Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000932.1 Hibiscus syriacus cultivar Beakdansim tig00001859_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: 68733
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2625 original size:18 final size:18
Alignment explanation
Indices: 2602--2636 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2592 CGTAGAAATT
*
2602 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
2620 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
2637 GATAATCCCT
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:0.23, C:0.34, G:0.23, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:4771 original size:63 final size:64
Alignment explanation
Indices: 4703--4858 Score: 165
Period size: 63 Copynumber: 2.5 Consensus size: 64
4693 CCTTTAACAT
* *
4703 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTT-TAATATT-AAGGG
1 GTGCATCGATGCACTACCTATGCATCGATACACAAATCACATTCGATGTTTGT-ATATTAAAGGG
* * * * * ** * * *
4766 GTGCATTGATGTACTACTTGTGCATTGATACACTGATGACATTCGATGTTTGTATTTTAAATGG
1 GTGCATCGATGCACTACCTATGCATCGATACACAAATCACATTCGATGTTTGTATATTAAAGGG
4830 GTGCATCGATGCACT-CCTTATGCATCGAT
1 GTGCATCGATGCACTACC-TATGCATCGAT
4859 GCACTATTGG
Statistics
Matches: 73, Mismatches: 17, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
63 46 0.63
64 27 0.37
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (64 bp):
GTGCATCGATGCACTACCTATGCATCGATACACAAATCACATTCGATGTTTGTATATTAAAGGG
Found at i:4873 original size:64 final size:62
Alignment explanation
Indices: 4703--4879 Score: 169
Period size: 64 Copynumber: 2.8 Consensus size: 62
4693 CCTTTAACAT
* * * *
4703 GTGCATCGATGCACTACC-CATGCATCGATACACAAATCACCTTCGATGTTTTAATATTAAGGG
1 GTGCATCGATGCACT-CCTTATGCATCGATACAC-TATGACATTCGATGTTTTAATATTAAGGG
* * * * * * *
4766 GTGCATTGATGTACTACTTGTGCATTGATACACTGATGACATTCGATGTTTGT-ATTTTAAATGG
1 GTGCATCGATGCACTCCTTATGCATCGATACACT-ATGACATTCGATGTTT-TAATATT-AAGGG
* *
4830 GTGCATCGATGCACTCCTTATGCATCGATGCACTATTGGCATTCGATGTT
1 GTGCATCGATGCACTCCTTATGCATCGATACACTA-TGACATTCGATGTT
4880 CAATATTTGA
Statistics
Matches: 91, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
62 1 0.01
63 44 0.48
64 46 0.51
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (62 bp):
GTGCATCGATGCACTCCTTATGCATCGATACACTATGACATTCGATGTTTTAATATTAAGGG
Found at i:6227 original size:20 final size:20
Alignment explanation
Indices: 6202--6252 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
6192 GAAATTTCCA
6202 TGCATCGATGCCTTCCTGTG
1 TGCATCGATGCCTTCCTGTG
6222 TGCATCGATGCCTTCCTGTG
1 TGCATCGATGCCTTCCTGTG
6242 TGCATCGATGC
1 TGCATCGATGC
6253 ACACTGAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.12, C:0.29, G:0.25, T:0.33
Consensus pattern (20 bp):
TGCATCGATGCCTTCCTGTG
Found at i:7268 original size:16 final size:17
Alignment explanation
Indices: 7247--7283 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
7237 ATAGCCTATT
7247 AATATTT-TCTAAAAAA
1 AATATTTATCTAAAAAA
*
7263 AATATTTATCTAAACAA
1 AATATTTATCTAAAAAA
7280 AATA
1 AATA
7284 ATCACATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (17 bp):
AATATTTATCTAAAAAA
Found at i:10850 original size:21 final size:22
Alignment explanation
Indices: 10808--10859 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
10798 AAATATAAAA
10808 TATAATAAA-TAATATTATTTAT
1 TATAA-AAATTAATATTATTTAT
10830 TATAAAAATTAATATTA-TTAT
1 TATAAAAATTAATATTATTTAT
*
10851 TTTAAAAAT
1 TATAAAAAT
10860 ATTAGAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TATAAAAATTAATATTATTTAT
Found at i:11004 original size:23 final size:21
Alignment explanation
Indices: 10978--11025 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
10968 AATATGATAA
10978 ATTATATTGATATCTATAAAAAT
1 ATTATATT-ATAT-TATAAAAAT
* *
11001 ATTATATTATATTTTAAAATT
1 ATTATATTATATTATAAAAAT
11022 ATTA
1 ATTA
11026 ATAAATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
22 4 0.17
23 8 0.35
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
ATTATATTATATTATAAAAAT
Found at i:11018 original size:21 final size:21
Alignment explanation
Indices: 10978--11040 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 21
10968 AATATGATAA
*
10978 ATTATATTGATATCTATAAAAAT
1 ATTATATT-ATAT-TTTAAAAAT
*
11001 ATTATATTATATTTTAAAATT
1 ATTATATTATATTTTAAAAAT
*
11022 ATTAATAAATATATTTTAA
1 ATT-AT-ATTATATTTTAA
11041 GGAATTTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 10 0.29
22 6 0.17
23 19 0.54
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
ATTATATTATATTTTAAAAAT
Found at i:11055 original size:23 final size:22
Alignment explanation
Indices: 10994--11056 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
10984 TTGATATCTA
* *
10994 TAAAAATA-TTATATTATATTT
1 TAAAATTATTTATAATATATTT
*
11015 TAAAATTATTAATAAATATATTT
1 TAAAATTATTTAT-AATATATTT
11038 TAAGGAATT-TTTATAATAT
1 TAA--AATTATTTATAATAT
11057 TATTAGACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.21
22 3 0.09
23 16 0.47
24 4 0.12
25 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (22 bp):
TAAAATTATTTATAATATATTT
Found at i:11213 original size:13 final size:13
Alignment explanation
Indices: 11190--11266 Score: 54
Period size: 13 Copynumber: 6.1 Consensus size: 13
11180 TTAAAATAAA
11190 AATATAATATTAT
1 AATATAATATTAT
