Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001752.1 Hibiscus syriacus cultivar Beakdansim tig00003543_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: 66782
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:705 original size:14 final size:14
Alignment explanation
Indices: 673--699 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
663 GGGATAAAAA
673 ATTAATTATTATTC
1 ATTAATTATTATTC
687 ATTAATTATTATT
1 ATTAATTATTATT
700 TTTTAAAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTAATTATTATTC
Found at i:1652 original size:15 final size:16
Alignment explanation
Indices: 1620--1652 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1610 TATTTTGTTT
1620 TTAATTTATTTAAATA
1 TTAATTTATTTAAATA
*
1636 TTAATTT-TTTTAATA
1 TTAATTTATTTAAATA
1651 TT
1 TT
1653 TTATTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTAATTTATTTAAATA
Found at i:4013 original size:35 final size:32
Alignment explanation
Indices: 3978--4058 Score: 83
Period size: 35 Copynumber: 2.3 Consensus size: 32
3968 TTTGGTTAAT
3978 TTTGTT-TATTACCATTTAATATCAGTTATTGTAA
1 TTTGTTATATTACCATTTAATA-C--TTATTGTAA
4012 TTTGTTTATCATTTACCATTTAATACTTATTGTAA
1 TTTG-TTAT-A-TTACCATTTAATACTTATTGTAA
*
4047 GTTTGTTGTATT
1 -TTTGTTATATT
4059 TAAAATTATA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
33 2 0.05
34 5 0.12
35 14 0.34
36 5 0.12
37 2 0.05
38 13 0.32
ACGTcount: A:0.26, C:0.09, G:0.10, T:0.56
Consensus pattern (32 bp):
TTTGTTATATTACCATTTAATACTTATTGTAA
Found at i:7502 original size:16 final size:16
Alignment explanation
Indices: 7483--7523 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
7473 TCAAATAATC
*
7483 ATAAT-AAACAATAAGT
1 ATAATAAAAAAAT-AGT
7499 ATAATAAAAAAATAGT
1 ATAATAAAAAAATAGT
7515 ATAATAAAA
1 ATAATAAAA
7524 TTACCTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.24
Consensus pattern (16 bp):
ATAATAAAAAAATAGT
Found at i:8842 original size:17 final size:17
Alignment explanation
Indices: 8820--8855 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
8810 CTTTTCAATC
8820 TTCACACCAAGAGTTTT
1 TTCACACCAAGAGTTTT
8837 TTCACACCAAGAGTTTT
1 TTCACACCAAGAGTTTT
8854 TT
1 TT
8856 TGTGAATAGG
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:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (17 bp):
TTCACACCAAGAGTTTT
Found at i:14656 original size:20 final size:20
Alignment explanation
Indices: 14631--14679 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
14621 AGAAGAAGTT
14631 GAAAAAGAGTGAACGGTGAG
1 GAAAAAGAGTGAACGGTGAG
*
14651 GAAAAAGAATGAACGGTGAG
1 GAAAAAGAGTGAACGGTGAG
*
14671 GAGAAAGAG
1 GAAAAAGAG
14680 GAAGTTAGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.49, C:0.04, G:0.39, T:0.08
Consensus pattern (20 bp):
GAAAAAGAGTGAACGGTGAG
Found at i:28069 original size:134 final size:133
Alignment explanation
Indices: 27807--28248 Score: 503
Period size: 134 Copynumber: 3.3 Consensus size: 133
27797 TCTTTCTTTA
* * *
27807 TTCCTAAAGAACAATGAAGCAAATCACATTAGATTTAATCTTCCATGAAGAGCAGCGAAGTGAAT
1 TTCCTAAAGAGCAATGAAGCAAATCACATTAGATTCAATATTCC-TGAAGAGCAGCGAAGTGAAT
* * * * * *
27872 CAAAATTTCCTCGAGTCTGAACTCCCC-TATAGAGTAGTGGAGA-AGATACTTCTTCATTCAGAT
65 CAAAATTTTCTCGAGTCTGACCTCCCCTTA-AGAGTAGCGGA-ACAGATTCTTTTTCTTTCAGAT
27935 TTGGTC
128 TTGGTC
* *
27941 TTCCTAAAGAGCAACGAAGCAAATCAAATCT-GATTCAATATTCTCTGAAGAGCAGCGAAGTGAA
1 TTCCTAAAGAGCAATGAAGCAAATCACAT-TAGATTCAATATTC-CTGAAGAGCAGCGAAGTGAA
* *
28005 TCAAAATTTTCTCGAGTCTGACCTCCCCTTAAGAGTAGCGGATCAGATTCTTTTTCTTTTAGATT
64 TCAAAATTTTCTCGAGTCTGACCTCCCCTTAAGAGTAGCGGAACAGATTCTTTTTCTTTCAGATT
28070 TGGTC
129 TGGTC
** * * * * * * *
28075 TTTTTGAAGAGTAGTGAAGCAAATCACATTTGATTCTATCTTCCCTGAAGAGCAACGAAGTGAAT
1 TTCCTAAAGAGCAATGAAGCAAATCACATTAGATTCAATATT-CCTGAAGAGCAGCGAAGTGAAT
* * * * * * * *
28140 CAAAATTTTCTCTAGTCTGGCCTCCCGTAAAGAGTAGCGAAACATATTCTTTTTATTTCATATTT
65 CAAAATTTTCTCGAGTCTGACCTCCCCTTAAGAGTAGCGGAACAGATTCTTTTTCTTTCAGATTT
