Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009162.1 Hibiscus syriacus cultivar Beakdansim tig00112697_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: 148633
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 2 of 2
Found at i:130374 original size:19 final size:19
Alignment explanation
Indices: 130359--130420 Score: 99
Period size: 19 Copynumber: 3.2 Consensus size: 19
130349 ATTAATAAAC
130359 ATAATAATAATAAATAATA
1 ATAATAATAATAAATAATA
130378 ATAATAATAATAAATAATA
1 ATAATAATAATAAATAATA
130397 ATAA-ATATATATAAATAATA
1 ATAATA-ATA-ATAAATAATA
130417 ATAA
1 ATAA
130421 AAAAGACCCG
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
18 1 0.02
19 26 0.63
20 14 0.34
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAATAATAATAAATAATA
Found at i:130376 original size:10 final size:10
Alignment explanation
Indices: 130361--130421 Score: 99
Period size: 10 Copynumber: 6.2 Consensus size: 10
130351 TAATAAACAT
130361 AATAATAATA
1 AATAATAATA
130371 AATAATAAT-
1 AATAATAATA
130380 AATAATAATA
1 AATAATAATA
130390 AATAATAATA
1 AATAATAATA
130400 AAT-ATATATA
1 AATAATA-ATA
130410 AATAATAATA
1 AATAATAATA
130420 AA
1 AA
130422 AAAGACCCGG
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
9 12 0.25
10 33 0.69
11 3 0.06
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AATAATAATA
Found at i:130378 original size:16 final size:16
Alignment explanation
Indices: 130359--130421 Score: 76
Period size: 16 Copynumber: 3.9 Consensus size: 16
130349 ATTAATAAAC
130359 ATAATAATAATAAATA
1 ATAATAATAATAAATA
130375 ATAATAATAAT-AATAA
1 ATAATAATAATAAAT-A
*
130391 ATAATAATAA-ATATA
1 ATAATAATAATAAATA
130406 TATAAATAATAATAAA
1 -AT-AATAATAATAAA
130422 AAAGACCCGG
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
15 4 0.10
16 26 0.65
17 8 0.20
18 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAATAATAATAAATA
Found at i:130754 original size:43 final size:41
Alignment explanation
Indices: 130696--130937 Score: 170
Period size: 40 Copynumber: 5.7 Consensus size: 41
130686 AAAGGTGATA
*
130696 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
1 ACACGGTTCCTACGTGATGAGGACGGCTGG--ATCTAGGGTTG
* * * *
130739 ACACGGCTCCTACGTGATAAGGA-GATCTGG-TCT-GGGAATG
1 ACACGGTTCCTACGTGATGAGGACG-GCTGGATCTAGGG-TTG
* * * * * *
130779 ACACGGCTCATACGTGATGAAGA-GTTCTGGCCATCTAAAGGTGATA
1 ACACGGTTCCTACGTGATGAGGACG-GCTGG--ATCT--AGG-GTTG
*
130825 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
1 ACACGGTTCCTACGTGATGAGGACGGCTGG--ATCTAGGGTTG
* *** * *
130868 ACACGGTTCCTACGTGATAAGGAAATCTGG-TCTGGGGATG
1 ACACGGTTCCTACGTGATGAGGACGGCTGGATCTAGGGTTG
*
130908 ACACGGTTCCTACATGATGAGGACGGCTGG
1 ACACGGTTCCTACGTGATGAGGACGGCTGG
130938 CCATCTTTAG
Statistics
Matches: 158, Mismatches: 31, Indels: 23
0.75 0.15 0.11
Matches are distributed among these distances:
39 2 0.01
40 63 0.40
42 1 0.01
43 56 0.35
44 2 0.01
46 32 0.20
47 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (41 bp):
ACACGGTTCCTACGTGATGAGGACGGCTGGATCTAGGGTTG
Found at i:130808 original size:40 final size:41
Alignment explanation
Indices: 130620--130927 Score: 130
Period size: 40 Copynumber: 7.2 Consensus size: 41
130610 ACGCGGTTCC
* * *
130620 TACGTGATGAGGACATCTGG-TC-GGGGAATGACACGGCTCA
1 TACGTGATGAAGAGATCTGGATCTAGGG-ATGACACGGCTCA
* * * *
