Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001772.1 Hibiscus syriacus cultivar Beakdansim tig00003573_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: 70703
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:1187 original size:21 final size:19
Alignment explanation
Indices: 1162--1258 Score: 90
Period size: 21 Copynumber: 4.9 Consensus size: 19
1152 TCAAACACTA
*
1162 AAATATTTTTTATTGTAAATT
1 AAATA-TTTTTATT-AAAATT
*
1183 AAATA-TTTTATTAAAAAT
1 AAATATTTTTATTAAAATT
* *
1201 AAATATTTTATTTGTAAATTT
1 AAATATTTT-TAT-TAAAATT
1222 AAATA-TTTTATTAAAATAT
1 AAATATTTTTATTAAAAT-T
1241 AAATATATTTTATTAAAA
1 AAATAT-TTTTATTAAAA
1259 ATATAAAATA
Statistics
Matches: 63, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
18 14 0.22
19 18 0.29
20 5 0.08
21 26 0.41
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
AAATATTTTTATTAAAATT
Found at i:1206 original size:39 final size:41
Alignment explanation
Indices: 1162--1254 Score: 147
Period size: 39 Copynumber: 2.3 Consensus size: 41
1152 TCAAACACTA
1162 AAATATTTTTTATTGTAAA-TTAAATATTTTATTAAAA-AT
1 AAATATTTTTTATTGTAAATTTAAATATTTTATTAAAATAT
*
1201 AAATATTTTAT-TTGTAAATTTAAATATTTTATTAAAATAT
1 AAATATTTTTTATTGTAAATTTAAATATTTTATTAAAATAT
*
1241 AAATATATTTTATT
1 AAATATTTTTTATT
1255 AAAAATATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
38 7 0.15
39 28 0.58
40 11 0.23
41 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (41 bp):
AAATATTTTTTATTGTAAATTTAAATATTTTATTAAAATAT
Found at i:1269 original size:21 final size:20
Alignment explanation
Indices: 1183--1269 Score: 99
Period size: 21 Copynumber: 4.3 Consensus size: 20
1173 ATTGTAAATT
1183 AAATATTTTATTAAAA-AT-
1 AAATATTTTATTAAAATATA
* *
1201 AAATATTTTATTTGTAAAT-TT
1 AAATATTTTA-TT-AAAATATA
1222 AAATATTTTATTAAAATATA
1 AAATATTTTATTAAAATATA
1242 AATATATTTTATTAAAAATATA
1 AA-ATATTTTATT-AAAATATA
1264 AAATAT
1 AAATAT
1270 AAAAAATATA
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
18 10 0.17
19 6 0.10
20 9 0.15
21 24 0.41
22 10 0.17
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (20 bp):
AAATATTTTATTAAAATATA
Found at i:5888 original size:32 final size:32
Alignment explanation
Indices: 5852--5919 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
5842 TCGGGTAGGA
* * *
5852 GTCGGGTGGAGGATATATATTTTTTAGGTCAG
1 GTCGGATGGAGGATATAAAATTTTTAGGTCAG
* *
5884 GTCGGATGTAGGATATAAAATTTTTAGGTCGG
1 GTCGGATGGAGGATATAAAATTTTTAGGTCAG
5916 GTCG
1 GTCG
5920 AGTTTGGATG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.24, C:0.07, G:0.34, T:0.35
Consensus pattern (32 bp):
GTCGGATGGAGGATATAAAATTTTTAGGTCAG
Found at i:12327 original size:23 final size:23
Alignment explanation
Indices: 12283--12327 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12273 TTAATTAGAT
*
12283 TTTAAAATATTAATGAGTTTAAG
1 TTTAAAATATTAATAAGTTTAAG
*
12306 TTTAAAAT-TTATTAAGTCTTAA
1 TTTAAAATATTAATAAGT-TTAA
12328 TATTTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (23 bp):
TTTAAAATATTAATAAGTTTAAG
Found at i:15725 original size:29 final size:29
Alignment explanation
Indices: 15663--15797 Score: 126
Period size: 29 Copynumber: 4.5 Consensus size: 29
15653 AACCCAACCA
* * **
15663 TAGGTCGCCAAGCACTCCAAGCGACCTAC
1 TAGGTCGCCATGCACTCCCAGCGACCTTG
*
15692 AAGGTCGCCATGCACTCCCAGCGACCTTG
1 TAGGTCGCCATGCACTCCCAGCGACCTTG
* * * *
15721 TAGGTCGCCAAGCAATCCCGGCGACCAAGATGG
1 TAGGTCGCCATGCACTCCCAGCGACC----TTG
* * *
15754 TAGGTCGCCATGTACGCCCAGCGACCTTA
1 TAGGTCGCCATGCACTCCCAGCGACCTTG
15783 TAGGTCGCCATGCAC
1 TAGGTCGCCATGCAC
15798 GCCGGCGTCC
Statistics
Matches: 84, Mismatches: 18, Indels: 8
0.76 0.16 0.07
Matches are distributed among these distances:
29 61 0.73
33 23 0.27
ACGTcount: A:0.24, C:0.35, G:0.25, T:0.16
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCTTG
Found at i:16448 original size:21 final size:21
Alignment explanation
Indices: 16423--16466 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
16413 AATTTAGTTA
16423 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
16444 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
16465 AT
1 AT
16467 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:16480 original size:28 final size:28
Alignment explanation
Indices: 16443--16496 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