* *
11203 TATATATTATTAT
1 AATATAATATTAT
*
11216 AATATAAT-TGAGT
1 AATATAATATTA-T
*
11229 -ATAT--TATTGT
1 AATATAATATTAT
11239 AATAATAATATTAT
1 AAT-ATAATATTAT
* *
11253 TATATTATATTAT
1 AATATAATATTAT
11266 A
1 A
11267 TTATTAAAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 12
0.67 0.16 0.17
Matches are distributed among these distances:
10 2 0.04
11 3 0.06
12 8 0.17
13 27 0.57
14 7 0.15
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (13 bp):
AATATAATATTAT
Found at i:11235 original size:23 final size:21
Alignment explanation
Indices: 11192--11272 Score: 73
Period size: 21 Copynumber: 4.0 Consensus size: 21
11182 AAAATAAAAA
*
11192 TATAATATTATTATATATTAT
1 TATAATATAATTATATATTAT
11213 TATAATATAATTGAGTATATTAT
1 TATAATATAATT-A-TATATTAT
*
11236 TGT-A-ATAA-TA-ATATTAT
1 TATAATATAATTATATATTAT
*
11253 TATATTAT-ATTATATTATTA
1 TATAATATAATTATA-TATTA
11273 AAAATATTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
17 9 0.18
18 1 0.02
19 5 0.10
20 2 0.04
21 20 0.41
22 2 0.04
23 10 0.20
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (21 bp):
TATAATATAATTATATATTAT
Found at i:11299 original size:11 final size:12
Alignment explanation
Indices: 11189--11304 Score: 64
Period size: 12 Copynumber: 9.8 Consensus size: 12
11179 ATTAAAATAA
*
11189 AAATATAATATT
1 AAATATATTATT
*
11201 ATTATATATTATT
1 A-AATATATTATT
11214 ATAATATA--ATT
1 A-AATATATTATT
* *
11225 GAGTATATTATT
1 AAATATATTATT
* *
11237 GTAATAATAATATT
1 -AAAT-ATATTATT
*
11251 -ATTATATTA-T
1 AAATATATTATT
*
11261 -ATTATATTATT
1 AAATATATTATT
* *
11272 AAAAATATTAAT
1 AAATATATTATT
11284 AAATATATT-TT
1 AAATATATTATT
11295 AAATATATTA
1 AAATATATTA
11305 ATAATTAATA
Statistics
Matches: 81, Mismatches: 15, Indels: 16
0.72 0.13 0.14
Matches are distributed among these distances:
10 15 0.19
11 19 0.23
12 22 0.27
13 18 0.22
14 7 0.09
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (12 bp):
AAATATATTATT
Found at i:11302 original size:23 final size:23
Alignment explanation
Indices: 11263--11319 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
11253 TATATTATAT
11263 TATATTATTAAAAATATTAATAAA
1 TATATT-TTAAAAATATTAATAAA
* *
11287 TATATTTTAAATATATTAATAAT
1 TATATTTTAAAAATATTAATAAA
11310 TAATATTTTA
1 T-ATATTTTA
11320 TTAAAATGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 16 0.53
24 14 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATAAA
Found at i:11954 original size:15 final size:16
Alignment explanation
Indices: 11919--11957 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
11909 AATCGGATAT
*
11919 CGGGTACCTGGTAATC
1 CGGGTACCTGATAATC
*
11935 CGGGTACCTGATTA-C
1 CGGGTACCTGATAATC
11950 CGGGTACC
1 CGGGTACC
11958 CGTAACATCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.18, C:0.28, G:0.31, T:0.23
Consensus pattern (16 bp):
CGGGTACCTGATAATC
Found at i:12039 original size:15 final size:16
Alignment explanation
Indices: 12007--12049 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
11997 ACCCGGAAGT
**
12007 TCCGGGTACCCGGGAA
1 TCCGGGTACCCGAAAA
12023 T-CGGGTACCCGAAAA
1 TCCGGGTACCCGAAAA
*
12038 TCCAGGTACCCG
1 TCCGGGTACCCG
12050 GATTTGCACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.23, C:0.33, G:0.30, T:0.14
Consensus pattern (16 bp):
TCCGGGTACCCGAAAA
Found at i:13197 original size:15 final size:16
Alignment explanation
Indices: 13170--13206 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
13160 TTAATTTTTA
13170 ATTAAAAATTTAAT-T
1 ATTAAAAATTTAATAT
13185 ATTAATAAA-TTAATAT
1 ATTAA-AAATTTAATAT
13201 ATTAAA
1 ATTAAA
13207 TTAAGGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATTAAAAATTTAATAT
Found at i:13282 original size:28 final size:28
Alignment explanation
Indices: 13229--13284 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
13219 TTATTCAAAT
**
13229 TTAGATTTAAACTTAATAGTGATAATAA
1 TTAGATTTAAACTTAATAAAGATAATAA
* *
13257 TTAGATTTAAATTTAATAAAGTTAATAA
1 TTAGATTTAAACTTAATAAAGATAATAA
13285 ATATTTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (28 bp):
TTAGATTTAAACTTAATAAAGATAATAA
Found at i:21136 original size:22 final size:22
Alignment explanation
Indices: 21105--21179 Score: 89
Period size: 22 Copynumber: 3.5 Consensus size: 22
21095 AACAACTATA
*
21105 AAATATTTAAATATTTATTATT
1 AAATAATTAAATATTTATTATT
* * * *
21127 AAATAATTAAAAATCT-CTATA
1 AAATAATTAAATATTTATTATT
*
21148 AAATATTTAAATATTTATTATT
1 AAATAATTAAATATTTATTATT
21170 AAATAATTAA
1 AAATAATTAA
21180 TAATCTTTAA
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
21 16 0.39
22 25 0.61
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (22 bp):
AAATAATTAAATATTTATTATT
Found at i:21147 original size:43 final size:43
Alignment explanation
Indices: 21100--21193 Score: 165
Period size: 43 Copynumber: 2.2 Consensus size: 43
21090 ACATTAACAA
21100 CTATAAAATATTTAAATATTTATTATTAAATAATTAAAAATCT
1 CTATAAAATATTTAAATATTTATTATTAAATAATTAAAAATCT
*
21143 CTATAAAATATTTAAATATTTATTATTAAATAATTAATAATCT
1 CTATAAAATATTTAAATATTTATTATTAAATAATTAAAAATCT
21186 -T-TAAAATA
1 CTATAAAATA
21194 GATAATACCC
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
41 7 0.14
42 1 0.02
43 42 0.84
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (43 bp):
CTATAAAATATTTAAATATTTATTATTAAATAATTAAAAATCT
Found at i:27240 original size:24 final size:23