130660 TACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCC
1 TACGTGATGAAGAGATCTGG--ATCT--AGG-GATGACACGGCTCA
* * * * *
130706 TACGTGATGAGGACG-GCTGGTTATCTATGGTTGACACGGCTCC
1 TACGTGATGAAGA-GATCTGG--ATCTAGGGATGACACGGCTCA
130749 TACGTGAT-AAGGAGATCTGG-TCT-GGGAATGACACGGCTCA
1 TACGTGATGAA-GAGATCTGGATCTAGGG-ATGACACGGCTCA
* * * *
130789 TACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCC
1 TACGTGATGAAGAGATCTGG--ATCT--AGG-GATGACACGGCTCA
* * * * * *
130835 TACGTGATGAGGACG-GCTGGTTATCTATGGTTGACACGGTTCC
1 TACGTGATGAAGA-GATCTGG--ATCTAGGGATGACACGGCTCA
* * * *
130878 TACGTGAT-AAGGAAATCTGG-TCTGGGGATGACACGGTTCC
1 TACGTGATGAA-GAGATCTGGATCTAGGGATGACACGGCTCA
*
130918 TACATGATGA
1 TACGTGATGA
130928 GGACGGCTGG
Statistics
Matches: 207, Mismatches: 38, Indels: 45
0.71 0.13 0.16
Matches are distributed among these distances:
39 2 0.01
40 71 0.34
41 3 0.01
42 3 0.01
43 56 0.27
44 4 0.02
46 64 0.31
47 4 0.02
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.26
Consensus pattern (41 bp):
TACGTGATGAAGAGATCTGGATCTAGGGATGACACGGCTCA
Found at i:130861 original size:46 final size:45
Alignment explanation
Indices: 130647--130930 Score: 170
Period size: 46 Copynumber: 6.6 Consensus size: 45
130637 TGGTCGGGGA
* * * ** **
130647 ATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTG
1 ATGACACGGTTCCTACGTGATGAGGAGAGCTGGTTATCT-AAGGTG
* *
130693 ATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGT-
1 ATGACACGGTTCCTACGTGATGAGGA-GAGCTGGTTATCTAAGGTG
* * *
130737 -TGACACGGCTCCTACGTGATAAGGAGATCTGG---TCT--GG-G
1 ATGACACGGTTCCTACGTGATGAGGAGAGCTGGTTATCTAAGGTG
* * * ** **
130775 AATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTG
1 -ATGACACGGTTCCTACGTGATGAGGAGAGCTGGTTATCT-AAGGTG
* *
130822 ATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGT-
1 ATGACACGGTTCCTACGTGATGAGGA-GAGCTGGTTATCTAAGGTG
* * * *
130866 -TGACACGGTTCCTACGTGATAAGGAAATCTGG---TCT--GGGG
1 ATGACACGGTTCCTACGTGATGAGGAGAGCTGGTTATCTAAGGTG
*
130905 ATGACACGGTTCCTACATGATGAGGA
1 ATGACACGGTTCCTACGTGATGAGGA
130931 CGGCTGGCCA
Statistics
Matches: 191, Mismatches: 31, Indels: 38
0.73 0.12 0.15
Matches are distributed among these distances:
38 4 0.02
40 57 0.30
42 1 0.01
43 56 0.29
45 8 0.04
46 62 0.32
47 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (45 bp):
ATGACACGGTTCCTACGTGATGAGGAGAGCTGGTTATCTAAGGTG
Found at i:130943 original size:129 final size:129
Alignment explanation
Indices: 130613--130927 Score: 542
Period size: 129 Copynumber: 2.4 Consensus size: 129
130603 AAGGTTAACG
* *
130613 CGGTTCCTACGTGATGAGGACATCTGGTC-GGGGAATGACACGGCTCATACGTGATGAAGAGTTC
1 CGGTTCCTACGTGATAAGGAAATCTGGTCTGGGG-ATGACACGGCTCATACGTGATGAAGAGTTC
130677 TGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACA
65 TGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACA
* * *
130742 CGGCTCCTACGTGATAAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGAGTTCT
1 CGGTTCCTACGTGATAAGGAAATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGAGTTCT
130807 GGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACA
66 GGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACA
* * *
130871 CGGTTCCTACGTGATAAGGAAATCTGGTCTGGGGATGACACGGTTCCTACATGATGA
1 CGGTTCCTACGTGATAAGGAAATCTGGTCTGGGGATGACACGGCTCATACGTGATGA
130928 GGACGGCTGG
Statistics
Matches: 175, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