16433 TAGTATAAAT
*
16443 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAATTTGTTAGTTTAAGTTATATTA
16471 TATTAATTTGTTAGTTTAAGTTATAT
1 TATTAATTTGTTAGTTTAAGTTATAT
16497 ATTAGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TATTAATTTGTTAGTTTAAGTTATATTA
Found at i:19642 original size:60 final size:59
Alignment explanation
Indices: 19570--20314 Score: 898
Period size: 60 Copynumber: 13.2 Consensus size: 59
19560 TTTATAAGAT
* *
19570 TTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAGTAATTTGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAA--TGA
19631 -TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
19689 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGA-TT--T-G--ATG-
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
* *
19742 ---GTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
* *
19798 TTTAGTAATGATTAGTAATAATGAAATCATTATTAATTTTTAATGATTTGATAATAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
19858 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
* * * * * * * * *
19918 TTAGTAATGATTAGTAATGATTAGTAATAATGAAATT-ATTATTAAT-TTTTAATAAT-TTGA
1 TTAGTAATGATTAGTAAT-AAT-GAAATTAT--TATTAATTTTTAATGATTTGATAGTAATGA
19978 -TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
20036 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTT-A--A-TT-AT--T--TGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
20087 -TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTT-A--A--TGAT--T--TGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
*
20136 -TAGTAATGATTAGTAATAATGAAACTATTATTAATTTTTAATGATTTGATAGTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
20194 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
* *
20254 TTAG---T-A--A-TAATAAT----TTATTATTAATATTTAATGATTTGATATTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
20302 TTTAGTAATGATT
1 -TTAGTAATGATT
20315 TGATAGTAAT
Statistics
Matches: 612, Mismatches: 31, Indels: 88
0.84 0.04 0.12
Matches are distributed among these distances:
48 33 0.05
49 130 0.21
50 3 0.00
51 3 0.00
52 10 0.02
53 3 0.00
54 7 0.01
55 9 0.01
56 13 0.02
57 15 0.02
58 11 0.02
59 42 0.07
60 309 0.50
61 13 0.02
62 8 0.01
63 3 0.00
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.47
Consensus pattern (59 bp):
TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
Found at i:19738 original size:109 final size:109
Alignment explanation
Indices: 19625--20261 Score: 867
Period size: 109 Copynumber: 5.7 Consensus size: 109
19615 TTTGATAGTA
19625 ATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGAT
1 ATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGAT
19690 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATG
66 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATG
* * *
19734 ATTTGATGGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGAT
1 ATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGAT
*
19799 TTAGTAATGATTAGTAATAATGAAATCATTATTAATTTTTAATGATTTG
66 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTT-A--A--TG
19848 ATAATAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGT
1 AT--T--TGA--TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGT
*
19913 AATGATTAGTAATGATTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATA
60 -A--A-T-G--AT--TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATG
19972 ATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGAT
1 ATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGAT
*
20037 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATT
66 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATG
20081 ATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-
1 ATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGAT
* * * * * *
20145 TTAGTAAT-AAT-GAAACTATTAT-TAATTTTTAATGATTTGATAGTAATG
66 TTAGTAATGATTAGTAA-TA--ATGAAATTATTATTAATTT--T--TAATG
20193 A-TT--TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-
1 ATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGAT
20254 TTAGTAAT
66 TTAGTAAT
20262 AATAATTTAT
Statistics
Matches: 484, Mismatches: 17, Indels: 54
0.87 0.03 0.10
Matches are distributed among these distances:
106 3 0.01
107 4 0.01
108 20 0.04
109 276 0.57
110 2 0.00
111 4 0.01
112 6 0.01
113 1 0.00
114 5 0.01
115 1 0.00
