Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002657.1 Hibiscus syriacus cultivar Beakdansim tig00005434_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: 49086
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Found at i:2753 original size:22 final size:21
Alignment explanation
Indices: 2711--2750 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2701 GAGTTTGTTT
*
2711 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
2732 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2751 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:11907 original size:26 final size:25
Alignment explanation
Indices: 11862--11917 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
11852 ACTTTCCCTT
*
11862 TTTTAATACCCTAATTAAAAATACA
1 TTTTGATACCCTAATTAAAAATACA
11887 TTTTGATACCCTAATTAAAAATACA
1 TTTTGATACCCTAATTAAAAATACA
11912 TTTTGA
1 TTTTGA
11918 ATCCATTTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.43, C:0.14, G:0.04, T:0.39
Consensus pattern (25 bp):
TTTTGATACCCTAATTAAAAATACA
Found at i:20098 original size:22 final size:22
Alignment explanation
Indices: 20073--20166 Score: 111
Period size: 22 Copynumber: 4.3 Consensus size: 22
20063 TTAAATTATG
* *
20073 AAAGTGCCTCTGCACTAGTACT
1 AAAGTGCCTCAGCACTAGTACA
* *
20095 AAAGTACCTCAGCACTAATACA
1 AAAGTGCCTCAGCACTAGTACA
*
20117 AAAGTGCCTCATCACT-GATACA
1 AAAGTGCCTCAGCACTAG-TACA
20139 AAAGTGCCTCAGCACT-GATACA
1 AAAGTGCCTCAGCACTAG-TACA
20161 AAAGTG
1 AAAGTG
20167 TTATAACACT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
22 63 1.00
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (22 bp):
AAAGTGCCTCAGCACTAGTACA
Found at i:20143 original size:44 final size:44
Alignment explanation
Indices: 20073--20166 Score: 129
Period size: 44 Copynumber: 2.1 Consensus size: 44
20063 TTAAATTATG
*
20073 AAAGTGCCTCTGCACTAGTACTAAAGTACCTCAGCACTAATACA
1 AAAGTGCCTCTGCACTAGTACAAAAGTACCTCAGCACTAATACA
* *
20117 AAAGTGCCTCAT-CACT-GATACAAAAGTGCCTCAGCACTGATACA
1 AAAGTGCCTC-TGCACTAG-TACAAAAGTACCTCAGCACTAATACA
20161 AAAGTG
1 AAAGTG
20167 TTATAACACT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 43 0.96
45 1 0.02
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (44 bp):
AAAGTGCCTCTGCACTAGTACAAAAGTACCTCAGCACTAATACA
Found at i:20578 original size:18 final size:21
Alignment explanation
Indices: 20535--20579 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 21
20525 TTTATTCTCA
*
20535 GAGTATCGATACTCTCCATAT
1 GAGTATCGATACTCTCCACAT
20556 G-GTATCGA-A-TCTCC-CAT
1 GAGTATCGATACTCTCCACAT
20573 GAGTATC
1 GAGTATC
20580 ACTACCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 3 0.14
18 10 0.45
19 1 0.05
20 7 0.32
21 1 0.05
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (21 bp):
GAGTATCGATACTCTCCACAT
Found at i:21928 original size:43 final size:43
Alignment explanation
Indices: 21719--22372 Score: 451
Period size: 43 Copynumber: 15.2 Consensus size: 43
21709 TATTTTTCTT
* * *
21719 CTTTATAATTGAGAG-CTCTAATTTTGT-AATCACAGTTTTTAC
1 CTTTATAATTGAG-GCCTCTAATTTTTTCAATCTCACTTTTTAC
* * * **
21761 CTTTTATGATTTAGGCCCCTAATTTTTTTTATCTCAC-TTTTAC
1 C-TTTATAATTGAGGCCTCTAATTTTTTCAATCTCACTTTTTAC
* * * * * * *
21804 ATTTACAATTGAGGCCCCCAATATTTTCAATCTCACTTTCTAG
1 CTTTATAATTGAGGCCTCTAATTTTTTCAATCTCACTTTTTAC
* * * * * * * * *
21847 TTTTATTATTGAAG-CTATTATTTTCTTTAAGCTTACTTTTTAT
1 CTTTATAATTGAGGCCTCTAATTTT-TTCAATCTCACTTTTTAC
* * **
21890 CTTTATAATGGAGGCCTCTAATTTTTTCAATCTCACTTTATGG
1 CTTTATAATTGAGGCCTCTAATTTTTTCAATCTCACTTTTTAC
* * * * * *
21933 CTTTATAATTGAAGCCCCAAATTTTTTTAATATTACTTTTTAC
1 CTTTATAATTGAGGCCTCTAATTTTTTCAATCTCACTTTTTAC
* * *
21976 ATTTATAACTGAGG-CTCCTAATTTTTTAAATC-CTACTTTTTAC
1 CTTTATAATTGAGGCCT-CTAATTTTTTCAATCTC-ACTTTTTAC
* *
22019 CTTTATAACTT-AGACCCCTAATTTTTTTCAATCTCAC-TTTTAC