129 172 0.98
130 3 0.02
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.26
Consensus pattern (129 bp):
CGGTTCCTACGTGATAAGGAAATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGAGTTCT
GGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACA
Found at i:131677 original size:31 final size:30
Alignment explanation
Indices: 131613--131687 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
131603 ATAGAAAATG
*
131613 TTTCAAGTGAAACGACTCAAAAATGGTTTTA
1 TTTCAAGTGAAACAACTCAAAAAT-GTTTTA
*
131644 TTTCAAGTGAAACAAACTCAAAGAT-TTTGTA
1 TTTCAAGTGAAAC-AACTCAAAAATGTTT-TA
* *
131675 TTTCTAGAGAAAC
1 TTTCAAGTGAAAC
131688 TGCCTCAAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 3 0.08
31 26 0.68
32 9 0.24
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (30 bp):
TTTCAAGTGAAACAACTCAAAAATGTTTTA
Found at i:131854 original size:63 final size:64
Alignment explanation
Indices: 131781--132289 Score: 215
Period size: 64 Copynumber: 8.2 Consensus size: 64
131771 AATGTGGGTA
* * *
131781 TTTTCAAAAGAAGTTGTC-TCGAGAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTT
* * *
131844 TTTTCAAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGA--T
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTT
*** * * * *
131906 GGATC-----ACA---TCTT-AAGTGAGACCAAA-TTTGTTTCAAATGAAACAATCTCAAA-AGT
1 TTTTCAAAAGAAATTGTCTTCAA--GAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGA-T
131960 TAGT
63 T--T
** * * * * *
131964 TTTTCATTAGAAACTGTC-TCAAGAGAGACAACA-TTTGTTT-TAAAGAAATAGACTCAAAGATG
1 TTTTCAAAAGAAATTGTCTTC-A-AGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT-
132026 ATT
63 -TT
* ** * * *
132029 TTGTT-AAGAGAAA-------CAA-ACTCAAAGA---T-TTTCAAGATG-AACATATTCAAAGAT
1 TT-TTCAAAAGAAATTGTCTTCAAGAGACAAA-ATTTTGTTTCAA-AAGAAACAAACTCAAAGAT
132080 TT
63 TT
** * * * * * * *
132082 ACTTCAAGAGAAACTGTC-TCAAGAGATACAAAATTCAT-TTT-AAGAGAAACAGATTCAAATAT
1 TTTTCAAAAGAAATTGTCTTCAAGAG--ACAAAATT-TTGTTTCAAAAGAAACAAACTCAAAGAT
132144 TT
63 TT
* * *
132146 TTTTCAAAAGAAATTATCTTAAAAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTT
1 TTTTCAAAAGAAATTGTCTT-CAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGA-TT
132211 T
64 T
* * * * *
132212 TGTTTTAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGA-T
1 T-TTTCAAAAGAAATTGTCTTCA-AGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATT
132276 T
64 T
132277 TTTTCAAAAGAAA
1 TTTTCAAAAGAAA
132290 CAATCTCAAA
Statistics
Matches: 339, Mismatches: 59, Indels: 95
0.69 0.12 0.19
Matches are distributed among these distances:
52 2 0.01
53 13 0.04
54 30 0.09
55 21 0.06
56 6 0.02
57 4 0.01
58 4 0.01
59 4 0.01
60 1 0.00
61 1 0.00
62 7 0.02
63 21 0.06
64 89 0.26
65 47 0.14
66 30 0.09
67 58 0.17
68 1 0.00
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.30
Consensus pattern (64 bp):
TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTT
Found at i:132017 original size:119 final size:119
Alignment explanation
Indices: 131803--132025 Score: 276
Period size: 119 Copynumber: 1.9 Consensus size: 119
131793 GTTGTCTCGA
* *
131803 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAATTGTCTTTAAG
1 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAACTGTCTTCAAG
*
131868 AGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATGGATCACATCTTAAGT
66 AGAGAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATGGATCACATCTTAAGT
* * * **
131922 GAGACCAAA-TTTGTTTCAAATGAAACAATCTCAAA-AGTTAGTTTTTCATTAGAAACTGTC-TC
1 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGA-TT--TTTTTCAAAAGAAACTGTCTTC
* *
131984 AAGAGAGACAACA-TTTGTTT-TAAAGAAATAGACTCAAAGATG
63 AAGAGAGA-AA-ATTTTGTTTCAAAAGAAACAGACTCAAAGATG
132026 ATTTTGTTAA
Statistics
Matches: 89, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
117 1 0.01
118 26 0.29
119 36 0.40
120 25 0.28
121 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (119 bp):
GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAACTGTCTTCAAG
AGAGAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATGGATCACATCTTAAGT
Found at i:132193 original size:37 final size:37
Alignment explanation
Indices: 132137--132263 Score: 108
Period size: 37 Copynumber: 3.6 Consensus size: 37
132127 GAAACAGATT
*
132137 CAAATATTTT-TTTCAAAAGAAATTATCTTAAAAGAGA
1 CAAA-ATTTTGTTTCAAAAGAAACTATCTTAAAAGAGA
* * * *
132174 CAAAATTTTGTTTCCAAAGAAACAAAC-T-CAA-AG-
1 CAAAATTTTGTTTCAAAAGAAACTATCTTAAAAGAGA
* * *
132207 ---ATTTTTGTTTTAAAAGAAACTATCTTAAGAGAGA
1 CAAAATTTTGTTTCAAAAGAAACTATCTTAAAAGAGA
*
132241 CAAAATTTTGTTTCCAAAGAAAC
1 CAAAATTTTGTTTCAAAAGAAAC
132264 AAACTCAAAG
Statistics
Matches: 67, Mismatches: 15, Indels: 16
0.68 0.15 0.16
Matches are distributed among these distances:
30 19 0.28
31 1 0.01
32 1 0.01
33 2 0.03
34 2 0.03
35 2 0.03
36 6 0.09
37 34 0.51
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (37 bp):
CAAAATTTTGTTTCAAAAGAAACTATCTTAAAAGAGA
Found at i:132243 original size:67 final size:68
Alignment explanation
Indices: 132146--132279 Score: 243
Period size: 67 Copynumber: 2.0 Consensus size: 68
132136 TCAAATATTT
*
132146 TTTTCAAAAGAAATTATCTTAAAAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTT
1 TTTTCAAAAGAAACTATCTTAAAAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTT
132211 TTG
66 TTG
*
132214 TTTT-AAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTT
1 TTTTCAAAAGAAACTATCTTAAAAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTT
132278 TT
66 TT
132280 TCAAAAGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
67 60 0.94
68 4 0.06
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (68 bp):
TTTTCAAAAGAAACTATCTTAAAAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTT
TTG
Found at i:132312 original size:67 final size:66
Alignment explanation
Indices: 132084--132298 Score: 226
Period size: 67 Copynumber: 3.3 Consensus size: 66
132074 AAAGATTTAC
* ** * * * * *
132084 TTCAAGAGAAACTGTCTCAAGAGATACAAAATTCAT-TTT--AAGAGAAACAGATTCAAATATTT
1 TTCAAAAGAAACAATCTCAAGAGAGACAAAATT-TTGTTTCCAA-AGAAACAAACTCAAAGATTT
132146 T-T
64 TGT
** * *
132148 TTCAAAAGAAATTATCTTAAAAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
1 TTCAAAAGAAACAATCTCAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGA-TTTT
132213 GT
65 GT
* * *
132215 TTTAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGA-TTT-
1 TTCAAAAGAAACAATCTCAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTG
132278 T
66 T
132279 TTCAAAAGAAACAATCTCAA
1 TTCAAAAGAAACAATCTCAA
132299 AGATTTTTTC
Statistics
Matches: 130, Mismatches: 16, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
63 1 0.01
64 48 0.37
65 17 0.13
66 6 0.05