Alignment explanation
Indices: 27188--27243 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
27178 AATAAGAATA
27188 TGTTCTTGTGACACATTTTTTCC
1 TGTTCTTGTGACACATTTTTTCC
* * *
27211 TATTCTTGTGAGA-AGTTTTTTCTT
1 TGTTCTTGTGACACA-TTTTTTC-C
27235 TGTTCTTGT
1 TGTTCTTGT
27244 AGTACGTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 1 0.04
23 18 0.67
24 8 0.30
ACGTcount: A:0.12, C:0.14, G:0.16, T:0.57
Consensus pattern (23 bp):
TGTTCTTGTGACACATTTTTTCC
Found at i:28562 original size:15 final size:15
Alignment explanation
Indices: 28542--28623 Score: 121
Period size: 15 Copynumber: 5.5 Consensus size: 15
28532 TTCCAGAAAA
28542 TGAATTACTGGAATT
1 TGAATTACTGGAATT
28557 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
28572 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
28587 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
28602 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
28616 TGAATTAC
1 TGAATTAC
28624 ATTTCTGTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 12 0.20
15 48 0.80
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:28576 original size:30 final size:30
Alignment explanation
Indices: 28542--28623 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
28532 TTCCAGAAAA
**
28542 TGAATTACTGGAATTTGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
28572 TGAATTACTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
28602 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
28624 ATTTCTGTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGGAATT
Found at i:28588 original size:45 final size:44
Alignment explanation
Indices: 28537--28623 Score: 147
Period size: 45 Copynumber: 2.0 Consensus size: 44
28527 TGGTTTTCCA
**
28537 GAAAATGAATTACTGGAATTTGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTGGAATTTGAATT-CTGGAAAATGAATTACTG
28582 GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
1 GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
28624 ATTTCTGTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (44 bp):
GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACTG
Found at i:28629 original size:20 final size:20
Alignment explanation
Indices: 28606--28675 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
28596 GGAATTTGAA
28606 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
28626 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
28646 TTCTGAAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
28666 TTCTGGAAAA
1 TTCTGGAAAA
28676 CATCTGGAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:28900 original size:22 final size:25
Alignment explanation
Indices: 28872--28920 Score: 68
Period size: 22 Copynumber: 2.1 Consensus size: 25
28862 AATATTATTC
28872 ATTATTAAATA-TA-TAAAA-AAAA
1 ATTATTAAATATTATTAAAATAAAA
*
28894 ATTATTATATATTATTAAAATAAAA
1 ATTATTAAATATTATTAAAATAAAA
28919 AT
1 AT
28921 ATAATATCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 10 0.43
23 2 0.09
24 5 0.22
25 6 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
ATTATTAAATATTATTAAAATAAAA
Found at i:28916 original size:29 final size:28
Alignment explanation
Indices: 28841--28944 Score: 86
Period size: 29 Copynumber: 3.5 Consensus size: 28
28831 CTTTACTAAA
* *
28841 ATATTATTGAAATATATAAATAATATTAT
1 ATATTATTAAAATA-AAAAATAATATTAT
*
28870 -TCATTATTAAATATATAAAAAAAAATTATTAT
1 AT-ATTATT-AA-A-ATAAAAAATAA-TATTAT
28902 ATATTATTAAAATAAAAATATAATATCT-T
1 ATATTATTAAAATAAAAA-ATAATAT-TAT
*
28931 ATATTATTATAATA
1 ATATTATTAAAATA
28945 TAATTGATTA
Statistics
Matches: 62, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
28 1 0.02
29 30 0.48
30 6 0.10
31 9 0.15
32 15 0.24
33 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (28 bp):
ATATTATTAAAATAAAAAATAATATTAT
Found at i:28927 original size:24 final size:24
Alignment explanation
Indices: 28885--28932 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
28875 ATTAAATATA
*
28885 TAAAAAAAAATTATTATATATTAT
1 TAAAAAAAAATTATAATATATTAT
*
28909 TAAAATAAAAA-TATAATATCTTAT
1 TAAAA-AAAAATTATAATATATTAT
28933 ATTATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
TAAAAAAAAATTATAATATATTAT
Found at i:28939 original size:32 final size:33
Alignment explanation
Indices: 28867--28940 Score: 82
Period size: 32 Copynumber: 2.3 Consensus size: 33
28857 TAAATAATAT
28867 TATTCATTATTAAATATATAAAAAAAAATTATTA
1 TATT-ATTATTAAATATATAAAAAAAAATTATTA
* * *
28901 TA-TATTATTAAA-ATA-AAAATATAATATCTTA
1 TATTATTATTAAATATATAAAAAAAAAT-TATTA
28932 TATTATTAT
1 TATTATTAT
28941 AATATAATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
30 8 0.23
31 9 0.26
32 15 0.43
33 1 0.03
34 2 0.06
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (33 bp):
TATTATTATTAAATATATAAAAAAAAATTATTA
Found at i:28985 original size:22 final size:23
Alignment explanation
Indices: 28960--29003 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
28950 GATTATTTTA
28960 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
28982 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
29004 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:29008 original size:22 final size:22
Alignment explanation
Indices: 28964--29020 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
28954 ATTTTATATA
* *
