Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005321.1 Hibiscus syriacus cultivar Beakdansim tig00012041_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: 74477
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:270 original size:22 final size:23
Alignment explanation
Indices: 228--270 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
218 AGTCGAGGGT
*
228 CTATATGGTCATTCAGTACAAAA
1 CTATATGGTCATTCAGGACAAAA
251 CTATATGGTC-TTCAGGACAA
1 CTATATGGTCATTCAGGACAA
271 TATGTGGCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (23 bp):
CTATATGGTCATTCAGGACAAAA
Found at i:13055 original size:19 final size:18
Alignment explanation
Indices: 13027--13062 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
13017 TGGAGGGGCA
13027 TTAAGGTTTAAGTAGAAT
1 TTAAGGTTTAAGTAGAAT
13045 TTAATGGTTTAAGTAGAA
1 TTAA-GGTTTAAGTAGAA
13063 AAGTCTACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.39, C:0.00, G:0.22, T:0.39
Consensus pattern (18 bp):
TTAAGGTTTAAGTAGAAT
Found at i:13964 original size:18 final size:17
Alignment explanation
Indices: 13925--13965 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
13915 GAATTCCAGA
13925 ATACCAAAATGGTAACG
1 ATACCAAAATGGTAACG
* *
13942 GTACCAAAATGGGTATCG
1 ATACCAAAAT-GGTAACG
13960 ATACCA
1 ATACCA
13966 TAAAAGGGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (17 bp):
ATACCAAAATGGTAACG
Found at i:14575 original size:23 final size:23
Alignment explanation
Indices: 14545--14626 Score: 146
Period size: 23 Copynumber: 3.6 Consensus size: 23
14535 GTCGAGGGTT
14545 CTATGTGGTCCTTCGGGACAAAA
1 CTATGTGGTCCTTCGGGACAAAA
14568 CTATGTGGTCCTTCGGGACAAAA
1 CTATGTGGTCCTTCGGGACAAAA
*
14591 CTATGTGGTCCTTCGGGAAAAAA
1 CTATGTGGTCCTTCGGGACAAAA
*
14614 CTATATGGTCCTT
1 CTATGTGGTCCTT
14627 AGTTACAAAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGACAAAA
Found at i:14635 original size:46 final size:45
Alignment explanation
Indices: 14545--14650 Score: 135
Period size: 46 Copynumber: 2.4 Consensus size: 45
14535 GTCGAGGGTT
* * *
14545 CTATGTGGTCCTTCGGGACAAAACTATGTGGTCCTTCGGGACAAAA
1 CTATGTGGTCCTTCGGGAAAAAACTATATGGTCCTTAGGGAC-AAA
**
14591 CTATGTGGTCCTTCGGGAAAAAACTATATGGTCCTTAGTTACAAA
1 CTATGTGGTCCTTCGGGAAAAAACTATATGGTCCTTAGGGACAAA
14636 -TATGTGG-CACTTCGG
1 CTATGTGGTC-CTTCGG
14651 TGCAAATTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
43 1 0.02
44 13 0.24
45 3 0.06
46 37 0.69
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (45 bp):
CTATGTGGTCCTTCGGGAAAAAACTATATGGTCCTTAGGGACAAA
Found at i:15421 original size:21 final size:21
Alignment explanation
Indices: 15395--15443 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
15385 ATTCTCTTCA
*
15395 TGAAAAGATTAA-ATCCTTTCG
1 TGAAAAGATTAAGCT-CTTTCG
*
15416 TGAAAAGGTTAAGCTCTTTCG
1 TGAAAAGATTAAGCTCTTTCG
15437 TGAAAAG
1 TGAAAAG
15444 GATAAGTCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (21 bp):
TGAAAAGATTAAGCTCTTTCG
Found at i:15444 original size:21 final size:21
Alignment explanation
Indices: 15410--15449 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
15400 AGATTAAATC
*
15410 CTTTCGTGAAAAGGTTAAGCT
1 CTTTCGTGAAAAGGATAAGCT
15431 CTTTCGTGAAAAGGATAAG
1 CTTTCGTGAAAAGGATAAG
15450 TCCCTTAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (21 bp):
CTTTCGTGAAAAGGATAAGCT
Found at i:15879 original size:19 final size:19
Alignment explanation
Indices: 15857--15894 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
15847 TTATTTTATT
15857 ATTA-TTATTTTATTTAGAA
1 ATTAGTTATTTTA-TTAGAA
15876 ATTAGTTATTTTATTAGAA
1 ATTAGTTATTTTATTAGAA
15895 CACTTGGTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (19 bp):
ATTAGTTATTTTATTAGAA
Found at i:19680 original size:20 final size:21
Alignment explanation
Indices: 19635--19680 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
19625 AATTTATTTA
*
19635 TTTTA-CTATTTTCTTTTTCT
1 TTTTATCTATTTTATTTTTCT
**
19655 AGTTATCTA-TTTATTTTTCT
1 TTTTATCTATTTTATTTTTCT
19675 TTTTAT
1 TTTTAT
19681 TTTTAGGTAC
Statistics
Matches: 20, Mismatches: 5, Indels: 2
0.74 0.19 0.07
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.72
Consensus pattern (21 bp):
TTTTATCTATTTTATTTTTCT
Found at i:20240 original size:19 final size:20
Alignment explanation
Indices: 20218--20257 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
20208 ATAGAGAGAA
20218 ACACAG-AAAAAGGGGGAGG
1 ACACAGAAAAAAGGGGGAGG
20237 ACACAGAAAAAAGGGGGAGG
1 ACACAGAAAAAAGGGGGAGG
20257 A
1 A
20258 AAAACAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.50, C:0.10, G:0.40, T:0.00
Consensus pattern (20 bp):
ACACAGAAAAAAGGGGGAGG
Found at i:20266 original size:20 final size:20
Alignment explanation
Indices: 20224--20268 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
20214 AGAAACACAG
* * *
20224 AAAAAGGGGGAGGACACAGA
1 AAAAAGGGGGAGGAAAAACA
20244 AAAAAGGGGGAGGAAAAACA
1 AAAAAGGGGGAGGAAAAACA
20264 AAAAA
1 AAAAA
20269 ATGAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.60, C:0.07, G:0.33, T:0.00