116 1 0.00
117 1 0.00
118 56 0.12
120 53 0.11
121 1 0.00
122 1 0.00
123 1 0.00
124 4 0.01
125 1 0.00
126 1 0.00
127 2 0.00
128 1 0.00
129 39 0.08
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (109 bp):
ATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGAT
TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATG
Found at i:19874 original size:10 final size:11
Alignment explanation
Indices: 19852--19945 Score: 52
Period size: 10 Copynumber: 8.4 Consensus size: 11
19842 GATTTGATAA
19852 TAATGATTTAG
1 TAATGATTTAG
*
19863 TAATGATTAGTAA
1 TAATGATT--TAG
* *
19876 TAATGAAATTAT
1 TAATG-ATTTAG
* * *
19888 TATTAATTT-T
1 TAATGATTTAG
19898 TAATGATTTGATAG
1 TAATGATTT---AG
19912 TAATGA-TTAG
1 TAATGATTTAG
19922 TAATGA-TTAG
1 TAATGATTTAG
19932 TAATGA-TTAG
1 TAATGATTTAG
19942 TAAT
1 TAAT
19946 AATGAAATTA
Statistics
Matches: 67, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
10 34 0.51
11 11 0.16
12 5 0.07
13 9 0.13
14 8 0.12
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (11 bp):
TAATGATTTAG
Found at i:19943 original size:69 final size:70
Alignment explanation
Indices: 19852--19994 Score: 270
Period size: 69 Copynumber: 2.1 Consensus size: 70
19842 GATTTGATAA
*
19852 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATAATTTGATAGTAATG
19917 ATTAG
66 ATTAG
19922 TAATGA-TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATAATTTGATAGTAATG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATAATTTGATAGTAATG
19986 ATTAG
66 ATTAG
19991 TAAT
1 TAAT
19995 AATGAAATTA
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
69 66 0.92
70 6 0.08
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.45
Consensus pattern (70 bp):
TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATAATTTGATAGTAATG
ATTAG
Found at i:20285 original size:21 final size:22
Alignment explanation
Indices: 20261--20330 Score: 63
Period size: 25 Copynumber: 3.1 Consensus size: 22
20251 TGATTAGTAA
20261 TAATAATTT-ATTATTAAT-ATT
1 TAATAATTTGA-TATTAATGATT
*
20282 TAATGATTTGATATTAATGATTT
1 TAATAATTTGATATTAATGA-TT
* *
20305 AGTAATGATTTGATAGTAATGATT
1 --TAATAATTTGATATTAATGATT
20329 TA
1 TA
20331 CGACTTGAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
21 15 0.36
22 4 0.10
23 2 0.05
24 2 0.05
25 19 0.45
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (22 bp):
TAATAATTTGATATTAATGATT
Found at i:20288 original size:48 final size:49
Alignment explanation
Indices: 19929--20310 Score: 451
Period size: 49 Copynumber: 7.3 Consensus size: 49
19919 TAGTAATGAT
* *
19929 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATAATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
19978 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTT-A--A--TGAT--T--TGA
* *
20036 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATTATTTGA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
20087 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
* *
20136 TAGTAATGATTAGTAATAATGAAACTATTATTAATTTTTAATGATTTGATAGTAATGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTT-A--A--TGAT--T--TGA
*
20194 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
20245 TAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
20293 TATTAATGATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
20311 GATTTGATAG
Statistics
Matches: 302, Mismatches: 8, Indels: 46
0.85 0.02 0.13
Matches are distributed among these distances:
48 34 0.11
49 153 0.51
50 2 0.01
51 6 0.02
52 2 0.01
53 2 0.01
54 7 0.02
55 7 0.02
56 2 0.01
57 2 0.01
58 6 0.02
59 2 0.01
60 77 0.25
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
Found at i:20298 original size:14 final size:14
Alignment explanation
Indices: 20282--20329 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
20272 TATTAATATT
*
20282 TAATGATTTGATAT
1 TAATGATTTGATAG
20296 TAATGA-TT--TAG
1 TAATGATTTGATAG
20307 TAATGATTTGATAG
1 TAATGATTTGATAG
20321 TAATGATTT
1 TAATGATTT
20330 ACGACTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 2 0.07
14 18 0.60
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:22674 original size:30 final size:30
Alignment explanation
Indices: 22640--22743 Score: 115
Period size: 30 Copynumber: 3.4 Consensus size: 30
22630 TCCCTTAAAC
*
22640 AACTAATAAACTATTCTTTAATATAACGTT-