67 58 0.45
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.30
Consensus pattern (66 bp):
TTCAAAAGAAACAATCTCAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTG
T
Found at i:132346 original size:29 final size:28
Alignment explanation
Indices: 132241--132671 Score: 311
Period size: 29 Copynumber: 14.8 Consensus size: 28
132231 TTAAGAGAGA
*
132241 CAAA-ATTTTGTTTCCAAAGAAACAAACT
1 CAAAGATTTT-TTTCAAAAGAAACAAACT
*
132269 CAAAGA-TTTTTTCAAAAGAAACAATCT
1 CAAAGATTTTTTTCAAAAGAAACAAACT
*
132296 CAAAGA-TTTTTTCAAAAGGAACAAACT
1 CAAAGATTTTTTTCAAAAGAAACAAACT
* *
132323 CCAAGATTTTTATTCAAAAGGAACAAACT
1 CAAAGATTTTT-TTCAAAAGAAACAAACT
* ***
132352 CAAAGA-TTTTTTCAAGAGAAACTGTCT
1 CAAAGATTTTTTTCAAAAGAAACAAACT
* * * *
132379 CAAGAGAGACAAAACTTTGTTTCAAAATAAATAGACT
1 C-A-A-AG-----A-TTTTTTTCAAAAGAAACAAACT
132416 CAAAGATTTTTTTCAAAAGAAAC-AACT
1 CAAAGATTTTTTTCAAAAGAAACAAACT
* *
132443 CAAAGATATTTATTCAAAAGGAACAAACT
1 CAAAGAT-TTTTTTCAAAAGAAACAAACT
* * *
132472 CCAAGATTTTTATTCAAAAGGAGCAAACT
1 CAAAGATTTTT-TTCAAAAGAAACAAACT
* ***
132501 CAAAGA-TTTTTTCAAGAGAAACTGTCT
1 CAAAGATTTTTTTCAAAAGAAACAAACT
* * * *
132528 CAAGAGAGACAAAACTTTGTTTCAAAATAAATAGACT
1 C-A-A-AG-----A-TTTTTTTCAAAAGAAACAAACT
132565 CAAAGA-TTTTTTCAAAAGAAAC-AACT
1 CAAAGATTTTTTTCAAAAGAAACAAACT
* *
132591 CAAAGATATTTATTCAAAAGGAACAAACT
1 CAAAGAT-TTTTTTCAAAAGAAACAAACT
* *
132620 CCAAGATTTTTATTCAAAAGGAACAAACT
1 CAAAGATTTTT-TTCAAAAGAAACAAACT
*
132649 CAAAGATTTTTTTCAAGAGAAAC
1 CAAAGATTTTTTTCAAAAGAAAC
132672 TGTCTCAAAA
Statistics
Matches: 323, Mismatches: 50, Indels: 60
0.75 0.12 0.14
Matches are distributed among these distances:
26 9 0.03
27 94 0.29
28 79 0.24
29 95 0.29
30 4 0.01
34 4 0.01
35 4 0.01
36 2 0.01
37 32 0.10
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (28 bp):
CAAAGATTTTTTTCAAAAGAAACAAACT
Found at i:132381 original size:27 final size:27
Alignment explanation
Indices: 132251--132373 Score: 174
Period size: 27 Copynumber: 4.5 Consensus size: 27
132241 CAAAATTTTG
*
132251 TTTCCAAAGAAACAAACTCAAAGATTT
1 TTTCAAAAGAAACAAACTCAAAGATTT
*
132278 TTTCAAAAGAAACAATCTCAAAGATTT
1 TTTCAAAAGAAACAAACTCAAAGATTT
* *
132305 TTTCAAAAGGAACAAACTCCAAGATTTT
1 TTTCAAAAGAAACAAACTCAAAGA-TTT
*
132333 TATTCAAAAGGAACAAACTCAAAGATTT
1 T-TTCAAAAGAAACAAACTCAAAGATTT
*
132361 TTTCAAGAGAAAC
1 TTTCAAAAGAAAC
132374 TGTCTCAAGA
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
27 56 0.65
28 8 0.09
29 22 0.26
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (27 bp):
TTTCAAAAGAAACAAACTCAAAGATTT
Found at i:132628 original size:148 final size:149
Alignment explanation
Indices: 132189--132690 Score: 832
Period size: 149 Copynumber: 3.4 Consensus size: 149
132179 TTTTGTTTCC
* * * * * *
132189 AAAGAAACAAACTCAAAGATTTTTGTTTTAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTT
1 AAAGGAACAAACTCAAAGA-TTTT-TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTT
* * * *
132254 CCAAAGAAACAAACTCAAAGATTTTTTCAAAAGAAACAATCTCAAAGAT-TTT-TTCAAAAGGAA
64 CAAAATAAATAGACTCAAAGATTTTTTCAAAAGAAACAA-CTCAAAGATATTTATTCAAAAGGAA
132317 CAAACTCCAAGATTTTTATTCA
128 CAAACTCCAAGATTTTTATTCA
132339 AAAGGAACAAACTCAAAGA-TTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 AAAGGAACAAACTCAAAGATTTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCA
132403 AAATAAATAGACTCAAAGATTTTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACA
66 AAATAAATAGACTCAAAGA-TTTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACA
132468 AACTCCAAGATTTTTATTCA
130 AACTCCAAGATTTTTATTCA
*
132488 AAAGGAGCAAACTCAAAGA-TTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 AAAGGAACAAACTCAAAGATTTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCA
132552 AAATAAATAGACTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAA
66 AAATAAATAGACTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAA
132617 ACTCCAAGATTTTTATTCA
131 ACTCCAAGATTTTTATTCA
*
132636 AAAGGAACAAACTCAAAGATTTTTTTCAAGAGAAACTGTCTCAAAAGAGACAAAA
1 AAAGGAACAAACTCAAAGATTTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
132691 AATATCGTTT
Statistics
Matches: 335, Mismatches: 13, Indels: 9
0.94 0.04 0.03
Matches are distributed among these distances:
147 61 0.18
148 107 0.32
149 149 0.44
150 18 0.05
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.27
Consensus pattern (149 bp):
AAAGGAACAAACTCAAAGATTTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCA
AAATAAATAGACTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAA
ACTCCAAGATTTTTATTCA
Found at i:132998 original size:36 final size:36
Alignment explanation
Indices: 132914--133219 Score: 144
Period size: 36 Copynumber: 8.8 Consensus size: 36
132904 GAGAAAATGA
* *
132914 TGTCTCAAGCGAGACAAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* **
132948 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
132984 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGGAAA-
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGA-GAAAT
* * * * *
133019 CGATCTCAAGTGAGATC-AACTTTG-TTTAATGTGAAA-
1 TG-TCTCAAGCGAGA-CAAAATTTGTTTTTA-GAGAAAT
** * * * *
133055 -----CAA---ATTCGAAATTTGTATCTCA-ATGAAAAA
1 TGTCTCAAGCGAGACAAAATTTGT-TTTTAGA-G-AAAT
* * * **
133085 TGTCTCCAGTGAGGCGGAATTTGTTTTTCA-AGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTT-AGAGAAAT
* *
133121 TGTCTCAAACGAGACAAAATTTGTTTTTAGA-AAGT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* * * *
133156 TGTCTCAATCGAGACAAAATTTGCTTTGAAAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
133192 TGTCTCAAGCTAGACAAAAATTTGTTTT
1 TGTCTCAAGCGAGAC-AAAATTTGTTTT
133220 AAAATTCTCA
Statistics
Matches: 205, Mismatches: 42, Indels: 47
0.70 0.14 0.16
Matches are distributed among these distances:
26 1 0.00
27 7 0.03
28 1 0.00
29 6 0.03
30 3 0.01
34 20 0.10
35 43 0.21
36 96 0.47
37 16 0.08
38 12 0.06
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:133814 original size:4 final size:4
Alignment explanation
Indices: 133765--133802 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
133755 TTTATGTATC
*
133765 ATGT ATGT ATG- -TGT ATGT ATGT ATAT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
133803 GTTGATGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 2 0.07
4 28 0.93
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:136822 original size:5 final size:5
Alignment explanation
Indices: 136812--136842 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
136802 CATTATGATG
136812 ATGCA ATGCA ATGCA ATGCA ATGCA ATGCA A
1 ATGCA ATGCA ATGCA ATGCA ATGCA ATGCA A
136843 ATGACAAAAT
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:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATGCA
Found at i:136910 original size:31 final size:32
Alignment explanation
Indices: 136854--136915 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
136844 TGACAAAATG
136854 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
136886 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
136916 CATGTAGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:139213 original size:9 final size:9
Alignment explanation
Indices: 139199--139225 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
139189 TGGCTTAAAA
139199 AAATATTAT
1 AAATATTAT
139208 AAATATTAT
1 AAATATTAT
139217 AAATATTAT
1 AAATATTAT
139226 TATTATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AAATATTAT
Found at i:139228 original size:3 final size:3
Alignment explanation
Indices: 139220--139251 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
139210 ATATTATAAA
139220 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
139252 AGTGTGTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:139232 original size:18 final size:18
Alignment explanation
Indices: 139199--139251 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
139189 TGGCTTAAAA
* *
139199 AAATATTATAAATATTAT
1 AAATATTATTATTATTAT
139217 AAATATTATTATTATTAT
1 AAATATTATTATTATTAT
* *
139235 TATTATTATTATTATTA
1 AAATATTATTATTATTA
139252 AGTGTGTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AAATATTATTATTATTAT
Found at i:140428 original size:15 final size:14
Alignment explanation
Indices: 140408--140445 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
140398 TTTGAGTTTA
*
140408 TATTTTGATATCTTT
1 TATTTT-ATATCCTT
140423 TATTTTA-ATCCTT
1 TATTTTATATCCTT
140436 TATTTTATAT
1 TATTTTATAT
140446 TTTAATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 12 0.57
14 3 0.14
15 6 0.29
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.66
Consensus pattern (14 bp):
TATTTTATATCCTT
Found at i:140446 original size:35 final size:35
Alignment explanation
Indices: 140404--140472 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
140394 TTATTTTGAG
* *
140404 TTTATATTTTGATATCTTTTATTTTAA-TCCTTTAT
1 TTTATATTTTAATATATTTTA-TTTAATTCCTTTAT
*
140439 TTTATATTTTAATTTATTTTATTTAATTCCTTTA
1 TTTATATTTTAATATATTTTATTTAATTCCTTTA
140473 ATTTCAGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 5 0.17
35 25 0.83
ACGTcount: A:0.25, C:0.07, G:0.01, T:0.67
Consensus pattern (35 bp):
TTTATATTTTAATATATTTTATTTAATTCCTTTAT
Found at i:140562 original size:22 final size:21
Alignment explanation
Indices: 140537--140584 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
140527 AAATTTAATC
*
140537 ATTTAACTATTATGTTTATTTT
1 ATTTAACTATT-TATTTATTTT
* *
140559 ATTTTAAGTGTTTATTTATTTT
1 A-TTTAACTATTTATTTATTTT
140581 ATTT
1 ATTT
140585 TTAGTCACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 3 0.14
22 11 0.50
23 8 0.36
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.67
Consensus pattern (21 bp):
ATTTAACTATTTATTTATTTT
Found at i:141566 original size:2 final size:2
Alignment explanation
Indices: 141561--141619 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
141551 TTTGTACGTG
141561 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
*
141603 TT TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
141620 TACAAATGAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Done.