Consensus pattern (20 bp):
AAAAAGGGGGAGGAAAAACA
Found at i:21011 original size:37 final size:39
Alignment explanation
Indices: 20934--21012 Score: 108
Period size: 40 Copynumber: 2.1 Consensus size: 39
20924 GATTTACGAT
*
20934 TTTTAGTTTGATTATTTAATTATTACTTTTTAATTTAAAA
1 TTTTAGTTTGATTATTTAATTATTAC-TTTTAATTGAAAA
* *
20974 TTTTGGTTTGATTATTTTATTATTA-TTTT-ATTGAAAA
1 TTTTAGTTTGATTATTTAATTATTACTTTTAATTGAAAA
21011 TT
1 TT
21013 AGTTATTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
37 9 0.25
38 4 0.11
40 23 0.64
ACGTcount: A:0.29, C:0.01, G:0.08, T:0.62
Consensus pattern (39 bp):
TTTTAGTTTGATTATTTAATTATTACTTTTAATTGAAAA
Found at i:21190 original size:19 final size:19
Alignment explanation
Indices: 21166--21210 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
21156 TTTGAAGTTA
21166 TACTTTTCTTTCATCT-TTT
1 TACTTTTCTTTCAT-TATTT
21185 TACTTTTCTTTCATTATTT
1 TACTTTTCTTTCATTATTT
21204 T-CTTTTC
1 TACTTTTC
21211 ACAATGCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.11, C:0.20, G:0.00, T:0.69
Consensus pattern (19 bp):
TACTTTTCTTTCATTATTT
Found at i:23196 original size:15 final size:15
Alignment explanation
Indices: 23178--23239 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
23168 TAGATTTACG
*
23178 ATTTTTAGTTTGATT
1 ATTTTTAGTTTAATT
*
23193 A-TTTTATTATTAATT
1 ATTTTTAGT-TTAATT
* *
23208 -TTTTTA-TTTTA-G
1 ATTTTTAGTTTAATT
23220 ATTTTTAGTTTAATT
1 ATTTTTAGTTTAATT
23235 ATTTT
1 ATTTT
23240 ATTATTATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
13 9 0.25
14 11 0.31
15 16 0.44
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.69
Consensus pattern (15 bp):
ATTTTTAGTTTAATT
Found at i:23226 original size:42 final size:43
Alignment explanation
Indices: 23172--23255 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 43
23162 ACCTTTTAGA
*
23172 TTTACGATTTTTAGTTTGATTATTTTATTATTAATTTT-TTTAT
1 TTTACGATTTTTAGTTTAATTATTTTATTATT-ATTTTATTTAT
23215 TTTA-GATTTTTAGTTTAATTATTTTATTATTATTTTATTTA
1 TTTACGATTTTTAGTTTAATTATTTTATTATTATTTTATTTA
23256 ATAATTAGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
41 5 0.13
42 30 0.77
43 4 0.10
ACGTcount: A:0.25, C:0.01, G:0.06, T:0.68
Consensus pattern (43 bp):
TTTACGATTTTTAGTTTAATTATTTTATTATTATTTTATTTAT
Found at i:27748 original size:20 final size:22
Alignment explanation
Indices: 27723--27777 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 22
27713 TAATGTAGGT
27723 ATCGATGCACTCT-AC-AGTGC
1 ATCGATGCACTCTAACGAGTGC
*
27743 ATCGATGCATCCTTTAACGAGTGC
1 ATCGATGCA--CTCTAACGAGTGC
27767 ATCGATGCACT
1 ATCGATGCACT
27778 ACTTATGCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 9 0.30
22 5 0.17
23 2 0.07
24 14 0.47
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (22 bp):
ATCGATGCACTCTAACGAGTGC
Found at i:34986 original size:52 final size:52
Alignment explanation
Indices: 34908--35011 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 52
34898 ATTATAATAT
* *
34908 CCTTGTAATTAGTTTTAATCCCCCAACTCTAGGCTAGTTTCTTATTTCTGTG
1 CCTTGTAATTAGTTGTAATCCCCCAACTCTAGGCTAGTTTCCTATTTCTGTG
34960 CCTTGTAATTAGTTGTAATCCCCCAACTCTAGGCTAGTTTCCTATTTCTGTG
1 CCTTGTAATTAGTTGTAATCCCCCAACTCTAGGCTAGTTTCCTATTTCTGTG
35012 TGCCCAATCT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.42
Consensus pattern (52 bp):
CCTTGTAATTAGTTGTAATCCCCCAACTCTAGGCTAGTTTCCTATTTCTGTG
Found at i:35175 original size:2 final size:2
Alignment explanation
Indices: 35168--35192 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35158 ATGATCCTTC
35168 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
35193 AACTATGCCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35881 original size:52 final size:52
Alignment explanation
Indices: 35818--35917 Score: 164
Period size: 52 Copynumber: 1.9 Consensus size: 52
35808 TGGGCACATA
*
35818 GAAATATGAAACTAGCCTAGAGTTGAGGGATTACAACTAATTAAAATGCATG
1 GAAATAGGAAACTAGCCTAGAGTTGAGGGATTACAACTAATTAAAATGCATG
* * *
35870 GAAATAGGAAACTAGCCTAGAGTTGGGGGATTGCAACTAATTACAATG
1 GAAATAGGAAACTAGCCTAGAGTTGAGGGATTACAACTAATTAAAATG
35918 ATGTTATAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (52 bp):
GAAATAGGAAACTAGCCTAGAGTTGAGGGATTACAACTAATTAAAATGCATG
Found at i:39229 original size:9 final size:9
Alignment explanation
Indices: 39219--39251 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
39209 TTCCATAAAT
*
39219 CACATATAT
1 CACATATAC
39228 CACATATAC
1 CACATATAC
39237 CACATATAC
1 CACATATAC
39246 CACATA
1 CACATA
39252 ACATAATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.24
Consensus pattern (9 bp):
CACATATAC
Found at i:42739 original size:32 final size:30
Alignment explanation
Indices: 42671--42743 Score: 85
Period size: 32 Copynumber: 2.4 Consensus size: 30
42661 TGTCTGAAGA
*
42671 ACATAGGTAACTGTCTATATGTCCCAAACG
1 ACATAGGTAACTGTCCATATGTCCCAAACG
*
42701 ACATAGGTAATCCTGTCCATATGT-CCATAAGG
1 ACATAGGTAA--CTGTCCATATGTCCCA-AACG
*
42733 ATATAGGTAAC
1 ACATAGGTAAC
42744 CCTCGACTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