1 CTTTATAA-TTGAGGCCTCTAA-TTTTTTCAATCTCACTTTTTAC
* * * * *
22062 CTTTATAATTAAAGCC-CATAATTTTTTAATATTTC-TTTTTTAC
1 CTTTATAATTGAGGCCTC-TAATTTTTTCA-ATCTCACTTTTTAC
* * * * * *
22105 TTTTATAATCGAGGCCT-TATTTTTTTTTCAATCCCGCCTTTTAC
1 CTTTATAATTGAGGCCTCTA--ATTTTTTCAATCTCACTTTTTAC
* * * * *
22149 CTTTATATTTGAAGCCTTTAA-TTTTT-AAGCTAACTTTTTAC
1 CTTTATAATTGAGGCCTCTAATTTTTTCAATCTCACTTTTTAC
*
22190 ATTTATAATTGAGG-CTCTTAATTTTTTTCAATCTCACTTTTTAC
1 CTTTATAATTGAGGCCTC-TAA-TTTTTTCAATCTCACTTTTTAC
* *
22234 CTTTATAATTGAAGTCC-CTAATTTTTTCAATCTCACTTTCTAC
1 CTTTATAATTG-AGGCCTCTAATTTTTTCAATCTCACTTTTTAC
* * *
22277 TTTTATAATTGAAGCCTCTCATTTTTT-AATCTCACTTTTTAC
1 CTTTATAATTGAGGCCTCTAATTTTTTCAATCTCACTTTTTAC
* * * *
22319 CTTTATAATTGAGACCCCT-ATTTTTTCCAACCTAACATTTTTAC
1 CTTTATAATTGAGGCCTCTAATTTTTT-CAATCTCAC-TTTTTAC
*
22363 TTTTATAATT
1 CTTTATAATT
22373 TAAGATCCTA
Statistics
Matches: 469, Mismatches: 112, Indels: 60
0.73 0.17 0.09
Matches are distributed among these distances:
40 2 0.00
41 31 0.07
42 85 0.18
43 249 0.53
44 95 0.20
45 6 0.01
46 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.49
Consensus pattern (43 bp):
CTTTATAATTGAGGCCTCTAATTTTTTCAATCTCACTTTTTAC
Found at i:22171 original size:87 final size:84
Alignment explanation
Indices: 22037--22330 Score: 256
Period size: 85 Copynumber: 3.4 Consensus size: 84
22027 CTTAGACCCC
* * * **
22037 TAATTTTTTTCAATCTCACTTTTACCTTTATAATTAAAGCCCATAATTTTTTAATATTTCTTTTT
1 TAATTTTTTTCAATCTCCCTTTTACCTTTATAATTGAAG-CCATAATTTTTTAAGATAAC-TTTT
*
22102 TACTTTTATAATCGAGGC-CT
64 TACATTTATAATCGAGGCTCT
* * * * *
22122 TATTTTTTTTTCAATCCCGCCTTTTACCTTTATATTTGAAGCCTTTAA-TTTTTAAGCTAACTTT
1 TA-ATTTTTTTCAATCTC-CCTTTTACCTTTATAATTGAAGCC-ATAATTTTTTAAGATAACTTT
*
22186 TTACATTTATAATTGAGGCTCT
63 TTACATTTATAATCGAGGCTCT
* * ** *
22208 TAATTTTTTTCAATCTCACTTTTTACCTTTATAATTGAAGTCCCTAATTTTTTCAATCTCACTTT
1 TAATTTTTTTCAATCTC-CCTTTTACCTTTATAATTGAAG-CCATAATTTTTT-AAGATAACTTT
* * * *
22273 CTACTTTTATAATTGAAGC-CT
63 TTACATTTATAATCGAGGCTCT
* *
22294 CTCA-TTTTTT-AATCTCACTTTTTACCTTTATAATTGA
1 -TAATTTTTTTCAATCTC-CCTTTTACCTTTATAATTGA
22331 GACCCCTATT
Statistics
Matches: 177, Mismatches: 24, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
85 85 0.48
86 43 0.24
87 49 0.28
ACGTcount: A:0.25, C:0.18, G:0.05, T:0.51
Consensus pattern (84 bp):
TAATTTTTTTCAATCTCCCTTTTACCTTTATAATTGAAGCCATAATTTTTTAAGATAACTTTTTA
CATTTATAATCGAGGCTCT
Found at i:24348 original size:24 final size:22
Alignment explanation
Indices: 24316--24364 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
24306 TTACTATTAT
* *
24316 ATATATATTTATGAATATATAAAA
1 ATATATATTCAT-AA-AAATAAAA
*
24340 ATATTTATTCATAAAAATAAAA
1 ATATATATTCATAAAAATAAAA
24362 ATA
1 ATA
24365 CTATTAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 10 0.45
23 2 0.09
24 10 0.45
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
ATATATATTCATAAAAATAAAA
Found at i:25770 original size:3 final size:3
Alignment explanation
Indices: 25762--25856 Score: 133
Period size: 3 Copynumber: 32.7 Consensus size: 3
25752 TTAATATATT
*
25762 TAA TAA TAA -AA TAA T-A TAA TAA TAA TAA AAA TAA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
25807 TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
25855 TA
1 TA
25857 TGGATAAAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
2 6 0.07
3 75 0.93
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:26463 original size:114 final size:114
Alignment explanation
Indices: 26001--26638 Score: 1057
Period size: 114 Copynumber: 5.5 Consensus size: 114
25991 ATTCTTCTTT
* * ** * * *
26001 TTCTCCAGATGAGTTCTTCTCATTACGAACTTTCTGCTGGGGATG-ATGTTCCATCAAATGATGA
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT-CTGGAAAAGAATGATCCATCAAGTGATGA
* *