28205 GGTC
130 GGTC
* * * *
28209 TTCCTGAAGACCAGTGAAGCAAATCACATTCGATTCAATA
1 TTCCTAAAGAGCAATGAAGCAAATCACATTAGATTCAATA
28249 ATCATGCAAC
Statistics
Matches: 262, Mismatches: 40, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
133 1 0.00
134 256 0.98
135 5 0.02
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Consensus pattern (133 bp):
TTCCTAAAGAGCAATGAAGCAAATCACATTAGATTCAATATTCCTGAAGAGCAGCGAAGTGAATC
AAAATTTTCTCGAGTCTGACCTCCCCTTAAGAGTAGCGGAACAGATTCTTTTTCTTTCAGATTTG
GTC
Found at i:28281 original size:22 final size:22
Alignment explanation
Indices: 28253--28303 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
28243 TCAATAATCA
28253 TGCAACAGTCTTGGATTGCACC
1 TGCAACAGTCTTGGATTGCACC
28275 TGCAACAGTCTTGGATTGCACC
1 TGCAACAGTCTTGGATTGCACC
28297 TGCAACA
1 TGCAACA
28304 AACAAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (22 bp):
TGCAACAGTCTTGGATTGCACC
Found at i:33534 original size:29 final size:29
Alignment explanation
Indices: 33492--33550 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
33482 ATCAGTTAAG
33492 CAAAAAAATCTTGCATAGGCTAAACTTAT
1 CAAAAAAATCTTGCATAGGCTAAACTTAT
33521 CAAAAAAATCTTGCATAGGCTAAACTTAT
1 CAAAAAAATCTTGCATAGGCTAAACTTAT
33550 C
1 C
33551 CACCACATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27
Consensus pattern (29 bp):
CAAAAAAATCTTGCATAGGCTAAACTTAT
Found at i:35021 original size:2 final size:2
Alignment explanation
Indices: 35014--35042 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35004 GGCCGGGGGC
35014 AT AT 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 AT AT A
35043 AAAACATGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36123 original size:2 final size:2
Alignment explanation
Indices: 36116--36142 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
36106 TAAAGATGAT
36116 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
36143 TTTGAAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36223 original size:4 final size:4
Alignment explanation
Indices: 36214--36241 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
36204 AGGAGACAAT
36214 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
36242 AAGAATACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:38888 original size:17 final size:16
Alignment explanation
Indices: 38850--38884 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
38840 CTTATTTCTC
38850 AAAA-TAAATAATGAA
1 AAAAGTAAATAATGAA
38865 AAAAGTAAATAATGAA
1 AAAAGTAAATAATGAA
38881 AAAA
1 AAAA
38885 AGTATAGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (16 bp):
AAAAGTAAATAATGAA
Found at i:38895 original size:15 final size:16
Alignment explanation
Indices: 38856--38888 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
38846 TCTCAAAATA
38856 AATAATG-AAAAAAGT
1 AATAATGAAAAAAAGT
38871 AAATAATGAAAAAAAGT
1 -AATAATGAAAAAAAGT
38888 A
1 A
38889 TAGTGAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.18
Consensus pattern (16 bp):
AATAATGAAAAAAAGT
Found at i:39810 original size:17 final size:17
Alignment explanation
Indices: 39762--39813 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
39752 TACAGTCTTG
* *
39762 AAATATCCTAAAGATAGA
1 AAATATACTAAAAATA-A
* *
39780 ATATATACTCAAAATAA
1 AAATATACTAAAAATAA
*
39797 AAATATTCTAAAAATAA
1 AAATATACTAAAAATAA
39814 TCCAAAAGAT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.60, C:0.10, G:0.04, T:0.27
Consensus pattern (17 bp):
AAATATACTAAAAATAA
Found at i:39880 original size:39 final size:39
Alignment explanation
Indices: 39835--39909 Score: 150
Period size: 39 Copynumber: 1.9 Consensus size: 39
39825 AATCCCAAAT
39835 TATTTTCAAATTCAAACTTAAGTTCCTAAGATAACTAAG
1 TATTTTCAAATTCAAACTTAAGTTCCTAAGATAACTAAG
39874 TATTTTCAAATTCAAACTTAAGTTCCTAAGATAACT
1 TATTTTCAAATTCAAACTTAAGTTCCTAAGATAACT
39910 CTACCCGTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (39 bp):
