACGCGATTCTGACT
1 TCGCAACGCGATACTGACT
46179 ATTGCAACCA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:46949 original size:24 final size:24
Alignment explanation
Indices: 46922--46975 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
46912 GTATTCGAAA
*
46922 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
46946 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
46970 TTTGAT
1 TTTGAT
46976 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:49521 original size:19 final size:19
Alignment explanation
Indices: 49499--49590 Score: 78
Period size: 19 Copynumber: 5.4 Consensus size: 19
49489 GGAAATTACT
49499 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
49518 ATCGTAAT--G--A-GAGA
1 ATCGCAATGCGAAATGAAA
49532 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
49551 ATCGTAAT--G--A-GAGA
1 ATCGCAATGCGAAATGAAA
49565 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
49584 ATCGCAA
1 ATCGCAA
49591 CGAGAGAATC
Statistics
Matches: 55, Mismatches: 8, Indels: 20
0.66 0.10 0.24
Matches are distributed among these distances:
14 20 0.36
15 2 0.04
16 2 0.04
17 2 0.04
18 2 0.04
19 27 0.49
ACGTcount: A:0.46, C:0.14, G:0.23, T:0.17
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:49541 original size:33 final size:33
Alignment explanation
Indices: 49499--49658 Score: 221
Period size: 33 Copynumber: 4.8 Consensus size: 33
49489 GGAAATTACT
* *
49499 ATCGCAATGCGAAATGAAAATCGTAATGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
49532 ATCGCAATGCGAAATGAAAATCGTAATGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
49565 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * * * *
49598 ATCGCAACGTGAAAAGAAAATCACAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
49631 ATCGCAAAGCGAAATGAAAATCACAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
49659 CGAATTTAGT
Statistics
Matches: 117, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 117 1.00
ACGTcount: A:0.47, C:0.16, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:49700 original size:19 final size:19
Alignment explanation
Indices: 49658--49701 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
49648 AAATCACAAC
*
49658 GCGAATTTAGTTCCGCGTT
1 GCGATTTTAGTTCCGCGTT
*
49677 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTCCGCGTT
49696 GCGATT
1 GCGATT
49702 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.14, C:0.18, G:0.27, T:0.41
Consensus pattern (19 bp):
GCGATTTTAGTTCCGCGTT
Found at i:51288 original size:42 final size:42
Alignment explanation
Indices: 51242--51321 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
51232 CGATGACAGT
* * *
51242 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
51284 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
51322 CAGGTGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:51713 original size:91 final size:90
Alignment explanation
Indices: 51543--51727 Score: 275
Period size: 91 Copynumber: 2.0 Consensus size: 90
51533 ATTTCAAACT
*
51543 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACATTATTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATTAAAGAAT--A-AGTTTAGC
51608 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
*
51636 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTTAATA-AAT-AGTTTAGC
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTATTAA-AGAATAAGTTTAGC
*
51699 AGTATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
51727 T
1 T
51728 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
91 36 0.42
93 19 0.22
95 30 0.35
96 1 0.01
ACGTcount: A:0.48, C:0.18, G:0.11, T:0.23
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATTAAAGAATAAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:53442 original size:20 final size:19
Alignment explanation
Indices: 53415--53536 Score: 84
Period size: 20 Copynumber: 6.8 Consensus size: 19
53405 TCTTTTGGTT
53415 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
53434 GATAATGAAAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
53455 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
53474 G--A-G--AACCGCAACGC
1 GAAATGAAAATCGCAACGA
**
53488 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
53507 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
53521 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