26065 ATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
65 ATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCC
*
26115 TTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATG-ATGATCCATCAAGTG
1 TTCTTCAGAT---GAGTTCTTCTCATTATGAA--CTTTCTCTGGAAAAGAATGATCCATCAAGTG
*
26179 ATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
61 ATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCC
26233 TTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAAAGAATGATCCATCAAGTG
1 TTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TT-CTCTGGAAAAGAATGATCCATCAAGTG
26298 ATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCC
61 ATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCC
26352 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATCAAGTGATGAA
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATCAAGTGATGAA
26417 TTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCC
66 TTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCC
26466 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG-AAAGAATGATCCATCAAGTGATGAA
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATCAAGTGATGAA
26530 TTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCC
66 TTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCC
26579 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATCAAGTG
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATCAAGTG
26639 GATTCGAAAT
Statistics
Matches: 506, Mismatches: 9, Indels: 18
0.95 0.02 0.03
Matches are distributed among these distances:
113 113 0.22
114 149 0.29
115 2 0.00
116 23 0.05
117 20 0.04
118 115 0.23
119 84 0.17
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (114 bp):
TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATCAAGTGATGAA
TTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCC
Found at i:26584 original size:227 final size:227
Alignment explanation
Indices: 26001--26638 Score: 1055
Period size: 227 Copynumber: 2.8 Consensus size: 227
25991 ATTCTTCTTT
* * * * * *
26001 TTCTCCAGATGAGTTCTTCTCATTACGAACTTTCTGCTGGGGATG-ATGTTCCATCAAATGATGA
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT-CT-GGAAAGAATGATCCATCAAGTGATGA
* *
26065 ATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGA
64 ATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGAT---GA
*
26130 GTTCTTCTCATTATGAACTCTTTCTCTGGAAATG-ATGATCCATCAAGTGATGAATTCAAGCAAA
126 GTTCTTCTCATTATGAA--CTTTCTCTGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAA
*
26194 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
189 AGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCC
26233 TTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAAAGAATGATCCATCAAGTG
1 TTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TT-CTCTGG-AAAGAATGATCCATCAAGTG
26298 ATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATG
60 ATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATG
26363 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAA
125 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAA
26428 GGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCC
190 GGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCC
26466 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGAATGATCCATCAAGTGATGAAT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGAATGATCCATCAAGTGATGAAT
26531 TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCT
66 TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCT
26596 TCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATCAAGTG
131 TCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATCAAGTG
26639 GATTCGAAAT
Statistics
Matches: 388, Mismatches: 10, Indels: 21
0.93 0.02 0.05
Matches are distributed among these distances:
227 134 0.35