1 AACTAATAAACTATTCTTTAATATAA-ATTA
22670 AACTAATAAACTATTCTTTAATATAAATTA
1 AACTAATAAACTATTCTTTAATATAAATTA
*
22700 AACTAATAAA-TGATT-TTTAATTATAATTTA
1 AACTAATAAACT-ATTCTTTAA-TATAAATTA
* *
22730 CTACTAAAAAACTA
1 -AACTAATAAACTA
22744 ATTAACTAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
29 8 0.12
30 47 0.72
31 9 0.14
32 1 0.02
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (30 bp):
AACTAATAAACTATTCTTTAATATAAATTA
Found at i:22947 original size:21 final size:21
Alignment explanation
Indices: 22923--22962 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
22913 TTTCTATATG
22923 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
22944 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
22963 ACTAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:23043 original size:18 final size:18
Alignment explanation
Indices: 22990--23044 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
22980 TTGTTTTACC
*
22990 CTAATTTATAATAATAAA
1 CTAATTTATAACAATAAA
23008 CTAA--T-TAAC--T-AA
1 CTAATTTATAACAATAAA
23020 -TAATTTATAACAATAAA
1 CTAATTTATAACAATAAA
23037 CTAATTTA
1 CTAATTTA
23045 AATAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 3 0.10
12 2 0.07
13 2 0.07
14 4 0.14
15 3 0.10
16 2 0.07
17 2 0.07
18 11 0.38
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
CTAATTTATAACAATAAA
Found at i:23103 original size:35 final size:37
Alignment explanation
Indices: 23064--23136 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 37
23054 TCTTTTATAT
23064 AACTT-AA-ACTAATAAACT-ATTTTTTATTATAATAA
1 AACTTAAACACTAATAAACTAATTTTTTA-TATAATAA
23099 AACTTAAACTACTAATAAACTAATTTTTTATATAATAA
1 AACTTAAAC-ACTAATAAACTAATTTTTTATATAATAA
23137 TATAAATTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
35 5 0.15
36 2 0.06
38 19 0.56
39 8 0.24
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (37 bp):
AACTTAAACACTAATAAACTAATTTTTTATATAATAA
Found at i:23687 original size:29 final size:28
Alignment explanation
Indices: 23640--23723 Score: 132
Period size: 29 Copynumber: 2.9 Consensus size: 28
23630 AAAGGCATAG
*
23640 GTCGTTGGGATCCCTTGGCGACCTACAAT
1 GTCGCTGGGATCCC-TGGCGACCTACAAT
23669 GTCGCTGGGATGCCCTGGCGACCTACAAT
1 GTCGCTGGGAT-CCCTGGCGACCTACAAT
23698 GTCGCTGGGATTCCCTGGCGACCTAC
1 GTCGCTGGGA-TCCCTGGCGACCTAC
23724 CCACGTTGCA
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
29 48 0.92
30 4 0.08
ACGTcount: A:0.15, C:0.31, G:0.30, T:0.24
Consensus pattern (28 bp):
GTCGCTGGGATCCCTGGCGACCTACAAT
Found at i:26695 original size:21 final size:23
Alignment explanation
Indices: 26665--26707 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
26655 TTCCTTGTTC
26665 TTTTAGTTTTTTA-GTTCTTTTT
1 TTTTAGTTTTTTATGTTCTTTTT
*
26687 TTTTA-TTTTTTATTTTCTTTT
1 TTTTAGTTTTTTATGTTCTTTT
26708 GAAAATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.09, C:0.05, G:0.05, T:0.81
Consensus pattern (23 bp):
TTTTAGTTTTTTATGTTCTTTTT
Found at i:27077 original size:6 final size:6
Alignment explanation
Indices: 27066--27116 Score: 56
Period size: 6 Copynumber: 9.0 Consensus size: 6
27056 TTTATGGTTG
*
27066 ATTTTT ATTTTT A-TTTT A-TCTT ATTTTT ATTTATT A-TTTT A-TTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTT-TT ATTTTT ATTTTT
27111 ATTTTT
1 ATTTTT
27117 TTATGTTATC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
5 17 0.43
6 20 0.50
7 3 0.08
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (6 bp):
ATTTTT
Found at i:27082 original size:5 final size:5
Alignment explanation
Indices: 27068--27115 Score: 51
Period size: 5 Copynumber: 8.8 Consensus size: 5
27058 TATGGTTGAT
*
27068 TTTTA TTTTTA TTTTA TCTTA TTTTTA TTTATTA TTTTA TTTTA TTTT
1 TTTTA -TTTTA TTTTA TTTTA -TTTTA -TT-TTA TTTTA TTTTA TTTT
27116 TTTATGTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
5 21 0.55
6 14 0.37
7 3 0.08
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:27091 original size:16 final size:15
Alignment explanation
Indices: 27069--27118 Score: 63
Period size: 16 Copynumber: 3.5 Consensus size: 15
27059 ATGGTTGATT
27069 TTTATTTTTATTTTA
1 TTTATTTTTATTTTA
27084 TCTTATTTTTA-TTTA
1 T-TTATTTTTATTTTA
27099 -TTA-TTTTATTTTA
1 TTTATTTTTATTTTA
27112 TTT-TTTT
1 TTTATTTT
27119 ATGTTATCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
12 5 0.16
13 7 0.23