30 11 0.30
31 3 0.08
32 23 0.62
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (30 bp):
ACATAGGTAACTGTCCATATGTCCCAAACG
Found at i:43680 original size:19 final size:19
Alignment explanation
Indices: 43641--43681 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
43631 CCTTCACTGG
* *
43641 TATATCGGTACACTACCTA
1 TATATCGATACACTAACTA
*
43660 TATATCGATACACTAATTA
1 TATATCGATACACTAACTA
43679 TAT
1 TAT
43682 GCGAAACTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.37
Consensus pattern (19 bp):
TATATCGATACACTAACTA
Found at i:45827 original size:12 final size:12
Alignment explanation
Indices: 45810--45834 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45800 ATGCAAACCC
45810 TTATCATATTCA
1 TTATCATATTCA
45822 TTATCATATTCA
1 TTATCATATTCA
45834 T
1 T
45835 ACTCTTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (12 bp):
TTATCATATTCA
Found at i:47320 original size:32 final size:30
Alignment explanation
Indices: 47239--47332 Score: 125
Period size: 30 Copynumber: 3.1 Consensus size: 30
47229 CCGAAGGACC
* *
47239 ACTATCCATATGTTCCGAAGAACATAGGTA
1 ACTATCCATATGTCCCGAAGGACATAGGTA
* * *
47269 ACTGTACATATGTCTCGAAGGACATAGGTA
1 ACTATCCATATGTCCCGAAGGACATAGGTA
47299 ATCCTATCCATATGTCCCGAAGGACATAGGTA
1 A--CTATCCATATGTCCCGAAGGACATAGGTA
47331 AC
1 AC
47333 CCTCGACTCT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
30 27 0.50
32 27 0.50
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (30 bp):
ACTATCCATATGTCCCGAAGGACATAGGTA
Found at i:49400 original size:64 final size:64
Alignment explanation
Indices: 49321--49449 Score: 249
Period size: 64 Copynumber: 2.0 Consensus size: 64
49311 CTTCTCCAAT
*
49321 TCCTCATTGAGTCTGGGTTCACAGACTCTCATGCAGACACTTCTCTATTCATTCTTCACTCAGG
1 TCCTCATTGAGTCTGGGTTCACAAACTCTCATGCAGACACTTCTCTATTCATTCTTCACTCAGG
49385 TCCTCATTGAGTCTGGGTTCACAAACTCTCATGCAGACACTTCTCTATTCATTCTTCACTCAGG
1 TCCTCATTGAGTCTGGGTTCACAAACTCTCATGCAGACACTTCTCTATTCATTCTTCACTCAGG
49449 T
1 T
49450 GACACTAGTA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.35
Consensus pattern (64 bp):
TCCTCATTGAGTCTGGGTTCACAAACTCTCATGCAGACACTTCTCTATTCATTCTTCACTCAGG
Found at i:54147 original size:24 final size:24
Alignment explanation
Indices: 54091--54189 Score: 123
Period size: 24 Copynumber: 4.2 Consensus size: 24
54081 TAAACGAAAG
** *
54091 ATAAACGAACATATTTGTGAACGT
1 ATAAACGAACATATTCCTGAACAT
54115 -TAAACGAACATATTCCTGAACAT
1 ATAAACGAACATATTCCTGAACAT
*
54138 ATAAACGAACATGTTCCTGAACAT
1 ATAAACGAACATATTCCTGAACAT
*
54162 ATAAACGAACATGTTCGC-GAACA-
1 ATAAACGAACATATTC-CTGAACAT
54185 ATAAA
1 ATAAA
54190 TAAACGAAGG
Statistics
Matches: 69, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
23 25 0.36
24 43 0.62
25 1 0.01
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.24
Consensus pattern (24 bp):
ATAAACGAACATATTCCTGAACAT
Found at i:54171 original size:12 final size:12
Alignment explanation
Indices: 54074--54173 Score: 55
Period size: 12 Copynumber: 8.5 Consensus size: 12
54064 ACTAAAAATT
54074 GAACATATAAAC
1 GAACATATAAAC
*
54086 GAA-AGATAAAC
1 GAACATATAAAC
****
54097 GAACATATTTGT
1 GAACATATAAAC
*
54109 GAACGT-TAAAC
1 GAACATATAAAC
**
54120 GAACATAT-TCC
1 GAACATATAAAC
54131 TGAACATATAAAC
1 -GAACATATAAAC
* **
54144 GAACATGT-TCC
1 GAACATATAAAC
54155 TGAACATATAAAC
1 -GAACATATAAAC
54168 GAACAT
1 GAACAT
54174 GTTCGCGAAC
Statistics
Matches: 60, Mismatches: 22, Indels: 12
0.64 0.23 0.13
Matches are distributed among these distances:
11 18 0.30
12 40 0.67
13 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (12 bp):
GAACATATAAAC
Found at i:54603 original size:29 final size:30
Alignment explanation
Indices: 54552--54634 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 30
54542 TAACTTTTAT
* * * *
54552 TTTTTTAAAAATTAAAATAAATC-CCAAAC
1 TTTTTTAAAAAATCAATTTAATCTCCAAAC
*
54581 TTTTTTAAAAAATCAATTTAATCTTCAAAC
1 TTTTTTAAAAAATCAATTTAATCTCCAAAC
** *
54611 AATATTAAAAAATCAATTT-ATCTC
1 TTTTTTAAAAAATCAATTTAATCTC
54635 ATTTATCATA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 23 0.52
30 21 0.48
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (30 bp):
TTTTTTAAAAAATCAATTTAATCTCCAAAC
Found at i:54779 original size:28 final size:29
Alignment explanation
Indices: 54744--54801 Score: 109
Period size: 28 Copynumber: 2.0 Consensus size: 29
54734 AGTCAACGAG
54744 AATAAATATTAATTG-AAAATCAGATCAA
1 AATAAATATTAATTGAAAAATCAGATCAA
54772 AATAAATATTAATTGAAAAATCAGATCAA
1 AATAAATATTAATTGAAAAATCAGATCAA
54801 A
1 A
54802 TCTATTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 15 0.52
29 14 0.48
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.28
Consensus pattern (29 bp):
AATAAATATTAATTGAAAAATCAGATCAA
Found at i:59481 original size:75 final size:75
Alignment explanation
Indices: 59345--59526 Score: 231
Period size: 75 Copynumber: 2.4 Consensus size: 75
59335 TTTAATCGGT
* * * * * * *
59345 TAAAATAAAATAGGCGCTACCTATTATGTTAAATTACCTACCGGTTTATTTGAATGTTACTAACA