28964 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATATAAT
28985 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
29007 ATATTTTAAATATT
1 ATATTATAAATATT
29021 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:29019 original size:52 final size:51
Alignment explanation
Indices: 28900--29020 Score: 133
Period size: 54 Copynumber: 2.3 Consensus size: 51
28890 AAAAATTATT
**
28900 ATATATTATTAAA-A-TAAAAATATAATATCTTATATTATTATAATATAATTG
1 ATATATT-TTAAATATTAAAAATATAATA-CTTATATTATTATAATATAATAA
28951 AT-TATTTTATATAATATTAAAAATATAATA-TTATATTATTATAAATATTAATAA
1 ATATA-TTT-TA-AATATTAAAAATATAATACTTATATTATTAT-AATA-TAATAA
29005 ATATATTTTAAATATT
1 ATATATTTTAAATATT
29021 TTAATAATTA
Statistics
Matches: 60, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 20 0.33
53 7 0.12
54 22 0.37
55 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (51 bp):
ATATATTTTAAATATTAAAAATATAATACTTATATTATTATAATATAATAA
Found at i:29268 original size:42 final size:42
Alignment explanation
Indices: 29209--29324 Score: 214
Period size: 42 Copynumber: 2.8 Consensus size: 42
29199 ATGAATTACA
*
29209 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
29251 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAATATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
29293 TTCCGGAAAACGAATTACGTGAAACAAACACG
1 TTCCGGAAAACGAATTACGTGAAACAAACACG
29325 TGAATTCGGG
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.44, C:0.19, G:0.20, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:31061 original size:13 final size:13
Alignment explanation
Indices: 31045--31120 Score: 54
Period size: 12 Copynumber: 6.1 Consensus size: 13
31035 AAATCAATGA
31045 AAAAAATAAAAAT
1 AAAAAATAAAAAT
*
31058 AAAAAAT-AAAAC
1 AAAAAATAAAAAT
**
31070 AAATGATAAAAAT
1 AAAAAATAAAAAT
* *
31083 AAGAAAT-AAATT
1 AAAAAATAAAAAT
31095 AAAGGAAA-AAAAAT
1 AAA--AAATAAAAAT
31109 --AAAATAAAAAT
1 AAAAAATAAAAAT
31120 A
1 A
31121 TAAAGCAAAC
Statistics
Matches: 47, Mismatches: 10, Indels: 13
0.67 0.14 0.19
Matches are distributed among these distances:
10 3 0.06
11 6 0.13
12 16 0.34
13 15 0.32
14 7 0.15
ACGTcount: A:0.78, C:0.01, G:0.05, T:0.16
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:31081 original size:25 final size:25
Alignment explanation
Indices: 31050--31117 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
31040 AATGAAAAAA
*
31050 ATAAAAATAAAAAATAAAACAAATG
1 ATAAAAATAAAAAATAAAACAAAGG
* **
31075 ATAAAAATAAGAAATAAATTAAAGG
1 ATAAAAATAAAAAATAAAACAAAGG
31100 A-AAAAA-AATAAAATAAAA
1 ATAAAAATAA-AAAATAAAA
31118 ATATAAAGCA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
23 2 0.06
24 12 0.33
25 22 0.61
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.16
Consensus pattern (25 bp):
ATAAAAATAAAAAATAAAACAAAGG
Found at i:31081 original size:31 final size:31
Alignment explanation
Indices: 31019--31092 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
31009 AAAATGTTAG
** *
31019 ATAAGAAATATTAAATAAATCAATGAAAAAA
1 ATAAGAAATAAAAAATAAAACAATGAAAAAA
*
31050 ATAA-AAATAAAAAATAAAACAAATGATAAAA
1 ATAAGAAATAAAAAATAAAAC-AATGAAAAAA
31081 ATAAGAAATAAA
1 ATAAGAAATAAA
31093 TTAAAGGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 13 0.35
31 17 0.46
32 7 0.19
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (31 bp):
ATAAGAAATAAAAAATAAAACAATGAAAAAA
Found at i:36377 original size:17 final size:17
Alignment explanation
Indices: 36355--36389 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
36345 AACCGAGTAC
36355 GGTAGAGGAGTCGAGGG
1 GGTAGAGGAGTCGAGGG
36372 GGTAGAGGAGTCGAGGG
1 GGTAGAGGAGTCGAGGG
36389 G
1 G
36390 CGATGGCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.60, T:0.11
Consensus pattern (17 bp):
GGTAGAGGAGTCGAGGG
Found at i:36810 original size:3 final size:3
Alignment explanation
Indices: 36793--36840 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
36783 AAAATAAAAA
* *
36793 AAT ATT AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
36840 A
1 A
36841 TATATATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:37251 original size:31 final size:31
Alignment explanation
Indices: 37216--37323 Score: 164
Period size: 33 Copynumber: 3.5 Consensus size: 31
37206 AGATAAAATT
*
37216 TGTTTCAAGAGAAACAATCTCAAAGGTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTG
* *
37247 TGTTTCAAGAGAAACATTTTCAAAGATTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAG--GTTTTG
37280 TGTTTCAAGAGAAACAATTTCAAAGG-TTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTG
37310 TGTTTCAAGAGAAA
1 TGTTTCAAGAGAAA
37324 TTGTCTTAGG
Statistics
Matches: 70, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
30 18 0.26
31 23 0.33
33 29 0.41
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (31 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTTTG
Found at i:37256 original size:67 final size:67
Alignment explanation
Indices: 37052--37617 Score: 260
Period size: 67 Copynumber: 8.6 Consensus size: 67
37042 CAGATGGTGC
** * ** * * * *
37052 TTCAAGAGAAGTTGTCTCAAAAGAGACAAAATTCATTTAAAGGGAAACGATCTCAAAGATATTTG
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGT-TTTG
37117 TTGT
65 -TGT
* * * * ** * *
37121 TTCATGAGAAACGGTCTCAAGGGAAACAAAATTT-TATT--TTA-ATA-AAT-TCAAAGATTTTG