14 5 0.16
15 5 0.16
16 9 0.29
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTATTTTTATTTTA
Found at i:27102 original size:23 final size:22
Alignment explanation
Indices: 27066--27116 Score: 84
Period size: 23 Copynumber: 2.3 Consensus size: 22
27056 TTTATGGTTG
27066 ATTTTTATTTTTATTTTATCTT
1 ATTTTTATTTTTATTTTATCTT
*
27088 ATTTTTATTTATTATTTTATTTT
1 ATTTTTATTT-TTATTTTATCTT
27111 ATTTTT
1 ATTTTT
27117 TTATGTTATC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (22 bp):
ATTTTTATTTTTATTTTATCTT
Found at i:27125 original size:18 final size:18
Alignment explanation
Indices: 27070--27117 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
27060 TGGTTGATTT
27070 TTATTTTTA--TTTTATC
1 TTATTTTTATTTTTTATC
* *
27086 TTATTTTTATTTATTATT
1 TTATTTTTATTTTTTATC
27104 TTA-TTTTATTTTTT
1 TTATTTTTATTTTTT
27118 TATGTTATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 9 0.33
17 10 0.37
18 8 0.30
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (18 bp):
TTATTTTTATTTTTTATC
Found at i:27125 original size:23 final size:23
Alignment explanation
Indices: 27067--27125 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
27057 TTATGGTTGA
*
27067 TTTTTATTTTTATTTTATCTTATT
1 TTTTTA-TATTATTTTATCTTATT
*
27091 TTTATT-TATTATTTTATTTTATT
1 TTT-TTATATTATTTTATCTTATT
*
27114 TTTTTATGTTAT
1 TTTTTATATTAT
27126 CATTTTATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 2 0.07
23 23 0.77
24 3 0.10
25 2 0.07
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.78
Consensus pattern (23 bp):
TTTTTATATTATTTTATCTTATT
Found at i:27132 original size:13 final size:12
Alignment explanation
Indices: 27068--27134 Score: 68
Period size: 13 Copynumber: 5.6 Consensus size: 12
27058 TATGGTTGAT
27068 TTTTATTT-TTA
1 TTTTATTTATTA
27079 TTTTATCTTA-T-
1 TTTTAT-TTATTA
27090 TTTTATTTATTA
1 TTTTATTTATTA
*
27102 TTTTATTTTATTT
1 TTTTA-TTTATTA
*
27115 TTTTATGTTATCA
1 TTTTAT-TTATTA
27128 TTTTATT
1 TTTTATT
27135 CATTTGTTGT
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
10 3 0.06
11 13 0.28
12 10 0.21
13 21 0.45
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.76
Consensus pattern (12 bp):
TTTTATTTATTA
Found at i:28641 original size:3 final size:3
Alignment explanation
Indices: 28633--28687 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
28623 TTAACTCGAG
* *
28633 ATA ATA ATA ATA ATA ATA ATA TTA ATA TTA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28681 ATA ATA A
1 ATA ATA A
28688 ATATTCTATC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:30406 original size:52 final size:52
Alignment explanation
Indices: 30292--30406 Score: 121
Period size: 52 Copynumber: 2.2 Consensus size: 52
30282 ATTTATTTAT
30292 TAATATTTATAATAATATAATATTATAATTTTAATATTATATAAAATAATCAA
1 TAAT-TTTATAATAATATAATATTATAATTTTAATATTATATAAAATAATCAA
* * * *
30345 TTATATTATAATAATATAAGATATTAT-ATTTTTATTTTA-ATAATATATAAT-AA
1 TAATTTTATAATAATAT-A-ATATTATAATTTTAATATTATATAA-A-ATAATCAA
30398 -AATTTTATA
1 TAATTTTATA
30407 TATTTAATAA
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
52 23 0.44
53 17 0.33
54 12 0.23
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (52 bp):
TAATTTTATAATAATATAATATTATAATTTTAATATTATATAAAATAATCAA
Found at i:30414 original size:26 final size:28
Alignment explanation
Indices: 30391--30466 Score: 61
Period size: 26 Copynumber: 2.8 Consensus size: 28
30381 TTAATAATAT
* *
30391 ATAATAAAATTTTATATATTTAATA-ATGA
1 ATAATAATA-TTTATATATATAATATAT-A
*
30420 ATAATATTATTTATATATAT-ATATAT-
1 ATAATAATATTTATATATATAATATATA
*
30446 AT-ATATATATATATATATATA
1 ATAATA-ATATTTATATATATA
30467 GAAAATTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
25 3 0.08
26 14 0.36
27 3 0.08
28 12 0.31
29 7 0.18
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (28 bp):
ATAATAATATTTATATATATAATATATA
Found at i:30416 original size:29 final size:29
Alignment explanation
Indices: 30294--30463 Score: 99
Period size: 29 Copynumber: 5.8 Consensus size: 29
30284 TTATTTATTA
*
30294 ATATTT-ATAATA-AT-ATAATATTATA-
1 ATATTTAATAATATATAATAATATTTTAT
* * **
30319 AT-TTTAATATTATATAA-AATAATCAATT
1 ATATTTAATAATATATAATAATATTTTA-T
30347 ATATTATAATAATATA-AGATATTATATTTT-T
1 ATATT-TAATAATATATA-ATA--ATATTTTAT
*
30378 AT-TTTAATAATATATAATAAAATTTTAT
1 ATATTTAATAATATATAATAATATTTTAT