1 TAAAATAAAATAGGTGCTACCTATTAAGTTAAAATACCGACCGGTTTATTTAAAGGCTACTAACA
*
59410 ATGTAAACGG
66 ATGTAAACGA
* * * * * *
59420 TAAAATAAAATAGGTGTTACCTATTACGTTAAAATATCGACTGGTTTGTTTAAAGGCTACTAATA
1 TAAAATAAAATAGGTGCTACCTATTAAGTTAAAATACCGACCGGTTTATTTAAAGGCTACTAACA
59485 ATGTAAACGA
66 ATGTAAACGA
59495 TAAAA-AAAATAGGTGCTACCTATTAAGTTAAA
1 TAAAATAAAATAGGTGCTACCTATTAAGTTAAA
59527 TAAGTGTTAC
Statistics
Matches: 92, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
74 25 0.27
75 67 0.73
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (75 bp):
TAAAATAAAATAGGTGCTACCTATTAAGTTAAAATACCGACCGGTTTATTTAAAGGCTACTAACA
ATGTAAACGA
Found at i:59541 original size:23 final size:23
Alignment explanation
Indices: 59501--59549 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
59491 ACGATAAAAA
* *
59501 AAATAGGTGCTACCTATTAAGTT
1 AAATAAGTGCTACATATTAAGTT
* *
59524 AAATAAGTGTTACATATTATGTT
1 AAATAAGTGCTACATATTAAGTT
59547 AAA
1 AAA
59550 CTAGCTACTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (23 bp):
AAATAAGTGCTACATATTAAGTT
Found at i:59542 original size:97 final size:98
Alignment explanation
Indices: 59427--59625 Score: 274
Period size: 97 Copynumber: 2.0 Consensus size: 98
59417 CGGTAAAATA
* * * *
59427 AAATAGGTGTTACCTATTACGTTAAAATATCGACTGGTTTGTTTAAAGGCTACTAATAATGTAAA
1 AAATAAGTGTTACATATTACGTTAAAATAGCGACTGGTTTGTTTAAAGGCTAATAATAATGTAAA
* *
59492 CGATAAAA-AAAATAGGTGCTACCTATTAAGTT
66 CGATAAAATAAAATAGGCGCTACCTACTAAGTT
* * * * *
59524 AAATAAGTGTTACATATTATGTTAAACTAGCTACTTGTTTGTTTAAATGCTAATAATAATGTAAA
1 AAATAAGTGTTACATATTACGTTAAAATAGCGACTGGTTTGTTTAAAGGCTAATAATAATGTAAA
* *
59589 CGGTAAAATAAAATAGGCGCTACCTACTATGTT
66 CGATAAAATAAAATAGGCGCTACCTACTAAGTT
59622 AAAT
1 AAAT
59626 TACCTACCGG
Statistics
Matches: 88, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
97 63 0.72
98 25 0.28
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (98 bp):
AAATAAGTGTTACATATTACGTTAAAATAGCGACTGGTTTGTTTAAAGGCTAATAATAATGTAAA
CGATAAAATAAAATAGGCGCTACCTACTAAGTT
Found at i:59660 original size:75 final size:75
Alignment explanation
Indices: 59534--59700 Score: 217
Period size: 75 Copynumber: 2.2 Consensus size: 75
59524 AAATAAGTGT
* * * ** * * *
59534 TACATATTATGTTAAACTAGCTACTTGTTTGTTTAAATGCTAATAATAATGTAAACGGTAAAATA
1 TACATACTATGTTAAATTACCTACCGGTTTGTTTAAAGGCTAATAACAATGTAAACGATAAAATA
*
59599 AAATAGGCGC
66 AAATAGACGC
* * *
59609 TACCTACTATGTTAAATTACCTACCGGTTTGTTTAAAGGTTATTAACAATGTAAACGATAAAATA
1 TACATACTATGTTAAATTACCTACCGGTTTGTTTAAAGGCTAATAACAATGTAAACGATAAAATA
59674 AAATAGACGC
66 AAATAGACGC
*
59684 TACATATTATGTTAAAT
1 TACATACTATGTTAAAT
59701 AAGCGCTACC
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
75 78 1.00
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (75 bp):
TACATACTATGTTAAATTACCTACCGGTTTGTTTAAAGGCTAATAACAATGTAAACGATAAAATA
AAATAGACGC
Found at i:59662 original size:172 final size:173
Alignment explanation
Indices: 59352--59771 Score: 529
Period size: 172 Copynumber: 2.4 Consensus size: 173
59342 GGTTAAAATA
* * * * * * * * *
59352 AAATAGGCGCTACCTATTATGTTAAATTACCTACCGGTTTATTTGAATGTTACTAACAATGTAAA
1 AAATAAGCGCTACATATTATGTTAAACTAACTACTGGTTTGTTTAAATGTTAATAATAATGTAAA
* * * * *
59417 CGGTAAAATAAAATAGGTGTTACCTATTACGTTAAAATATCGACTGGTTTGTTTAAAGGCTACTA
66 CGGTAAAATAAAATAGGCGCTACCTACTACGTTAAAATACCGACCGGTTTGTTTAAAGGCTACTA
* ** *
59482 ATAATGTAAACGATAAAA-AAAATAGGTGCTACCTATTAAGTT
131 ACAATGTAAACGATAAAATAAAATAGACGCTACATATTAAGTT
* * * * *
59524 AAATAAGTGTTACATATTATGTTAAACTAGCTACTTGTTTGTTTAAATGCTAATAATAATGTAAA
1 AAATAAGCGCTACATATTATGTTAAACTAACTACTGGTTTGTTTAAATGTTAATAATAATGTAAA
* * * * *
59589 CGGTAAAATAAAATAGGCGCTACCTACTATGTTAAATTACCTACCGGTTTGTTTAAAGGTTATTA
66 CGGTAAAATAAAATAGGCGCTACCTACTACGTTAAAATACCGACCGGTTTGTTTAAAGGCTACTA
*
59654 ACAATGTAAACGATAAAATAAAATAGACGCTACATATTATGTT
131 ACAATGTAAACGATAAAATAAAATAGACGCTACATATTAAGTT
* * *
59697 AAATAAGCGCTACCTATTACGTTAAACTAACTA-TCGGTTTGTTTAAAGGTTAATAATAATGTAA
1 AAATAAGCGCTACATATTATGTTAAACTAACTACT-GGTTTGTTTAAATGTTAATAATAATGTAA
59761 ACGGTAAAATA
65 ACGGTAAAATA
59772 TATACAACTT
Statistics
Matches: 210, Mismatches: 36, Indels: 3
0.84 0.14 0.01
Matches are distributed among these distances:
172 125 0.60
173 85 0.40
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.34
Consensus pattern (173 bp):
AAATAAGCGCTACATATTATGTTAAACTAACTACTGGTTTGTTTAAATGTTAATAATAATGTAAA
CGGTAAAATAAAATAGGCGCTACCTACTACGTTAAAATACCGACCGGTTTGTTTAAAGGCTACTA
ACAATGTAAACGATAAAATAAAATAGACGCTACATATTAAGTT
Found at i:59997 original size:153 final size:151
Alignment explanation
Indices: 59753--60039 Score: 414
Period size: 153 Copynumber: 1.9 Consensus size: 151
59743 AGGTTAATAA
* * ** * *
59753 TAATGTAAACGGTAAAATATATACAACTTAATTGTTTGATTTTTTTTTTAAATTCGAAAGTATGA
1 TAATATAAACGGTAAAAAATATACAACTTAACCGTTTGATATTTTTTTAAAATTCGAAAGTATGA
* *
59818 ATACTTACACGAAAAGTATGGATACTCTAAGGGTAAATAATAATGTATCCATACTTACTCTAAAA
66 ATACTTACACGAAAAATATGGATACTCTAAAGGTAAATAATAATGTATCCATACTTACTCTAAAA
59883 GTATGGGTACTGTTTCGACAG