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT-TTCAAGAGAAACAATCTCAAAGGTTTTG
37180 TGT
65 TGT
*
37183 TTCAAGAGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTTGT
37248 GT
66 GT
* **** *
37250 TTCAAGAGAAACAT-TTTC-A-A-AGA-TTTTTTGTGTTTCAAGAGAAACAATTTCAAAGG-TTT
1 TTCAAGAGAAAC-TGTCTCAAGAGAGACAAAATT-TGTTTCAAGAGAAACAATCTCAAAGGTTTT
37309 GTGT
64 GTGT
* * * * ** * *
37313 TTCAAGAGAAATTGTCTTAGGGGAGGTAAAATTTTGTTTCAAGAGAAAC-ATGTTCAAA-G-ATT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACAAT-CTCAAAGGTTTT
37375 GATGT
64 G-TGT
* * * ***
37380 TTCAAGAGAAACTGTCTCAAGAGAGACAACACTTTGTTTTAAGGGAAATTGTCTCAAGAGAGACA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAA-AATTTGTTTCAAGAGAAACAATCTCAA-AG-G---
**
37445 AAATT-TGT
60 -TTTTGTGT
* * *
37453 TTCAAGAGAAATTGTCT---TA-AG---AAA---G--ACAAGAGAAACAATCTCAAAGGTTTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTTGT
37506 GT
66 GT
* ****** *
37508 TTCAAGAGAAACATTTC-CAA-AGA-TTTTTTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTT
1 TTCAAGAGAAAC-TGTCTCAAGAGAGACAAAATT-TGTTTCAAGAGAAACAATCTCAAAGG----
37570 TTTTGTGT
60 TTTTGTGT
37578 TTCAAGAGAAACTGTCTCAAGAGA-ACAAAATTTGTTTCAA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAA
37618 AGGAAACTGC
Statistics
Matches: 373, Mismatches: 76, Indels: 95
0.69 0.14 0.17
Matches are distributed among these distances:
54 2 0.01
55 14 0.04
56 3 0.01
57 1 0.00
58 2 0.01
59 2 0.01
60 13 0.03
62 36 0.10
63 27 0.07
64 38 0.10
65 6 0.02
66 35 0.09
67 94 0.25
68 7 0.02
69 33 0.09
70 33 0.09
71 5 0.01
73 19 0.05
75 3 0.01
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.33
Consensus pattern (67 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTTGT
GT
Found at i:37480 original size:36 final size:37
Alignment explanation
Indices: 37377--37481 Score: 149
Period size: 36 Copynumber: 2.9 Consensus size: 37
37367 CAAAGATTGA
* *
37377 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAACACTT
1 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAACAATT
* *
37414 TGTTTTAAGGGAAATTGTCTCAAGAGAGACAA-AATT
1 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAACAATT
* *
37450 TGTTTCAAGAGAAATTGTCTTAAGAAAGACAA
1 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAA
37482 GAGAAACAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
36 31 0.52
37 29 0.48
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (37 bp):
TGTTTCAAGAGAAATTGTCTCAAGAGAGACAACAATT
Found at i:37546 original size:35 final size:35
Alignment explanation
Indices: 37500--37589 Score: 155
Period size: 35 Copynumber: 2.6 Consensus size: 35
37490 ATCTCAAAGG
37500 TTTTGTGTTTCAAGAGAAAC-ATTTCCAAAGATTTT
1 TTTTGTGTTTCAAGAGAAACAATTT-CAAAGATTTT
*
37535 TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTT
1 TTTTGTGTTTCAAGAGAAACAATTTCAAAGATTTT
37570 TTTTGTGTTTCAAGAGAAAC
1 TTTTGTGTTTCAAGAGAAAC
37590 TGTCTCAAGA
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
35 49 0.92
36 4 0.08
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (35 bp):
TTTTGTGTTTCAAGAGAAACAATTTCAAAGATTTT
Found at i:37614 original size:35 final size:37
Alignment explanation
Indices: 37575--37654 Score: 121
Period size: 35 Copynumber: 2.2 Consensus size: 37
37565 GTTTTTTTTG
*
37575 TGTTTCAAGA-GAAACTGTCTCAAGAGA-ACAAAATT
1 TGTTTCAAGAGGAAACTGCCTCAAGAGAGACAAAATT
*
37610 TGTTTCAA-AGGAAACTGCCTTAAGAGAGACAAAATT
1 TGTTTCAAGAGGAAACTGCCTCAAGAGAGACAAAATT
37646 TGTTTCAAG
1 TGTTTCAAG
37655 TAAATTAGTC
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
34 1 0.03
35 23 0.57
36 16 0.40
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.28
Consensus pattern (37 bp):
TGTTTCAAGAGGAAACTGCCTCAAGAGAGACAAAATT
Found at i:37675 original size:36 final size:36
Alignment explanation
Indices: 37575--37675 Score: 118
Period size: 35 Copynumber: 2.8 Consensus size: 36
37565 GTTTTTTTTG
37575 TGTTTC-AAGAGAAACTGTCTCAAGAGA-ACAAAATT
1 TGTTTCAAAG-GAAACTGTCTCAAGAGAGACAAAATT
* *
37610 TGTTTCAAAGGAAACTGCCTTAAGAGAGACAAAATT
1 TGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATT
* * *
37646 TGTTTC-AAGTAAATTAGTCTCAAGCGAGAC
1 TGTTTCAAAGGAAACT-GTCTCAAGAGAGAC
37676 GACCCCTTGT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
35 28 0.50
36 28 0.50
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.27
Consensus pattern (36 bp):
TGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:39350 original size:10 final size:9
Alignment explanation
Indices: 39334--39400 Score: 55
Period size: 9 Copynumber: 7.0 Consensus size: 9
39324 TCTTGTTTTC
39334 TTTTTTCTT
1 TTTTTTCTT
39343 TATTTTTCCTGT
1 T-TTTTT-CT-T
*
39355 GTTTTTGCTT
1 -TTTTTTCTT
*
39365 TTTTTT-TC
1 TTTTTTCTT
39373 TTTTTTCTT
1 TTTTTTCTT
*
39382 TGTTTTTCTC
1 T-TTTTTCTT
39392 TTTTTTCTT
1 TTTTTTCTT
39401 CTCTTTTTGT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
8 7 0.15
9 15 0.33
10 14 0.30
11 4 0.09
12 5 0.11
13 1 0.02
ACGTcount: A:0.01, C:0.13, G:0.06, T:0.79
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:39365 original size:29 final size:28
Alignment explanation
Indices: 39329--39396 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
39319 ACGCGTCTTG
39329 TTTTCTTTTTTCTTTATTTTTCCTGTGT
1 TTTTCTTTTTTCTTTATTTTTCCTGTGT
* * *
39357 TTTTGCTTTTTT-TTTCTTTTTTCTTTGT
1 TTTT-CTTTTTTCTTTATTTTTCCTGTGT
39385 TTTTCTCTTTTT