228 6 0.02
229 2 0.01
230 21 0.05
232 23 0.06
233 78 0.20
234 19 0.05
235 22 0.06
236 6 0.02
237 77 0.20
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (227 bp):
TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGAATGATCCATCAAGTGATGAAT
TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCT
TCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGA
ACAAGTTCTTCTCATTATGAACTTCCTCTTCC
Found at i:27353 original size:52 final size:52
Alignment explanation
Indices: 27275--27742 Score: 807
Period size: 52 Copynumber: 9.0 Consensus size: 52
27265 CAATACTTGA
*
27275 TTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
*
27327 TTCTGTCCAACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
*
27379 TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATG
1 TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
27431 TTCTGAT-CAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 TTCTG-TCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
* *
27483 TTCTGTCCAACCAGATCAGATAACTCAAAAAACACTTCCAGAAGATGTTATG
1 TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
*
27535 TTCTGAT-CAACCAGATAAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 TTCTG-TCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
* *
27587 TTCTGTCCAACCAGATCAGATAACTCAAAAAACACTTCCAGAAGATGTTATG
1 TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
27639 TTCTGAT-CAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 TTCTG-TCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
*
27691 TTCTGTCCAACCAGATCAGATAACTCAAAGAACAATTCCAGAAGATGCTATG
1 TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
27743 AGCACATTCA
Statistics
Matches: 394, Mismatches: 16, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
51 3 0.01
52 388 0.98
53 3 0.01
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (52 bp):
TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
Found at i:28918 original size:16 final size:17
Alignment explanation
Indices: 28899--28968 Score: 72
Period size: 17 Copynumber: 4.1 Consensus size: 17
28889 TTTTCTATTA
* *
28899 TTTTTTCCTCTTTTTTT
1 TTTTTTCTTCTTTTCTT
**
28916 TTTTTTCTT-TTCCCTT
1 TTTTTTCTTCTTTTCTT
28932 TTTTTTCTTTCTTTTCTT
1 TTTTTTC-TTCTTTTCTT
28950 TTTTCTTCTTC-TTTCTT
1 TTTT-TTCTTCTTTTCTT
28967 TT
1 TT
28969 CTTCAAGCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
16 11 0.25
17 18 0.41
18 12 0.27
19 3 0.07
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTTCTTCTTTTCTT
Found at i:28922 original size:35 final size:36
Alignment explanation
Indices: 28883--28965 Score: 91
Period size: 35 Copynumber: 2.3 Consensus size: 36
28873 ACCTTGACCC
28883 TTTTCTTTTTCTATTATTTTTTC-CTCTTTT-TTTTT
1 TTTTCTTTTTCTATT-TTTTTTCTCTCTTTTCTTTTT
** *
28918 TTTTC-TTTTCCCTTTTTTTTCTTTCTTTTCTTTTT
1 TTTTCTTTTTCTATTTTTTTTCTCTCTTTTCTTTTT
*
28953 TCTTCTTCTTTCT
1 TTTTCTT-TTTCT
28966 TTTCTTCAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
33 7 0.18
34 13 0.33
35 14 0.36
36 1 0.03
37 4 0.10
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.78
Consensus pattern (36 bp):
TTTTCTTTTTCTATTTTTTTTCTCTCTTTTCTTTTT
Found at i:28926 original size:22 final size:22
Alignment explanation
Indices: 28901--28969 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 22
28891 TTCTATTATT
*
28901 TTTTCCTCTTTTTTTTTTTTTC
1 TTTTCCTCTTTTTTTTTCTTTC
28923 TTTTCC-C-TTTTTTTTCTTTC
1 TTTTCCTCTTTTTTTTTCTTTC
28943 TTTT-CT-TTTTTCTTCTTCTTTC
1 TTTTCCTCTTTTT-TT-TTCTTTC
28965 TTTTC
1 TTTTC
28970 TTCAAGCATA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
19 1 0.02
20 20 0.49
21 3 0.07
22 17 0.41
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTCCTCTTTTTTTTTCTTTC
Found at i:28958 original size:15 final size:14
Alignment explanation
Indices: 28907--28972 Score: 53