131 GTATGGGTACTGTTTCGACAG
*
59904 TAATATAAACGGTAAAAAATATACAACTTAACCGTTTGAAATATTTTTTTAAAATTTGAAAGTAT
1 TAATATAAACGGTAAAAAATATACAACTTAACCGTTTG--ATATTTTTTTAAAATTCGAAAGTAT
* ** * *
59969 GGATACTTATTCTAAAAATAT-GAGTACTCTAAAGGTTAATAATAATGTATCCATACTTACTCTA
64 GAATACTTACACGAAAAATATGGA-TACTCTAAAGGTAAATAATAATGTATCCATACTTACTCTA
60033 AAAGTAT
128 AAAGTAT
60040 TGATATTTCT
Statistics
Matches: 119, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
151 34 0.29
152 2 0.02
153 83 0.70
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (151 bp):
TAATATAAACGGTAAAAAATATACAACTTAACCGTTTGATATTTTTTTAAAATTCGAAAGTATGA
ATACTTACACGAAAAATATGGATACTCTAAAGGTAAATAATAATGTATCCATACTTACTCTAAAA
GTATGGGTACTGTTTCGACAG
Found at i:61396 original size:23 final size:23
Alignment explanation
Indices: 61349--61398 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
61339 AATAACATAT
* * **
61349 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGAGCTTATAAAATAAAA
61372 TAGGTAGAGCTTATAAAATAAAA
1 TAGGTAGAGCTTATAAAATAAAA
61395 TAGG
1 TAGG
61399 CATTTAACCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.30
Consensus pattern (23 bp):
TAGGTAGAGCTTATAAAATAAAA
Found at i:61453 original size:23 final size:23
Alignment explanation
Indices: 61427--61474 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
61417 ATCAAGTACA
61427 ATAA-CAAATTAGGTAGCGCTTAT
1 ATAATCAAA-TAGGTAGCGCTTAT
**
61450 ATAATGTAATAGGTAGCGCTTAT
1 ATAATCAAATAGGTAGCGCTTAT
61473 AT
1 AT
61475 TGACCTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAATCAAATAGGTAGCGCTTAT
Found at i:61458 original size:87 final size:84
Alignment explanation
Indices: 61315--61473 Score: 264
Period size: 87 Copynumber: 1.9 Consensus size: 84
61305 TATATTATAT
*
61315 CATTTAACCGGTATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAGA
1 CATTTAACCGGTATTATCAAGCACAATAACAAATTAGGTAGCGCTTATATAATGTAATAGGTAGA
61380 GCTTATAAAATAAAATAGG
66 GCTTATAAAATAAAATAGG
*
61399 CATTTAACCGGAAATATTATCAAGTACAATAACAAATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGG---TATTATCAAGCACAATAACAAATTAGGTAGCGCTTATATAATGTAATAGGT
*
61464 AGCGCTTATA
63 AGAGCTTATA
61474 TTGACCTATT
Statistics
Matches: 69, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
84 11 0.16
87 58 0.84
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (84 bp):
CATTTAACCGGTATTATCAAGCACAATAACAAATTAGGTAGCGCTTATATAATGTAATAGGTAGA
GCTTATAAAATAAAATAGG
Found at i:61826 original size:198 final size:199
Alignment explanation
Indices: 61510--61991 Score: 523
Period size: 198 Copynumber: 2.4 Consensus size: 199
61500 AAATTTAAAA
* * * * *
61510 CGGTTACATTATACATTGACCTATTACATTAT-GTATATCGGTTTCGATGTTTTCG-GGATCGAT
1 CGGTTACATTGTAAATTTACCTATTACATTATAAT-TATCGGTTTCGATGATTTCGAGGATCGAT
* * * * * *
61573 ACAATTTT-AAATGTATCGACACTTTATGTGTGCAACTCGTTTGTGCTTTATTTTGGAAAAAAGT
65 AC-TTTTTAAAATGTATCGACACTTTAAGCGTACAACTCGTTTGTCCTTCATTTTGGAAAAAAGT
* * * *
61637 ATAGACACATATTTAAAGAGTGTCGATACATAATGTAAACCTATT-TGCTAATTAA-CCGATATA
129 ATAGACACAAATTAAAAAAGTGTCGATACATAATGTAAACCTATTCT-CTAATGAACCCGATATA
61700 TTT-TAAC
193 TTTCT-AC
* * *
61707 CGGTTACATTGTAAATTTACCTGTTACATAATAATTATCGATTTCGATG-TTTCGAGGATCGATA
1 CGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGATTTCGAGGATCGATA
* *
61771 CTTTTTACAAATGTATCGACACTTTAAGCGTACACCTCGTTT-TCCATTCATTTTGGAAAAATGT
66 CTTTTTA-AAATGTATCGACACTTTAAGCGTACAACTCGTTTGTCC-TTCATTTTGGAAAAAAGT
* * * ** * * *
61835 ATCGACACAAATTAAAAAAGTGTCGATACTTTATGTTGACTTATTCTCTCATGAACCCGGTATAT
129 ATAGACACAAATTAAAAAAGTGTCGATACATAATGTAAACCTATTCTCTAATGAACCCGATATAT
61900 TTCTAC
194 TTCTAC
* * * ** *
61906 CGGTTACATTGGAAATTTACCTATTACATTATAATTATTGGTCTCTTTGATTTTGA-GATCGATA
1 CGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGATTTCGAGGATCGATA
*
61970 CTTGTTATAAATGTATCGACAC
66 CTTTTTA-AAATGTATCGACAC
61992 AAAATCTAAT
Statistics
Matches: 238, Mismatches: 38, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
196 9 0.04
197 52 0.22
198 89 0.37
199 82 0.34
200 6 0.03
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (199 bp):
CGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGATTTCGAGGATCGATA
CTTTTTAAAATGTATCGACACTTTAAGCGTACAACTCGTTTGTCCTTCATTTTGGAAAAAAGTAT
AGACACAAATTAAAAAAGTGTCGATACATAATGTAAACCTATTCTCTAATGAACCCGATATATTT
CTAC
Found at i:65542 original size:197 final size:198
Alignment explanation
Indices: 65133--66158 Score: 1145
Period size: 201 Copynumber: 5.1 Consensus size: 198
65123 GTAATTTTAA
* * * * * * * * *
65133 AAAGTATCGACATAAATTTAAAAAGTGTCGATGCATTATGTAGACCTATTTTCTCATGAAACCGG
1 AAAGTATCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTTTTTTAAT--AACCGG
* * * * * * *
65198 -AAAATTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTACGGGTTTCGATGTTTTT
64 TATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTTTTT
* * * **
65262 AGGATCGACACTTTTTCTAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATG
129 GGGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATACATTATG
65327 GACAT
194 GACAT