53537 TGCGATTTTG
Statistics
Matches: 79, Mismatches: 12, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
14 19 0.24
16 4 0.05
17 4 0.05
19 20 0.25
20 30 0.38
21 2 0.03
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:53496 original size:33 final size:33
Alignment explanation
Indices: 53446--53536 Score: 146
Period size: 33 Copynumber: 2.7 Consensus size: 33
53436 TAATGAAAAT
53446 CGCAACGCGGAAATGACTATCGCAACGAGAGAAC
1 CGCAACGC-GAAATGACTATCGCAACGAGAGAAC
*
53480 CGCAACGCGAAATGACTATCGCAACGAGAGAAT
1 CGCAACGCGAAATGACTATCGCAACGAGAGAAC
**
53513 CGCAACGCGAAATGAAAATCGCAA
1 CGCAACGCGAAATGACTATCGCAA
53537 TGCGATTTTG
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 46 0.85
34 8 0.15
ACGTcount: A:0.41, C:0.25, G:0.24, T:0.10
Consensus pattern (33 bp):
CGCAACGCGAAATGACTATCGCAACGAGAGAAC
Found at i:53585 original size:33 final size:32
Alignment explanation
Indices: 53537--53625 Score: 97
Period size: 33 Copynumber: 2.7 Consensus size: 32
53527 AAAATCGCAA
*
53537 TGCGATTTTGGTTTCGCGTTGCAATTATCTCGT
1 TGCGATTTT-ATTTCGCGTTGCAATTATCTCGT
* * *
53570 TGCGATTTTCATTTCGAGTTGCGATTCTCTCGT
1 TGCGATTTT-ATTTCGCGTTGCAATTATCTCGT
*
53603 TGCGATAGTTATTTCCGCGTTGC
1 TGCGAT-TTTATTT-CGCGTTGC
53626 GATTTTCATT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
33 38 0.81
34 9 0.19
ACGTcount: A:0.12, C:0.20, G:0.24, T:0.44
Consensus pattern (32 bp):
TGCGATTTTATTTCGCGTTGCAATTATCTCGT
Found at i:54237 original size:20 final size:20
Alignment explanation
Indices: 54164--54293 Score: 120
Period size: 20 Copynumber: 6.5 Consensus size: 20
54154 GCTATGTAAA
* *
54164 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTACGTAT
* *
54184 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTACGTAT
*
54204 TCGCATTGCAATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* *
54224 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
* *
54245 TCGCATTGCGATTTACTTAA
1 TCGCATTGCGATTTACGTAT
*
54265 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
*
54285 TTGCATTGC
1 TCGCATTGC
54294 AAATTATGAA
Statistics
Matches: 94, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
19 3 0.03
20 73 0.78
21 18 0.19
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:54349 original size:21 final size:20
Alignment explanation
Indices: 54295--54357 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
54285 TTGCATTGCA
*
54295 AATTATGAAAATCGCAACGCG
1 AATTA-GAAAATCGCAATGCG
*
54316 AA-TACATAAATCGCAATGCG
1 AATTAGA-AAATCGCAATGCG
*
54336 AATTAGGAAAATCGCATTGCG
1 AATTA-GAAAATCGCAATGCG
54357 A
1 A
54358 TAGTCATAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 1 0.03
20 16 0.46
21 17 0.49
22 1 0.03
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.21
Consensus pattern (20 bp):
AATTAGAAAATCGCAATGCG
Found at i:57099 original size:4 final size:4
Alignment explanation
Indices: 57083--57121 Score: 69
Period size: 4 Copynumber: 9.5 Consensus size: 4
57073 TCATTTGTAA
57083 TCAT TCAAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TC
1 TCAT TC-AT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TC
57122 TCGCTCTCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 30 0.88
5 4 0.12
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (4 bp):
TCAT
Found at i:58036 original size:2 final size:2
Alignment explanation
Indices: 58029--58057 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
58019 GTCATATGCG
58029 TA TA 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 TA TA T
58058 TCAGTCAAGC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:62356 original size:3 final size:3
Alignment explanation
Indices: 62348--62382 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
62338 TATTTCTTGT
62348 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
62383 AGTTACTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:63963 original size:18 final size:18
Alignment explanation
Indices: 63918--63963 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
63908 GTTTGATATC
*
63918 GTTTAAGTTAAGTCTCAG
1 GTTTAAGTTCAGTCTCAG
63936 GTTTAAGTTCAGTCTCAG
1 GTTTAAGTTCAGTCTCAG
63954 GTTTAAGTTC
1 GTTTAAGTTC
63964 TTGTGTATGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.24, C:0.13, G:0.22, T:0.41
Consensus pattern (18 bp):
GTTTAAGTTCAGTCTCAG
Done.