TATTTTCAAATTCAAACTTAAGTTCCTAAGATAACTAAG
Found at i:40200 original size:17 final size:17
Alignment explanation
Indices: 40135--40238 Score: 63
Period size: 17 Copynumber: 6.1 Consensus size: 17
40125 ATATAGCATG
*
40135 TAGTTTTTGAAAACATA
1 TAGTTTTTGAAAATATA
*
40152 TAGTTTTT-AAAA-ATG
1 TAGTTTTTGAAAATATA
* * ***
40167 T-GTGTGTGTGTATATA
1 TAGTTTTTGAAAATATA
40183 TAGTTTTTGAAAATATA
1 TAGTTTTTGAAAATATA
*
40200 TAGTATATTAT-ATAATTTATA
1 TAGT-T-TT-TGA-AA-ATATA
40221 TAGTTTTTGAAAATATA
1 TAGTTTTTGAAAATATA
40238 T
1 T
40239 TATATAATTT
Statistics
Matches: 64, Mismatches: 14, Indels: 18
0.67 0.15 0.19
Matches are distributed among these distances:
14 4 0.06
15 4 0.06
16 7 0.11
17 27 0.42
18 4 0.06
19 6 0.09
20 4 0.06
21 8 0.12
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (17 bp):
TAGTTTTTGAAAATATA
Found at i:40243 original size:60 final size:63
Alignment explanation
Indices: 40179--40310 Score: 184
Period size: 60 Copynumber: 2.1 Consensus size: 63
40169 TGTGTGTGTA
40179 TATATAGTTTTTGAAAATATATAGTATAT-TAT-ATAATT-TATATAGTTTTTG-AAA-ATATAT
1 TATATAGTTTTTGAAAATATATA-TATATATATAAT-ATTATATATAGTTTTTGAAAAGATATAT
* *
40239 TATATAATTTTTGAATATATATATATATATATAATATTATATATAGTTTTTGAAAAGATATAT
1 TATATAGTTTTTGAAAATATATATATATATATAATATTATATATAGTTTTTGAAAAGATATAT
*
40302 AATATAGTT
1 TATATAGTT
40311 ATATATATAT
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
59 5 0.08
60 27 0.43
61 15 0.24
62 3 0.05
63 13 0.21
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (63 bp):
TATATAGTTTTTGAAAATATATATATATATATAATATTATATATAGTTTTTGAAAAGATATAT
Found at i:40244 original size:22 final size:22
Alignment explanation
Indices: 40216--40310 Score: 83
Period size: 22 Copynumber: 4.5 Consensus size: 22
40206 ATTATATAAT
40216 TTATATAGTTTTTGAAAATATA
1 TTATATAGTTTTTGAAAATATA
* *
40238 TTATATAATTTTTGAATATATA
1 TTATATAGTTTTTGAAAATATA
* * *
40260 -TATATA-TATAT-AATAT-TA
1 TTATATAGTTTTTGAAAATATA
40278 -TATATAGTTTTTGAAAAGATATA
1 TTATATAGTTTTTG-AAA-ATATA
*
40301 TAATATAGTT
1 TTATATAGTT
40311 ATATATATAT
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
18 8 0.14
19 8 0.14
20 3 0.05
21 8 0.14
22 22 0.37
23 2 0.03
24 8 0.14
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.49
Consensus pattern (22 bp):
TTATATAGTTTTTGAAAATATA
Found at i:40244 original size:24 final size:23
Alignment explanation
Indices: 40209--40270 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 23
40199 ATAGTATATT
40209 ATATAATT-TATATAGTTTTTGAAA
1 ATAT-ATTATATATA-TTTTTGAAA
*
40233 ATATATTATATA-ATTTTTGAAT
1 ATATATTATATATATTTTTGAAA
40255 ATATATATATATATAT
1 ATATAT-TATATATAT
40271 AATATTATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
22 14 0.41
23 10 0.29
24 10 0.29
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.52
Consensus pattern (23 bp):
ATATATTATATATATTTTTGAAA
Found at i:40258 original size:2 final size:2
Alignment explanation
Indices: 40253--40326 Score: 50
Period size: 2 Copynumber: 38.0 Consensus size: 2
40243 TAATTTTTGA
* * *
40253 AT AT AT AT AT AT AT AT AT A- AT AT -T AT AT AT AGT TT TT GA- AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT -AT AT
*
40294 AG AT AT AT A- AT AT AGT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
40327 TCCTATTATT
Statistics
Matches: 60, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
1 5 0.08
2 53 0.88
3 2 0.03
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Found at i:40275 original size:39 final size:40
Alignment explanation
Indices: 40232--40323 Score: 118
Period size: 39 Copynumber: 2.4 Consensus size: 40
40222 AGTTTTTGAA
* *
40232 AATATAT-TATATAATTTTTGAATATATATATATATATA-T
1 AATATATATATATAATTTTTGAAAAGATATATA-ATATAGT
*
40271 AATAT-TATATATAGTTTTTGAAAAGATATATAATATAGT
1 AATATATATATATAATTTTTGAAAAGATATATAATATAGT
*
40310 TATATATATATATA
1 AATATATATATATA
40324 TATTCCTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