*
65332 AAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTTTTTTAATAACCGGTA
1 AAAGTATCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTTTTTTAATAACCGGTA
* * * *
65397 TGTTTAGACCGGTTATATTTTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTT-G
66 TATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGG
**
65461 GATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGA
131 GATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATACATTATGGA
65526 CAT
196 CAT
* *
65529 AAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTAAACCTTTCTTTTTTAATAACCGG
1 AAAGTATCGACACAAATGTATAAAGTATCGATACATTATGTATACC-TT-TTTTTTAATAACCGG
* *
65594 TATATTTAGACCGGTTACATTGTTATGTTATCTATTACATTATAATTATGTGTTTCGATGTTTTT
64 TATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTTTTT
* * *
65659 GGGATCGACACTTGTTATAAATGTATCGACACTTTTTTTGTGCACTTGGTTTGG-AAATACATTC
129 GGGATCGACACTTGTTATAAATGTATCGACAC-TTTTTCGTGAACTT-GTTTGGAAAATACATTA
*
65723 TTG--AT
192 TGGACAT
* * * *
65728 AACATGTATCGACACAAATGAATAAAGTGTCGATACA-TATTGTAGACCTATTTTCTCATAA-AA
1 AA-A-GTATCGACACAAATGTATAAAGTATCGATACATTA-TGTATACCT-TTTT-T-TTAATAA
* * * * * * * * * * *
65791 CTGATAAATTTAAACTGGTTACATTGTAAAGTGACCTATTACATTATAGTTACGGGTTTCAATGT
60 CCGGTATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGT
* * *
65856 TTTTTGGATCGACACTTGATATAAATGTGTCGACACTTATTT-GTGAACTTGTTTTGGTTGGAAA
125 TTTTGGGATCGACACTTGTTATAAATGTATCGACACTT-TTTCGTGAACTTG---T--TTGGAAA
*
65920 ATACATTATGGACAC
184 ATACATTATGGACAT
* * * * * * *
65935 AAAGTATCGACACAAATCTATAAAGTGTCGATACTTTATGTATATCTCTTTTCTCATAAACCGGT
1 AAAGTATCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTTTTTTAAT-AACCGGT
* * *
66000 ATATTTAGACTGGTTACATTGTTATTTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTG
65 ATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
* * *
66065 GGATCGATACTTTTTATAAATGTATCGACACTTTGTTCGTGCACTTGGTTTGG-AAATACATTAT
130 GGATCGACACTTGTTATAAATGTATCGACACTTT-TTCGTGAACTT-GTTTGGAAAATACATTAT
66129 GGACA-
193 GGACAT
* * *
66134 ACATGTATCGACACGAATGAATAAA
1 A-AAGTATCGACACAAATGTATAAA
66159 ACAAATTCAT
Statistics
Matches: 710, Mismatches: 89, Indels: 55
0.83 0.10 0.06
Matches are distributed among these distances:
197 118 0.17
198 55 0.08
199 129 0.18
200 82 0.12
201 153 0.22
202 12 0.02
203 3 0.00
204 97 0.14
205 54 0.08
206 4 0.01
207 3 0.00
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (198 bp):
AAAGTATCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTTTTTTAATAACCGGTA
TATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGG
GATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATACATTATGGA
CAT
Found at i:66059 original size:405 final size:397
Alignment explanation
Indices: 65133--66158 Score: 1251
Period size: 405 Copynumber: 2.6 Consensus size: 397
65123 GTAATTTTAA
* * * * * * *
65133 AAAGTATCGACATAAATTTAAAAAGTGTCGATGCATTATGTAGACCTATTTTCTCATGAAACCGG
1 AAAGTATCGACACAAATCTATAAAGTGTCGATACATTATGTAAATCTCTTTTCTCAT-AAACCGG
* * * * * * *
65198 -AAAATTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTACGGGTTTCGATGTTTTT
65 TATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTTTTT
* * * **
65262 AGGATCGACACTTTTTCTAAATGTATCGACAC-TTTTTCGTGAACTT-GTTTGGAAAATTTATTA
130 GGGATCGACACTTTTTATAAATGTATCGACACTTTTTTCGTGCACTTGGTTTGG-AAATACATTA
* * * *
65325 TGGACATAA-A-GTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTTTTTTAA
194 TGG--ATAACATGTATCGACACAAATGAATAAAGTATCGATACATTATGTAGACCTTTTTTATAA
* ** * * * * * * * * *
65388 TAACCGGTATGTTTAGACCGGTTATATTTTTATGTTACCTATTACATTATAATTATGTGTTTCGA
257 TAACCGATAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTACGGGTTTCAA
* **
65453 TGTTTTTGGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTT
322 TGTTTTTGGATCGACACTTGATATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATAC
*
65518 ATTATGGACAT
387 ATTATGGACAC
* * * * * *
65529 AAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTAAACCTTTCTTTTTTAAT-AACCG
1 AAAGTATCGACACAAATCTATAAAGTGTCGATACATTATGTAAA--TCTCTTTTCTCATAAACCG
* *
65593 GTATATTTAGACCGGTTACATTGTTATGTTATCTATTACATTATAATTATGTGTTTCGATGTTTT
64 GTATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTTTT
* * *
65658 TGGGATCGACACTTGTTATAAATGTATCGACACTTTTTTTGTGCACTTGGTTTGGAAATACATTC
129 TGGGATCGACACTTTTTATAAATGTATCGACACTTTTTTCGTGCACTTGGTTTGGAAATACATTA
* *
65723 TTGATAACATGTATCGACACAAATGAATAAAGTGTCGATACA-TATTGTAGACCTATTTTCTCAT
194 TGGATAACATGTATCGACACAAATGAATAAAGTATCGATACATTA-TGTAGACCT-TTTT-T-AT
* * *
65787 AA-AACTGATAAATTTAAACTGGTTACATTGTAAAGTGACCTATTACATTATAGTTACGGGTTTC
255 AATAACCGATAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTACGGGTTTC
*
65851 AATGTTTTTTGGATCGACACTTGATATAAATGTGTCGACACTTATTT-GTGAACTTGTTTTGGTT
320 AATG-TTTTTGGATCGACACTTGATATAAATGTATCGACACTT-TTTCGTGAACTTG---T--TT
65915 GGAAAATACATTATGGACAC
378 GGAAAATACATTATGGACAC
* *
65935 AAAGTATCGACACAAATCTATAAAGTGTCGATACTTTATGTATATCTCTTTTCTCATAAACCGGT
1 AAAGTATCGACACAAATCTATAAAGTGTCGATACATTATGTAAATCTCTTTTCTCATAAACCGGT