1 TTTTCT-TTTTT
39397 TCTTCTCTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 2 0.06
28 26 0.74
29 7 0.20
ACGTcount: A:0.01, C:0.13, G:0.06, T:0.79
Consensus pattern (28 bp):
TTTTCTTTTTTCTTTATTTTTCCTGTGT
Found at i:39370 original size:11 final size:10
Alignment explanation
Indices: 39334--39414 Score: 56
Period size: 10 Copynumber: 7.9 Consensus size: 10
39324 TCTTGTTTTC
39334 TTTTTTCTTT
1 TTTTTTCTTT
* *
39344 ATTTTTCCTGTG
1 -TTTTTTCT-TT
*
39356 TTTTTGCTTT
1 TTTTTTCTTT
39366 TTTTTTCTTT
1 TTTTTTCTTT
* *
39376 TTTCTT-TGT
1 TTTTTTCTTT
*
39385 TTTTCTCTTT
1 TTTTTTCTTT
*
39395 TTTCTTCTCTT
1 TTTTTTCT-TT
*
39406 TTTGTTCTT
1 TTTTTTCTT
39415 GATTGGATCT
Statistics
Matches: 54, Mismatches: 13, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
9 6 0.11
10 24 0.44
11 23 0.43
12 1 0.02
ACGTcount: A:0.01, C:0.15, G:0.06, T:0.78
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:39376 original size:17 final size:19
Alignment explanation
Indices: 39356--39396 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
39346 TTTTCCTGTG
39356 TTTTTGCTTT-TTTTT-TC
1 TTTTTGCTTTGTTTTTCTC
*
39373 TTTTTTCTTTGTTTTTCTC
1 TTTTTGCTTTGTTTTTCTC
39392 TTTTT
1 TTTTT
39397 TCTTCTCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.43
18 5 0.24
19 7 0.33
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.83
Consensus pattern (19 bp):
TTTTTGCTTTGTTTTTCTC
Found at i:39397 original size:29 final size:28
Alignment explanation
Indices: 39329--39408 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 28
39319 ACGCGTCTTG
* *
39329 TTTTCTTTTTTCTTTATTTTTCCTGTGTT
1 TTTTCTTTTTT-TTTCTTTTTTCTGTGTT
* *
39358 TTTGCTTTTTTTTTCTTTTTTCTTTGTT
1 TTTTCTTTTTTTTTCTTTTTTCTGTGTT
*
39386 TTTCTCTTTTTTCTTCTCTTTTT
1 TTT-TCTTTTTTTTTCT-TTTTT
39409 GTTCTTGATT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
28 17 0.40
29 21 0.49
30 5 0.12
ACGTcount: A:0.01, C:0.15, G:0.05, T:0.79
Consensus pattern (28 bp):
TTTTCTTTTTTTTTCTTTTTTCTGTGTT
Found at i:39408 original size:39 final size:39
Alignment explanation
Indices: 39324--39414 Score: 105
Period size: 39 Copynumber: 2.3 Consensus size: 39
39314 TGCATACGCG
*
39324 TCTTGTTTTCTTTTTTCTTTATTTTTCCTGTGTTTTTGC
1 TCTTTTTTTCTTTTTTCTTTATTTTTCCTGTGTTTTTGC
* * *
39363 TTTTTTTTTCTTTTTTCTTTGTTTTTCTCT-T-TTTTCTTC
1 TCTTTTTTTCTTTTTTCTTTATTTTTC-CTGTGTTTT-TGC
39402 TCTTTTTGTTCTT
1 TCTTTTT-TTCTT
39415 GATTGGATCT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
38 4 0.09
39 33 0.75
40 7 0.16
ACGTcount: A:0.01, C:0.15, G:0.07, T:0.77
Consensus pattern (39 bp):
TCTTTTTTTCTTTTTTCTTTATTTTTCCTGTGTTTTTGC
Found at i:40542 original size:64 final size:64
Alignment explanation
Indices: 40432--40569 Score: 179
Period size: 64 Copynumber: 2.2 Consensus size: 64
40422 TTCAGTGTGT
* * *
40432 ATCGATGCACCCCTTAAAAATGGAAACATCGAATGCAATTGGTGTATCGATGCATAAGG-AGTGC
1 ATCGATGCATCCCTTAAAAATGAAAACATCGAAGGCAATTGGTGTATCGATGCAT-AGGTAGTGC
* * * ** *
40496 ATCGATGCATCCCTTTAAGATGAAAACATCGAAGGTAATTTTTGTATCGATGCATGGGTAGTGC
1 ATCGATGCATCCCTTAAAAATGAAAACATCGAAGGCAATTGGTGTATCGATGCATAGGTAGTGC
40560 ATCGATGCAT
1 ATCGATGCAT
40570 ATGTTAAAGA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
63 2 0.03
64 62 0.97
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (64 bp):
ATCGATGCATCCCTTAAAAATGAAAACATCGAAGGCAATTGGTGTATCGATGCATAGGTAGTGC
Found at i:40610 original size:20 final size:20
Alignment explanation
Indices: 40577--40614 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40567 CATATGTTAA
*
40577 AGAATACATTGATGCACTGT
1 AGAATACATCGATGCACTGT
*
40597 AGAATGCATCGATGCACT
1 AGAATACATCGATGCACT
40615 TAAAGGGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
AGAATACATCGATGCACTGT
Found at i:41730 original size:23 final size:23
Alignment explanation
Indices: 41698--41758 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
41688 TCTTATATGA
*
41698 CACTTCGGTGTATTTCTACGCGG
1 CACTTCGGTGCATTTCTACGCGG
* * *
41721 CACTTAGGTGCAATTCTACGTGG
1 CACTTCGGTGCATTTCTACGCGG
41744 CACTTCGGTGCATTT
1 CACTTCGGTGCATTT
41759 ATATGAGCTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.16, C:0.25, G:0.25, T:0.34
Consensus pattern (23 bp):
CACTTCGGTGCATTTCTACGCGG
Found at i:42113 original size:2 final size:2
Alignment explanation
Indices: 42106--42150 Score: 63
Period size: 2 Copynumber: 22.0 Consensus size: 2
42096 TTGTGAAACA
* *
42106 AT AT AT AT GT AC AT GAT 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
42149 AT
1 AT
42151 GTTTGGATGC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:45137 original size:20 final size:22
Alignment explanation
Indices: 45092--45149 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
45082 GCATGGGTTG
45092 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
45116 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
45136 TGCATCGATGCACT
1 TGCATCGATGCACT
45150 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:46221 original size:45 final size:45
Alignment explanation
Indices: 46170--46268 Score: 114
Period size: 46 Copynumber: 2.2 Consensus size: 45
46160 CTTACGGAAT
*
46170 TTTCTACGTGGTC-CTTAGG-GACATATTTTA-TGGCACTTCAGTGCA
1 TTTCTACGTGG-CACTTAGGTG-CA-ATTCTACTGGCACTTCAGTGCA
*
46215 TTTCTACGTGGCACTTAGGTGCAATTCTACTTGGCACTTCGGTGCA