*
30406 ATATTTAATAATGA-ATAATATTATTTATAT
1 ATATTTAATAAT-ATATAATAATATTT-TAT
*
30436 ATATATATATATATATATATATATATAT
1 ATATTTA-ATA-ATATATA-ATA-ATAT
30464 ATAGAAAATT
Statistics
Matches: 111, Mismatches: 13, Indels: 33
0.71 0.08 0.21
Matches are distributed among these distances:
24 3 0.03
25 7 0.06
26 8 0.07
27 7 0.06
28 5 0.05
29 35 0.32
30 23 0.21
31 8 0.07
32 5 0.05
33 7 0.06
34 3 0.03
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (29 bp):
ATATTTAATAATATATAATAATATTTTAT
Found at i:30438 original size:2 final size:2
Alignment explanation
Indices: 30431--30466 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
30421 TAATATTATT
30431 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
30467 GAAAATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35381 original size:15 final size:14
Alignment explanation
Indices: 35343--35378 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
35333 AATATTATTT
35343 ATATATTTAAAT-A
1 ATATATTTAAATAA
35356 ATAT-TTT-AATAA
1 ATATATTTAAATAA
35368 ATATATTTAAA
1 ATATATTTAAA
35379 ATATACTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
11 3 0.15
12 8 0.40
13 7 0.35
14 2 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATATATTTAAATAA
Found at i:35381 original size:23 final size:23
Alignment explanation
Indices: 35343--35406 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
35333 AATATTATTT
**
35343 ATATATTTAAATAATATTTTAATAA
1 ATATATTT-AA-AATATACTAATAA
*
35368 ATATATTTAAAATATACTAATTA
1 ATATATTTAAAATATACTAATAA
*
35391 ATATTTTTAAAATATA
1 ATATATTTAAAATATA
35407 ATATAACACT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 25 0.71
24 2 0.06
25 8 0.23
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATATTTAAAATATACTAATAA
Found at i:35487 original size:32 final size:29
Alignment explanation
Indices: 35447--35516 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
35437 AATATAATTT
*
35447 ATAATA-TTTTATTTCACTAAAATATAAAAAA
1 ATAATATTTTTA-TT-AATAAAAT-TAAAAAA
*
35478 ATTAATATTTTTATTAATAAAATTATAAAA
1 A-TAATATTTTTATTAATAAAATTAAAAAA
35508 ATAATATTT
1 ATAATATTT
35517 AATAATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 8 0.23
30 7 0.20
31 8 0.23
32 7 0.20
33 5 0.14
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (29 bp):
ATAATATTTTTATTAATAAAATTAAAAAA
Found at i:35782 original size:15 final size:15
Alignment explanation
Indices: 35737--35782 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
35727 TTCCGAAAAT
35737 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
*
35752 G-AATTCAAATTT-CA
1 GTAATTC-ATTTTCCA
35766 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
35781 GT
1 GT
35783 TCCAGTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.43
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:36818 original size:16 final size:16
Alignment explanation
Indices: 36778--36820 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
36768 AAAACAAATT
36778 ATTTTAAAATATTTAAA
1 ATTTTAAAA-ATTTAAA
* * *
36795 AATATAAAAATTTAGA
1 ATTTTAAAAATTTAAA
36811 ATTTTAAAAA
1 ATTTTAAAAA
36821 GAATGACCGA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
ATTTTAAAAATTTAAA
Found at i:38743 original size:20 final size:20
Alignment explanation
Indices: 38720--38775 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
38710 ACTCATGTTC
*
38720 CAAATTCACAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
38740 CAAATTCGCAATGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
38760 CGAAATTCGCAACGCG
1 C-AAATTCGCAACGCG
38776 GTTTTAAGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 19 0.59
21 13 0.41
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:39480 original size:18 final size:19
Alignment explanation
Indices: 39444--39480 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
39434 CACGGAATGT
39444 AAGATTACCAGTAGGAATAA
1 AAGATTACCAG-AGGAATAA
39464 AAGATTACCAG-GGAATA
1 AAGATTACCAGAGGAATA
39481 GGATTATTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.49, C:0.11, G:0.22, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGAGGAATAA
Found at i:40085 original size:21 final size:21
Alignment explanation
Indices: 40061--40103 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
40051 TTGTGATTAT
40061 TTTAGTTTGTAAATTTAGAAA