* * *
66000 ATATTTAGACTGGTTACATTGTTATTTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTG
66 ATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
* *
66065 GGATCGATACTTTTTATAAATGTATCGACACTTTGTTCGTGCACTTGGTTTGGAAATACATTATG
131 GGATCGACACTTTTTATAAATGTATCGACACTTTTTTCGTGCACTTGGTTTGGAAATACATTATG
* *
66130 GACAACATGTATCGACACGAATGAATAAA
196 GATAACATGTATCGACACAAATGAATAAA
66159 ACAAATTCAT
Statistics
Matches: 535, Mismatches: 76, Indels: 29
0.84 0.12 0.05
Matches are distributed among these distances:
396 47 0.09
397 87 0.16
398 66 0.12
399 10 0.02
400 52 0.10
401 48 0.09
402 3 0.01
404 11 0.02
405 153 0.29
406 58 0.11
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (397 bp):
AAAGTATCGACACAAATCTATAAAGTGTCGATACATTATGTAAATCTCTTTTCTCATAAACCGGT
ATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
GGATCGACACTTTTTATAAATGTATCGACACTTTTTTCGTGCACTTGGTTTGGAAATACATTATG
GATAACATGTATCGACACAAATGAATAAAGTATCGATACATTATGTAGACCTTTTTTATAATAAC
CGATAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTACGGGTTTCAATGTT
TTTGGATCGACACTTGATATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATACATTA
TGGACAC
Found at i:67932 original size:18 final size:18
Alignment explanation
Indices: 67911--67945 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
67901 ATCATCATCA
67911 TCATCATCATCTTCATTT
1 TCATCATCATCTTCATTT
*
67929 TCATCGTCATCTTCATT
1 TCATCATCATCTTCATT
67946 GACCGCTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.29, G:0.03, T:0.49
Consensus pattern (18 bp):
TCATCATCATCTTCATTT
Found at i:69080 original size:15 final size:15
Alignment explanation
Indices: 69060--69112 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
69050 TGATTTCCTC
69060 AGAAGAGCTGGGTTG
1 AGAAGAGCTGGGTTG
* *
69075 AGAAGAGGTGAGTTG
1 AGAAGAGCTGGGTTG
*
69090 AGAAGAGATGGGTTG
1 AGAAGAGCTGGGTTG
69105 AGAAGAGC
1 AGAAGAGC
69113 CCCGATTTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.34, C:0.04, G:0.45, T:0.17
Consensus pattern (15 bp):
AGAAGAGCTGGGTTG
Found at i:69753 original size:198 final size:198
Alignment explanation
Indices: 69504--70410 Score: 1403
Period size: 198 Copynumber: 4.6 Consensus size: 198
69494 TTACAAAATG
*
69504 ACCTATTACATTATAATTATGGGTCTCGATGTTTTTTGGATCGAAACTTTTTATAAATGTATCGA
1 ACCTATTACATTATAATTATGGGTCTCGATGTTTTTTGGATCGATACTTTTTATAAATGTATCGA
* * * *
69569 CACATTGTGGTGACCTTGGTAAGGAAATCATTCTGAATACAAAGTATCGACACAAATTCTAAAAG
66 CACATTATGGTGACCTTGGTAAGGAAATCATTCTGGACACAAAGTATCGACACAAATTCAAAAAG
* * *
69634 TGTCGATACTTCATGTATACCTGTTTTCTCATAAACCAGTTTATTTAGACCGGTGAGATTGATAA
131 TGTCGATACTTCATGTACACCTGTTTTCTCATAAACCAGTGTATTTAGACCGGTTAGATTGATAA
69699 TTT
196 TTT
*
69702 ACCTATTACATTATAATTATGGGTCTCGTTGTTTTTTGGATCGATACTTTTTATAAATGTATCGA
1 ACCTATTACATTATAATTATGGGTCTCGATGTTTTTTGGATCGATACTTTTTATAAATGTATCGA
* * *
69767 CACATTGTGGTGATCTTGGTAAGGAAATCATTCTGGACACAAAGTATCGACACAAATTCAAAACG
66 CACATTATGGTGACCTTGGTAAGGAAATCATTCTGGACACAAAGTATCGACACAAATTCAAAAAG
* *
69832 TGTCGATACTTCATGTACACCTGTTTT-TCATAAACCAGTGTATTTATACCGGTTACATTGCA-A
131 TGTCGATACTTCATGTACACCTGTTTTCTCATAAACCAGTGTATTTAGACCGGTTAGATTG-ATA
* *
69895 AATG
195 ATTT
* *
69899 ACCTATTACATTATAATTATGGGTCTCGATGTTTTTGGGATCGATACTTTTTATAAAGGTATCGA
1 ACCTATTACATTATAATTATGGGTCTCGATGTTTTTTGGATCGATACTTTTTATAAATGTATCGA
* *
69964 GACATTATGGTGACCTTGGTAAGGAAATCATTCTGGACACAAAGTATAGACACAAATTCAAAAAG
66 CACATTATGGTGACCTTGGTAAGGAAATCATTCTGGACACAAAGTATCGACACAAATTCAAAAAG
* *
70029 TGTCGATACTTCATGTACACCTGTTTTCTCATAAACCGGTGTATTTAGACCGGTTAAATTGATAA
131 TGTCGATACTTCATGTACACCTGTTTTCTCATAAACCAGTGTATTTAGACCGGTTAGATTGATAA
70094 TTT
196 TTT
* *
70097 ACCTATTACATTATAATTATGGGTCTCGATGTTTTTGGGATCGATACTTTTTATAAAGGTATCGA
1 ACCTATTACATTATAATTATGGGTCTCGATGTTTTTTGGATCGATACTTTTTATAAATGTATCGA
* *
70162 CATATTATGGTGACCTTGGTAAGGAAATCATTCTGGACACAAAGTATGGGATCAACACAAATT-A
66 CACATTATGGTGACCTTGGTAAGGAAATCATTCTGGACACAAAG--T---ATCGACACAAATTCA
* *
70226 AACAAGTGTCGATACTTTATGTACACCTGTTTTCTCATAAACCGGT-TATTTAGACCGGTTAGAT
126 AA-AAGTGTCGATACTTCATGTACACCTGTTTTCTCATAAACCAGTGTATTTAGACCGGTTAGAT
70290 TGATAATTT
190 TGATAATTT
*
70299 ACCTATTATATTATAATTATGGGTCTCGATGTTTTTTGGATCGATACTTTTTATAAATGTATCGA
1 ACCTATTACATTATAATTATGGGTCTCGATGTTTTTTGGATCGATACTTTTTATAAATGTATCGA
** *
70364 CACATT-TCCAT-ACACTTGGTAAGGAAATCATTTTGGACACAAAGTAT
66 CACATTAT-GGTGAC-CTTGGTAAGGAAATCATTCTGGACACAAAGTAT
70411 ACTTGGAATG
Statistics
Matches: 658, Mismatches: 40, Indels: 23
0.91 0.06 0.03
Matches are distributed among these distances:
197 184 0.28
198 290 0.44
200 2 0.00
201 3 0.00
202 126 0.19
203 53 0.08
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.36
Consensus pattern (198 bp):
ACCTATTACATTATAATTATGGGTCTCGATGTTTTTTGGATCGATACTTTTTATAAATGTATCGA
CACATTATGGTGACCTTGGTAAGGAAATCATTCTGGACACAAAGTATCGACACAAATTCAAAAAG
TGTCGATACTTCATGTACACCTGTTTTCTCATAAACCAGTGTATTTAGACCGGTTAGATTGATAA
TTT
Found at i:70207 original size:395 final size:396
Alignment explanation
Indices: 69477--70411 Score: 1450