38 6 0.13
39 32 0.70
40 8 0.17
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (40 bp):
AATATATATATATAATTTTTGAAAAGATATATAATATAGT
Found at i:40301 original size:58 final size:59
Alignment explanation
Indices: 40178--40326 Score: 166
Period size: 60 Copynumber: 2.6 Consensus size: 59
40168 GTGTGTGTGT
* * *
40178 ATATATAGTTTTTGAAAATATATAGTATAT-TATATAATTTATATAGTTTTTGAAAATAT
1 ATATATAATTTTTGAATATATATA-TATATATATATAATTTATATAGTTTTTGAAAATAG
40237 ATTATATAATTTTTGAATATATATATATATATATA-ATATTATATATAGTTTTTG-AAA-AG
1 A-TATATAATTTTTGAATATATATATATATATATATA-ATT-TATATAGTTTTTGAAAATAG
* * *
40296 ATATATAA-TATAG-TTATATATATATATATAT
1 ATATATAATTTTTGAATATATATATATATATAT
40327 TCCTATTATT
Statistics
Matches: 80, Mismatches: 6, Indels: 11
0.82 0.06 0.11
Matches are distributed among these distances:
56 17 0.21
57 3 0.04
58 7 0.09
59 9 0.11
60 31 0.39
61 13 0.16
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (59 bp):
ATATATAATTTTTGAATATATATATATATATATATAATTTATATAGTTTTTGAAAATAG
Found at i:40344 original size:9 final size:9
Alignment explanation
Indices: 40332--40373 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 9
40322 TATATTCCTA
40332 TTATTATTT
1 TTATTATTT
40341 TTATTATGTT
1 TTATTAT-TT
40351 TTATTAGTTT
1 TTATTA-TTT
*
40361 TT-TTGTTT
1 TTATTATTT
40369 TTATT
1 TTATT
40374 TTTAATTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
8 5 0.17
9 11 0.38
10 12 0.41
11 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (9 bp):
TTATTATTT
Found at i:40356 original size:19 final size:17
Alignment explanation
Indices: 40332--40377 Score: 51
Period size: 19 Copynumber: 2.7 Consensus size: 17
40322 TATATTCCTA
40332 TTATTATTTTTATTATGTT
1 TTATTATTTTTATT-TG-T
*
40351 TTATTAGTTTT-TTTGT
1 TTATTATTTTTATTTGT
40367 TT-TTATTTTTA
1 TTATTATTTTTA
40378 ATTTCAGGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 7 0.29
16 3 0.12
17 2 0.08
18 2 0.08
19 10 0.42
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (17 bp):
TTATTATTTTTATTTGT
Found at i:44891 original size:20 final size:20
Alignment explanation
Indices: 44853--44891 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
44843 CGTTAGACTT
*
44853 GCAAGATAAATCTTGCCTTG
1 GCAAGATAAATCTTCCCTTG
44873 GCAAGA-AAATCTGTCCCTT
1 GCAAGATAAATCT-TCCCTT
44892 ATTGCCGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (20 bp):
GCAAGATAAATCTTCCCTTG
Found at i:46173 original size:6 final size:6
Alignment explanation
Indices: 46158--46199 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
46148 TTACTTGATC
*
46158 ATGCAG ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA
1 ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA
46200 TAATGGTACC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.48, C:0.17, G:0.19, T:0.17
Consensus pattern (6 bp):
ATGCAA
Found at i:49680 original size:21 final size:21
Alignment explanation
Indices: 49654--49693 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
49644 CAGAACCCCA
*
49654 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
49675 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
49694 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:53585 original size:22 final size:21
Alignment explanation
Indices: 53543--53582 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
53533 GAGTTTGTTT
*
53543 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
53564 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
53583 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:63223 original size:21 final size:21
Alignment explanation
Indices: 63180--63223 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
63170 TGATGAATTA
**
63180 TGGCTTTATAATAAAGCTTCT
1 TGGCTTTATAATAAAGCACCT
*
63201 TGGCTTTGTAATAAAGCACCT
1 TGGCTTTATAATAAAGCACCT
63222 TG
1 TG
63224 ATTCTTGACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (21 bp):
TGGCTTTATAATAAAGCACCT
Done.