1 TTTCTACGTGGCACTTAGGTGCAATTCTAC-TGGCACTTCAGTGCA
*
46261 TTTATACG
1 TTTCTACG
46269 AGCTGTGGTG
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
44 6 0.13
45 19 0.40
46 22 0.47
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.37
Consensus pattern (45 bp):
TTTCTACGTGGCACTTAGGTGCAATTCTACTGGCACTTCAGTGCA
Found at i:46226 original size:23 final size:23
Alignment explanation
Indices: 46200--46268 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
46190 ACATATTTTA
46200 TGGCACTTCAGTGCATTTCTACG
1 TGGCACTTCAGTGCATTTCTACG
* *
46223 TGGCACTT-AGGTGCAATTCTACT
1 TGGCACTTCA-GTGCATTTCTACG
* *
46246 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCAGTGCATTTCTACG
46269 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
22 1 0.03
23 37 0.97
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (23 bp):
TGGCACTTCAGTGCATTTCTACG
Found at i:46627 original size:2 final size:2
Alignment explanation
Indices: 46620--46684 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
46610 AATATGTATG
46620 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
46662 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
46685 GTTTGGATGC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:49852 original size:30 final size:32
Alignment explanation
Indices: 49794--49870 Score: 104
Period size: 31 Copynumber: 2.4 Consensus size: 32
49784 AAGAAATATT
*
49794 AAATAAATATTAAATCATCAATGAAAAAAATAA
1 AAATAAAAATTAAATCA-CAATGAAAAAAATAA
*
49827 AAATAAAAAATAAATCA-AATGAAAAAAATAA
1 AAATAAAAATTAAATCACAATGAAAAAAATAA
*
49858 GAA-AAAAATTAAA
1 AAATAAAAATTAAA
49871 GGAAAAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
30 9 0.22
31 16 0.40
33 15 0.38
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.19
Consensus pattern (32 bp):
AAATAAAAATTAAATCACAATGAAAAAAATAA
Found at i:49854 original size:18 final size:16
Alignment explanation
Indices: 49813--49862 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 16
49803 TTAAATCATC
49813 AATGAAAAAAAT-AAA
1 AATGAAAAAAATAAAA
49828 AAT--AAAAAATAAATCA
1 AATGAAAAAAATAAA--A
49844 AATGAAAAAAATAAGAA
1 AATGAAAAAAATAA-AA
49861 AA
1 AA
49863 AAATTAAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 7 0.24
14 2 0.07
15 3 0.10
16 4 0.14
17 3 0.10
18 9 0.31
19 1 0.03
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (16 bp):
AATGAAAAAAATAAAA
Found at i:49855 original size:14 final size:14
Alignment explanation
Indices: 49813--49890 Score: 65
Period size: 14 Copynumber: 5.6 Consensus size: 14
49803 TTAAATCATC
*
49813 AATGAAAAAAATAAA
1 AATGAAAAAAAT-TA
* *
49828 AATAAAAAATAAATCA
1 AAT-GAAAA-AAATTA
49844 AATGAAAAAAA-T-
1 AATGAAAAAAATTA
49856 AA-GAAAAAAATTA
1 AATGAAAAAAATTA
*
49869 AAGGAAAAAAATTA
1 AATGAAAAAAATTA
49883 AAT-AAAAA
1 AATGAAAAA
49891 TATAAAGCAA
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
11 8 0.15
12 3 0.06
13 7 0.13
14 16 0.30
15 7 0.13
16 8 0.15
17 4 0.08
ACGTcount: A:0.77, C:0.01, G:0.06, T:0.15
Consensus pattern (14 bp):
AATGAAAAAAATTA
Found at i:49889 original size:25 final size:24
Alignment explanation
Indices: 49825--49897 Score: 83
Period size: 25 Copynumber: 2.9 Consensus size: 24
49815 TGAAAAAAAT
* *
49825 AAAAATAAAAAATAAATCAAATGAA
1 AAAAATAAAAAA-AAATTAAAGGAA
49850 AAAAATAAGAAAAAAATTAAAGGAA
1 AAAAATAA-AAAAAAATTAAAGGAA
*
49875 AAAAATTAAATAAAAATATAAAG
1 AAAAA-TAAAAAAAAAT-TAAAG
49898 CAAACGTATG
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
25 30 0.71
26 12 0.29
ACGTcount: A:0.75, C:0.01, G:0.07, T:0.16
Consensus pattern (24 bp):
AAAAATAAAAAAAAATTAAAGGAA
Found at i:50848 original size:3 final size:3
Alignment explanation
Indices: 50835--50883 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
50825 TGTCTGCAAA
50835 AAT AGAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT -AT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
50879 -AT AAT
1 AAT AAT
50884 TTTTCTGTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
2 6 0.14
3 33 0.79
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:51098 original size:19 final size:18
Alignment explanation
Indices: 51063--51126 Score: 51
Period size: 18 Copynumber: 3.5 Consensus size: 18
51053 CTTCTGATTA
51063 AAAAATTAATATATTTTT
1 AAAAATTAATATATTTTT
* * *
51081 AAAAATTCATGATCTTTTA
1 AAAAATTAAT-ATATTTTT
*
51100 AGAAAAGTTAAGA-A-TTTT
1 A-AAAA-TTAATATATTTTT
51118 AAAAATTAA
1 AAAAATTAA
51127 ATTAGTGAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
16 4 0.11
17 4 0.11
18 13 0.36
19 7 0.19
20 5 0.14
21 3 0.08
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (18 bp):
AAAAATTAATATATTTTT
Found at i:53883 original size:36 final size:36
Alignment explanation
Indices: 53837--54014 Score: 279
Period size: 36 Copynumber: 5.0 Consensus size: 36
53827 GTGCGATACA
* *
53837 TCCTTCCGTTCAACTTGAATCGGAAGTGCTGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
53873 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
* * *
53909 TCCCTCCGTTCGACTTGAATCGGGAGTGCCGACGCTT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGC-T
*
53946 TCC-TCCGTTCGACTTGAATCGGAAGTGTCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
53981 TCCTTCCGTTCGACTTGAATCGGAAGTG-CGATGC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGC
54015 ATTCTTTCGT
Statistics