1 TTTAGTTTGTAAATTTAGAAA
40082 TTTAGTTTGTAAATTTAGAAA
1 TTTAGTTTGTAAATTTAGAAA
40103 T
1 T
40104 ATTAAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (21 bp):
TTTAGTTTGTAAATTTAGAAA
Found at i:47585 original size:23 final size:23
Alignment explanation
Indices: 47559--47606 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
47549 TTGTCCTACG
* *
47559 TCAGTAGAAATTTCTTGTGAAAT
1 TCAGGAGAAATTTCTAGTGAAAT
47582 TCAGGAGAAATTTCTAGTGAAAT
1 TCAGGAGAAATTTCTAGTGAAAT
47605 TC
1 TC
47607 TACATCAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (23 bp):
TCAGGAGAAATTTCTAGTGAAAT
Found at i:54698 original size:23 final size:22
Alignment explanation
Indices: 54646--54695 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
54636 GTCGAAAGTT
*
54646 AAAACCTTGCCCGACTTTGATA
1 AAAACCTTGCCCGACTTTAATA
54668 AAAACCTTGCCCGACTTTAATA
1 AAAACCTTGCCCGACTTTAATA
54690 AAAACC
1 AAAACC
54696 CTTTTGTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.24
Consensus pattern (22 bp):
AAAACCTTGCCCGACTTTAATA
Found at i:54751 original size:18 final size:18
Alignment explanation
Indices: 54728--54773 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
54718 GTTTATGAGG
54728 GAATTAAAATCTGT-AAA
1 GAATTAAAATCTGTCAAA
*
54745 TGAATTAGAATCTGTCAAA
1 -GAATTAAAATCTGTCAAA
54764 -AATTAAAATC
1 GAATTAAAATC
54774 AAATTTCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 9 0.36
18 13 0.52
19 3 0.12
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (18 bp):
GAATTAAAATCTGTCAAA
Found at i:55949 original size:259 final size:258
Alignment explanation
Indices: 55143--56251 Score: 1749
Period size: 258 Copynumber: 4.4 Consensus size: 258
55133 CCTCCATCCG
* * * *
55143 AGACCTGACCCGACCAAAATAAAGTTTTA-CCGACCCGACCCGACTATATGAATTAGAAACCTGA
1 AGACCTGACCCAACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGA
55207 CCCGACCCGAAATAATAAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAA
66 CCCGACCCGAAATAATAAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAA
* *
55272 -TATATATATAGGGGTATTATTGTAATTATTTCTAAATATATAAGGTAAAATTATATATATTTT-
131 TTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTC
** *
55335 GGGTTAGGTATTTTTCACCCTAAACCCGA----ACCCGACCCGAATATCACACTTAAAAAAAC
196 GGGTCGGGTATTTTTCACCCTAAACCCAACTCGACCCGACCCGAATATCACACTTAAAAAAAC
* * * * *
55394 CGATCC-GACCCCACCAAAATAAAGTTTCACCCAACCCGACCCGAATATATGGATTAGAAATCCG
1 AGA-CCTGACCCAACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCG
*
55458 ACCCGACCCGAAATAAT-AAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGAAAAAA
65 ACCCGACCCGAAATAATAAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTG-AAAAA
55522 AATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTT
129 AATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTT
* * * *
55587 TCGGGTTGAGTATTTTTCACCCTAAGCCTCAACTCGACCCAACCCGAATATCACACTT-AAAAAA
194 TCGGGTCGGGTATTTTTCACCCTAAACC-CAACTCGACCCGACCCGAATATCACACTTAAAAAAA
55651 C
258 C
*
55652 CGACCTGACCCAACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGA
1 AGACCTGACCCAACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGA
55717 CCCGACCCGAAATAATAAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAA
66 CCCGACCCGAAATAATAAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAA
*
55782 TTATATGTAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTC
131 TTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTC
* *
55847 GGGTCGGGTATTTTTCACCCTAAACCCAAACTCGACCCGACACGAATATCACACTTAAAAAAGC
196 GGGTCGGGTATTTTTCACCCTAAACCC-AACTCGACCCGACCCGAATATCACACTTAAAAAAAC
*
55911 AGACCCGACCCAACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAG--A--C-A
1 AGACCTGACCCAACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGA
55971 CCCGACCCGAAATAAT----AAAATTATTTTTATTCAATAAAAACAGTGACTTAATTG-AAAAAA
66 CCCGACCCGAAATAATAAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAA
*
56031 TTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAATGTAAAATTATATATATTTTC
131 TTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTC
*
56096 GGGTCGGGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACATTTAAAAAAAC
196 GGGTCGGGTATTTTTCACCCTAAACCC-AACTCGACCCGACCCGAATATCACACTTAAAAAAAC
* * * *
56160 TGACCTGACCCGACCAAAATAAAGTTTCTCCCGACCTGACCCGAATATATGAATTAGAAACCCGA
1 AGACCTGACCCAACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGA
56225 CCCGACCCGAAAT-A-AAAAAAAATTATT
66 CCCGACCCGAAATAATAAAAAAAATTATT
56252 CAATATATGA
Statistics
Matches: 794, Mismatches: 41, Indels: 41
0.91 0.05 0.05
Matches are distributed among these distances:
249 181 0.23
250 38 0.05
251 64 0.08
252 55 0.07
253 63 0.08
254 54 0.07
255 3 0.00
256 9 0.01
257 4 0.01
258 201 0.25
259 122 0.15
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (258 bp):
AGACCTGACCCAACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGA
CCCGACCCGAAATAATAAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAA
TTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTC
GGGTCGGGTATTTTTCACCCTAAACCCAACTCGACCCGACCCGAATATCACACTTAAAAAAAC
Found at i:57105 original size:33 final size:33
Alignment explanation
Indices: 57055--57230 Score: 108
Period size: 32 Copynumber: 5.1 Consensus size: 33
57045 CCCTAAACCG
* * *
57055 ACCCAAATATCACACTTAAAAAACTCCGACCCA
1 ACCCGAATATCAAACTTAAAAAAATCCGACCCA
*
57088 ACCCGAATATCAAACTT-AAAAAACCCTGACCCGA
1 ACCCGAATATCAAACTTAAAAAAATCC-GACCC-A
* ** *
57122 CTCTACCC-AA-ACCCGAATTTTTTAAAAAAAATCCGACCCG
1 ----ACCCGAATA-TC-AA--ACTTA-AAAAAATCCGACCCA
* ***
57162 ACCCGAATATCACACTTAAAAAAA-CCGACATG
1 ACCCGAATATCAAACTTAAAAAAATCCGACCCA
57194 ACCCGAATATCAAACTTAAAAAAATCCGACCCGA
1 ACCCGAATATCAAACTTAAAAAAATCCGACCC-A
57228 ACC
1 ACC
57231 TAATTTTTAA
Statistics
Matches: 108, Mismatches: 19, Indels: 31
0.68 0.12 0.20
Matches are distributed among these distances:
32 36 0.33
33 31 0.29
34 7 0.06
36 6 0.06
37 6 0.06
38 7 0.06
40 2 0.02
41 5 0.05
42 8 0.07
ACGTcount: A:0.44, C:0.32, G:0.07, T:0.16
Consensus pattern (33 bp):
ACCCGAATATCAAACTTAAAAAAATCCGACCCA
Found at i:57168 original size:30 final size:30
Alignment explanation
Indices: 57132--57280 Score: 79
Period size: 32 Copynumber: 4.8 Consensus size: 30
57122 CTCTACCCAA
57132 ACCCGAATTTTTTAAAAAAAATCCGACCCG
1 ACCCGAATTTTTTAAAAAAAATCCGACCCG
** **
57162 ACCCGAATATCACACTT-AAAAAAA-CCGACATG
1 ACCCGAAT-T---TTTTAAAAAAAATCCGACCCG
**
57194 ACCCGAATATCAAACTT-AAAAAAATCCGACCCG
1 ACCCGAAT-T---TTTTAAAAAAAATCCGACCCG
* * * * *
57227 AACCTAATTTTTAAAAAAAAATCCGATCTG
1 ACCCGAATTTTTTAAAAAAAATCCGACCCG
* *
57257 ATCCCGAAATTTTAAAAAAAAATC
1 A-CCCGAATTTTTTAAAAAAAATC
57281 TAACTTAAAT
Statistics
Matches: 95, Mismatches: 17, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
29 1 0.01
30 23 0.24
31 20 0.21
32 30 0.32
33 19 0.20
34 2 0.02
ACGTcount: A:0.46, C:0.24, G:0.08, T:0.21
Consensus pattern (30 bp):
ACCCGAATTTTTTAAAAAAAATCCGACCCG
Found at i:57190 original size:32 final size:33
Alignment explanation
Indices: 57146--57227 Score: 130
Period size: 32 Copynumber: 2.5 Consensus size: 33
57136 GAATTTTTTA
*
57146 AAAAAAATCCGACCCGACCCGAATATCACACTT
1 AAAAAAATCCGACCCGACCCGAATATCAAACTT
**
57179 AAAAAAA-CCGACATGACCCGAATATCAAACTT
1 AAAAAAATCCGACCCGACCCGAATATCAAACTT
57211 AAAAAAATCCGACCCGA
1 AAAAAAATCCGACCCGA
57228 ACCTAATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
32 29 0.67
33 14 0.33
ACGTcount: A:0.48, C:0.29, G:0.10, T:0.13
Consensus pattern (33 bp):
AAAAAAATCCGACCCGACCCGAATATCAAACTT
Found at i:58333 original size:22 final size:22
Alignment explanation
Indices: 58305--58352 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
58295 CGATCCGAAA
*
58305 CGCGTTCCAGTTGTTTCAAAAT
1 CGCGTTCCAGTCGTTTCAAAAT
*
58327 CGCGTTCCAGTCGTTTTAAAAT
1 CGCGTTCCAGTCGTTTCAAAAT
58349 CGCG
1 CGCG
58353 ATTCGGTACG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (22 bp):
CGCGTTCCAGTCGTTTCAAAAT
Found at i:60564 original size:5 final size:5
Alignment explanation
Indices: 60556--60586 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
60546 AATGCTCATT
60556 TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC T
1 TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC T
60587 TCTTTTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (5 bp):
TCTTC
Found at i:68871 original size:2 final size:2
Alignment explanation
Indices: 68859--68909 Score: 93
Period size: 2 Copynumber: 25.0 Consensus size: 2
68849 TCTAATAAGC
68859 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
68902 AT AT AT AT
1 AT AT AT AT
68910 CAATGTTAGT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 46 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.