Period size: 395 Copynumber: 2.4 Consensus size: 396
69467 TAAATAGGTA
*
69477 TATTTATACCGGTTACATTACAAAATGACCTATTACATTATAATTATGGGTCTCGATGTTTTTTG
1 TATTTATACCGGTTACATTGCAAAATGACCTATTACATTATAATTATGGGTCTCGATGTTTTTTG
* * *
69542 GATCGAAACTTTTTATAAATGTATCGACACATTGTGGTGACCTTGGTAAGGAAATCATTCTGAAT
66 GATCGATACTTTTTATAAATGTATCGACACATT-TGGTGACCTTGGTAAGGAAATCATTCTGGAC
* * *
69607 ACAAAGTATCGACACAAATTCTAAAAGTGTCGATACTTCATGTATACCTGTTTTCTCATAAACCA
130 ACAAAGTATAGACACAAATTCAAAAAGTGTCGATACTTCATGTACACCTGTTTTCTCATAAACCA
* * *
69672 GTTTATTTAGACCGGTGAGATTGATAATTTACCTATTACATTATAATTATGGGTCTCGTTGTTTT
195 GTGTATTTAGACCGGTGAAATTGATAATTTACCTATTACATTATAATTATGGGTCTCGATGTTTT
* * * *
69737 TTGGATCGATACTTTTTATAAATGTATCGACACATTGTGGTGATCTTGGTAAGGAAATCATTCTG
260 TGGGATCGATACTTTTTATAAAGGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATTCTG
* *
69802 GACACAAAG-T-ATCGACACAAATTCAAA-ACGTGTCGATACTTCATGTACACCTGTTTT-TCAT
325 GACACAAAGATGATCAACACAAATT-AAACAAGTGTCGATACTTCATGTACACCTGTTTTCTCAT
69863 AAACCAGT
389 AAACCAGT
*
69871 GTATTTATACCGGTTACATTGCAAAATGACCTATTACATTATAATTATGGGTCTCGATGTTTTTG
1 -TATTTATACCGGTTACATTGCAAAATGACCTATTACATTATAATTATGGGTCTCGATGTTTTTT
* *
69936 GGATCGATACTTTTTATAAAGGTATCGAGACATTATGGTGACCTTGGTAAGGAAATCATTCTGGA
65 GGATCGATACTTTTTATAAATGTATCGACACATT-TGGTGACCTTGGTAAGGAAATCATTCTGGA
70001 CACAAAGTATAGACACAAATTCAAAAAGTGTCGATACTTCATGTACACCTGTTTTCTCATAAACC
129 CACAAAGTATAGACACAAATTCAAAAAGTGTCGATACTTCATGTACACCTGTTTTCTCATAAACC
* *
70066 GGTGTATTTAGACCGGTTAAATTGATAATTTACCTATTACATTATAATTATGGGTCTCGATGTTT
194 AGTGTATTTAGACCGGTGAAATTGATAATTTACCTATTACATTATAATTATGGGTCTCGATGTTT
*
70131 TTGGGATCGATACTTTTTATAAAGGTATCGACATATTATGGTGACCTTGGTAAGGAAATCATTCT
259 TTGGGATCGATACTTTTTATAAAGGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATTCT
*
70196 GGACACAAAGTATGGGATCAACACAAATTAAACAAGTGTCGATACTTTATGTACACCTGTTTTCT
324 GGACACAAAG-AT--GATCAACACAAATTAAACAAGTGTCGATACTTCATGTACACCTGTTTTCT
*
70261 CATAAACCGGT
386 CATAAACCAGT
* * * * *
70272 TATTTAGACCGGTTAGATTG-ATAATTTACCTATTATATTATAATTATGGGTCTCGATGTTTTTT
1 TATTTATACCGGTTACATTGCA-AAATGACCTATTACATTATAATTATGGGTCTCGATGTTTTTT
** *
70336 GGATCGATACTTTTTATAAATGTATCGACACATTTCCAT-ACACTTGGTAAGGAAATCATTTTGG
65 GGATCGATACTTTTTATAAATGTATCGACACATTT-GGTGAC-CTTGGTAAGGAAATCATTCTGG
70400 ACACAAAGTATA
128 ACACAAAGTATA
70412 CTTGGAATGG
Statistics
Matches: 494, Mismatches: 36, Indels: 15
0.91 0.07 0.03
Matches are distributed among these distances:
395 313 0.63
397 1 0.00
399 7 0.01
400 162 0.33
401 11 0.02
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.36
Consensus pattern (396 bp):
TATTTATACCGGTTACATTGCAAAATGACCTATTACATTATAATTATGGGTCTCGATGTTTTTTG
GATCGATACTTTTTATAAATGTATCGACACATTTGGTGACCTTGGTAAGGAAATCATTCTGGACA
CAAAGTATAGACACAAATTCAAAAAGTGTCGATACTTCATGTACACCTGTTTTCTCATAAACCAG
TGTATTTAGACCGGTGAAATTGATAATTTACCTATTACATTATAATTATGGGTCTCGATGTTTTT
GGGATCGATACTTTTTATAAAGGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATTCTGG
ACACAAAGATGATCAACACAAATTAAACAAGTGTCGATACTTCATGTACACCTGTTTTCTCATAA
ACCAGT
Found at i:70595 original size:20 final size:20
Alignment explanation
Indices: 70552--70602 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
70542 TTACATTCAC
* *
70552 ATACAAAATT-ATAAATCGT
1 ATACAAAATTAAAAAAACGT
*
70571 ATACAAAATTAAAAAAACTT
1 ATACAAAATTAAAAAAACGT
70591 ATACAAAATTAA
1 ATACAAAATTAA
70603 CCTACATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.61, C:0.10, G:0.02, T:0.27
Consensus pattern (20 bp):
ATACAAAATTAAAAAAACGT
Found at i:71756 original size:17 final size:17
Alignment explanation
Indices: 71734--71769 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
71724 GAATCATTAG
71734 GATTAATATCTTTTCAT
1 GATTAATATCTTTTCAT
71751 GATTAATATCTTTTCAT
1 GATTAATATCTTTTCAT
71768 GA
1 GA
71770 AATATTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (17 bp):
GATTAATATCTTTTCAT
Found at i:72774 original size:22 final size:24
Alignment explanation
Indices: 72748--72802 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
72738 CAACCTGCAT
72748 TATAATAAAAT-TA-ATCATTTTA
1 TATAATAAAATATACATCATTTTA
*
72770 TATAAT-AACTATACCATCATTTTA
1 TATAATAAAATATA-CATCATTTTA
72794 TATAA-AAAA
1 TATAATAAAA
72803 CAAAAACATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 3 0.11
22 8 0.30
24 16 0.59
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (24 bp):
TATAATAAAATATACATCATTTTA
Found at i:74083 original size:19 final size:19
Alignment explanation
Indices: 74028--74086 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
74018 CTAAAAAATC
74028 ATTTTCTACCTATAATATT
1 ATTTTCTACCTATAATATT
* * ** *
74047 ATATAC-ATGTATCCATATT
1 ATTTTCTACCTAT-AATATT
74066 ATTTTCTACCTATAATATT
1 ATTTTCTACCTATAATATT
74085 AT
1 AT
74087 AATATAATCG
Statistics
Matches: 28, Mismatches: 10, Indels: 4
0.67 0.24 0.10
Matches are distributed among these distances:
18 4 0.14
19 20 0.71
20 4 0.14
ACGTcount: A:0.34, C:0.15, G:0.02, T:0.49
Consensus pattern (19 bp):
ATTTTCTACCTATAATATT
Done.