Matches: 132, Mismatches: 8, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
35 10 0.08
36 118 0.89
37 4 0.03
ACGTcount: A:0.17, C:0.28, G:0.25, T:0.30
Consensus pattern (36 bp):
TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
Found at i:60224 original size:19 final size:19
Alignment explanation
Indices: 60183--60226 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
60173 AAACAAAGAT
* * *
60183 ATCAGAAATCAGAGCAGAG
1 ATCAGAAATCAGAACAAAA
*
60202 ATCAGAAATCATAACAAAA
1 ATCAGAAATCAGAACAAAA
60221 ATCAGA
1 ATCAGA
60227 GAAAACTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.55, C:0.16, G:0.16, T:0.14
Consensus pattern (19 bp):
ATCAGAAATCAGAACAAAA
Found at i:62757 original size:32 final size:32
Alignment explanation
Indices: 62711--62827 Score: 166
Period size: 32 Copynumber: 3.7 Consensus size: 32
62701 TACGGAATAT
* *
62711 ATATGGATAGAATTACCTATGTCTTTCGGGAC
1 ATATGGACATAATTACCTATGTCTTTCGGGAC
62743 ATATGGACATAATTACCTATGTCTTTCGGGAC
1 ATATGGACATAATTACCTATGTCTTTCGGGAC
* * *
62775 ATATGAACATAATTACCTATGTCTTTTGAGAC
1 ATATGGACATAATTACCTATGTCTTTCGGGAC
62807 ATATGGACAGT-A-TACCTATGT
1 ATATGGACA-TAATTACCTATGT
62828 TCTCAGAAAC
Statistics
Matches: 78, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
31 9 0.12
32 68 0.87
33 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (32 bp):
ATATGGACATAATTACCTATGTCTTTCGGGAC
Found at i:62826 original size:31 final size:31
Alignment explanation
Indices: 62724--62910 Score: 148
Period size: 31 Copynumber: 6.0 Consensus size: 31
62714 TGGATAGAAT
*
62724 TACCTATGTCTTTCGGGACATATGGACA-TAA
1 TACCTATGTCTTTCGAGACATATGGACAGT-A
* *
62755 TTACCTATGTCTTTCGGGACATATGAACA-TAA
1 -TACCTATGTCTTTCGAGACATATGGACAGT-A
*
62787 TTACCTATGTCTTTTGAGACATATGGACAGTA
1 -TACCTATGTCTTTCGAGACATATGGACAGTA
* * *
62819 TACCTATGT-TCTCAGAAACATATGGACAATA
1 TACCTATGTCTTTC-GAGACATATGGACAGTA
*** * *
62850 TACCTATGTTCTAAGGA-ACATATGAACAGTT
1 TACCTATG-TCTTTCGAGACATATGGACAGTA
* * * *
62881 TACCTAGGTTTTTCGGGACCTATGGACAGT
1 TACCTATGTCTTTCGAGACATATGGACAGT
62911 TGTCGAGGTT
Statistics
Matches: 128, Mismatches: 22, Indels: 11
0.80 0.14 0.07
Matches are distributed among these distances:
30 5 0.04
31 61 0.48
32 60 0.47
33 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (31 bp):
TACCTATGTCTTTCGAGACATATGGACAGTA
Found at i:63766 original size:12 final size:14
Alignment explanation
Indices: 63749--63780 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
63739 ATTTTTTCAC
63749 TGTTCATG-G-TAT
1 TGTTCATGCGATAT
63761 TGTTCATGCGATAT
1 TGTTCATGCGATAT
63775 TGTTCA
1 TGTTCA
63781 CTGTTCATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.44
13 1 0.06
14 9 0.50
ACGTcount: A:0.19, C:0.12, G:0.22, T:0.47
Consensus pattern (14 bp):
TGTTCATGCGATAT
Found at i:67143 original size:21 final size:21
Alignment explanation
Indices: 67114--67153 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
67104 GGTAAAAAAT
*
67114 TACCTAAAATATTATTATTTC
1 TACCAAAAATATTATTATTTC
67135 TACCAAAAATATTATTATT
1 TACCAAAAATATTATTATT
67154 GGGCATTTTA
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:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (21 bp):
TACCAAAAATATTATTATTTC
Found at i:67258 original size:79 final size:80
Alignment explanation
Indices: 67112--67258 Score: 181
Period size: 79 Copynumber: 1.9 Consensus size: 80
67102 TCGGTAAAAA
* * * * * **
67112 ATTACCTAAAATATTATTATTTCTACCAAAAATATTATTATTGGGCATTTTACTGGATTTATTAA
1 ATTACCTAAAATATTATTATTTCTACCAAAAATATTAATATTGAGCACTTTACCGGATTAAAAAA
67177 CATATCTGGTAAAGT
66 CATATCTGGTAAAGT
* * *
67192 ATTATCTAAAATATTATT-TTTTTACCGAAAATATTAATATTGAGCACTTTACCGTG-TTAAAAA
1 ATTACCTAAAATATTATTATTTCTACCAAAAATATTAATATTGAGCACTTTACCG-GATTAAAAA
67255 ACAT
65 ACAT
67259 TAATATTTTA
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
79 38 0.68
80 18 0.32
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (80 bp):
ATTACCTAAAATATTATTATTTCTACCAAAAATATTAATATTGAGCACTTTACCGGATTAAAAAA
CATATCTGGTAAAGT
Found at i:67276 original size:21 final size:21
Alignment explanation
Indices: 67251--67294 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
67241 TACCGTGTTA
*
67251 AAAAACATTAATATTTTAGGT
1 AAAAACAATAATATTTTAGGT
*
67272 AAAAATAATAATATTTTAGGT
1 AAAAACAATAATATTTTAGGT
67293 AA
1 AA
67295 TTTTTTATCA
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:0.52, C:0.02, G:0.09, T:0.36
Consensus pattern (21 bp):
AAAAACAATAATATTTTAGGT
Found at i:68502 original size:14 final size:14
Alignment explanation
Indices: 68483--68521 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
68473 GGATTGAGTG
* *
68483 TTTAGGGTTTATGT
1 TTTAGGGTTTAGGA
68497 TTTAGGGTTTAGGA
1 TTTAGGGTTTAGGA
68511 TTTAGGGTTTA
1 TTTAGGGTTTA
68522 AGGTTCATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.31, T:0.51
Consensus pattern (14 bp):
TTTAGGGTTTAGGA
Found at i:68507 original size:7 final size:7
Alignment explanation
Indices: 68482--68526 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
68472 CGGATTGAGT
68482 GTTTAGG
1 GTTTAGG
*
68489 GTTTATG
1 GTTTAGG
*
68496 TTTTAGG
1 GTTTAGG
68503 GTTTAGG
1 GTTTAGG
*
68510 ATTTAGG
1 GTTTAGG
*
68517 GTTTAAG
1 GTTTAGG
68524 GTT
1 GTT
68527 CATTACAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.49
Consensus pattern (7 bp):
GTTTAGG
Done.