Period size: 16 Copynumber: 4.4 Consensus size: 14
28897 TATTTTTTCC
*
28907 TCTTTTTTTTTTTT
1 TCTTCTTTTTTTTT
28921 TCTT-TTCCCTTTTTTT
1 TCTTCTT---TTTTTTT
28937 TCTTTCTTTTCTTTTT
1 TC-TTCTTTT-TTTTT
*
28953 TCTTCTTCTTTCTTT
1 TCTTCTT-TTTTTTT
28968 TCTTC
1 TCTTC
28973 AAGCATAATA
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
13 2 0.05
14 4 0.09
15 16 0.36
16 18 0.41
17 2 0.05
18 2 0.05
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TCTTCTTTTTTTTT
Found at i:28970 original size:12 final size:12
Alignment explanation
Indices: 28931--28972 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
28921 TCTTTTCCCT
*
28931 TTTTTTTCTTTC
1 TTTTCTTCTTTC
28943 TTTTCTT-TTT-
1 TTTTCTTCTTTC
*
28953 TCTTCTTCTTTC
1 TTTTCTTCTTTC
28965 TTTTCTTC
1 TTTTCTTC
28973 AAGCATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
10 6 0.24
11 6 0.24
12 13 0.52
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTCTTCTTTC
Found at i:28970 original size:31 final size:29
Alignment explanation
Indices: 28907--28971 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 29
28897 TATTTTTTCC
*
28907 TCTTTTTTTTTTTTTCTTTTCCCTTTTTTT
1 TCTTTTTTTTTTTTTCTTTT-CCTTTCTTT
28937 TCTTTCTTTTCTTTTTTCTTCTT-CTTTCTTT
1 TCTTT-TTTT-TTTTTTCTT-TTCCTTTCTTT
28968 TCTT
1 TCTT
28972 CAAGCATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
30 5 0.16
31 15 0.48
32 9 0.29
33 2 0.06
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (29 bp):
TCTTTTTTTTTTTTTCTTTTCCTTTCTTT
Found at i:40359 original size:24 final size:22
Alignment explanation
Indices: 40327--40375 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
40317 TTACTATTAT
* *
40327 ATATATATTTATGAATATATAAAA
1 ATATATATTCAT-AA-AAATAAAA
*
40351 ATATTTATTCATAAAAATAAAA
1 ATATATATTCATAAAAATAAAA
40373 ATA
1 ATA
40376 CTATTAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 10 0.45
23 2 0.09
24 10 0.45
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
ATATATATTCATAAAAATAAAA
Found at i:41787 original size:3 final size:3
Alignment explanation
Indices: 41779--41878 Score: 157
Period size: 3 Copynumber: 33.7 Consensus size: 3
41769 TTAATATATT
*
41779 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA AAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
41826 TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
41874 TAA TA
1 TAA TA
41879 TGGATAAAAA
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
2 2 0.02
3 86 0.98
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:46509 original size:152 final size:154
Alignment explanation
Indices: 46255--46557 Score: 583
Period size: 152 Copynumber: 2.0 Consensus size: 154
46245 CACTCTACCT
46255 TTTCTTTTTACGTTTCATTCTTATTCTTGATTCATCTTCTTATTGTACTTTGCATGTTAGTTGAT
1 TTTCTTTTTACGTTTCATTCTTATTCTTGATTCATCTTCTTATTGTACTTTGCATGTTAGTTGAT
46320 GTGATTAGTAATTGACAGCTACATTTCATTGTTGTTTTCTGTCAATTATGTGGAAGTTTGGGTCT
66 GTGATTAGTAATTGACAGCTACATTTCATTGTTGTTTTCTGTCAATTATGTGGAAGTTTGGGTCT
46385 TTTCTTATTGTTTAAGGGTCAGTG
131 TTTCTTATTGTTTAAGGGTCAGTG
46409 TTTC-TTTTACGTTTCATTCTTATTCTTGATTC-TCTTCTTATTGTACTTTGCATGTTAGTTGAT
1 TTTCTTTTTACGTTTCATTCTTATTCTTGATTCATCTTCTTATTGTACTTTGCATGTTAGTTGAT
*
46472 GTGATTAGTAATTGAGAGCTACATTTCATTGTTGTTTTCTGTCAATTATGTGGAAGTTTGGGTCT
66 GTGATTAGTAATTGACAGCTACATTTCATTGTTGTTTTCTGTCAATTATGTGGAAGTTTGGGTCT
46537 TTTCTTATTGTTTAAGGGTCA
131 TTTCTTATTGTTTAAGGGTCA
46558 ATGTGTTACA
Statistics
Matches: 148, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
152 116 0.78
153 28 0.19
154 4 0.03
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.51
Consensus pattern (154 bp):
TTTCTTTTTACGTTTCATTCTTATTCTTGATTCATCTTCTTATTGTACTTTGCATGTTAGTTGAT
GTGATTAGTAATTGACAGCTACATTTCATTGTTGTTTTCTGTCAATTATGTGGAAGTTTGGGTCT
TTTCTTATTGTTTAAGGGTCAGTG
Done.