Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002787.1 Hibiscus syriacus cultivar Beakdansim tig00005742_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: 53687
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:487 original size:2 final size:2
Alignment explanation
Indices: 480--548 Score: 115
Period size: 2 Copynumber: 35.5 Consensus size: 2
470 AGAGTGTTGA
480 AT AT AT AT AT AT AT AT A- 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
*
521 AA AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
549 ATAAAGAAAG
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
1 2 0.03
2 61 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13189 original size:19 final size:19
Alignment explanation
Indices: 13167--13212 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
13157 TCTATTACCC
13167 TTCCAAATGTATATATTCA
1 TTCCAAATGTATATATTCA
13186 TTCCAAATGTATATATTCA
1 TTCCAAATGTATATATTCA
13205 TTCCAAAT
1 TTCCAAAT
13213 TTTCTTTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.41
Consensus pattern (19 bp):
TTCCAAATGTATATATTCA
Found at i:15524 original size:28 final size:28
Alignment explanation
Indices: 15493--15560 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
15483 TACCTCGAGA
*
15493 AGAGAAAATCATAATTGAAACCTCAAAT
1 AGAGAAAATCATAATTCAAACCTCAAAT
*
15521 AGAGAAAATCACAATTCAAACCTCAAAT
1 AGAGAAAATCATAATTCAAACCTCAAAT
15549 AGAGAAAATCAT
1 AGAGAAAATCAT
15561 GTTTGGAGTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.54, C:0.16, G:0.10, T:0.19
Consensus pattern (28 bp):
AGAGAAAATCATAATTCAAACCTCAAAT
Found at i:16056 original size:101 final size:101
Alignment explanation
Indices: 15878--16217 Score: 361
Period size: 101 Copynumber: 3.4 Consensus size: 101
15868 ACGATAAAAA
** * * *
15878 TTATCTCACTTGAGATCCTTTTTCTTAAAATCAATTTCGTCTCACTTGAGACAGATTCCTTTGAA
1 TTATCTCACTTGAGATTATTTTTCTTAAAATCAATTTCGTCTCGCTTGAGATAGTTTCCTTTGAA
*
15943 GCACAAAATTTGGAATTGCTTCACTTGAAACAAGAT
66 ACACAAAATTTGGAATTGCTTCACTTGAAACAAGAT
* * *
15979 TTATCTCACTCGATATTGTTTTTCTTAAAATCAATTTCGTCTCGCTTGAGATAGTTTCCTTTGAA
1 TTATCTCACTTGAGATTATTTTTCTTAAAATCAATTTCGTCTCGCTTGAGATAGTTTCCTTTGAA
**
16044 ACACAAGTTTTGGGAA-TGCTTCA-TTCGAAACAAGAT
66 ACACAAAATTT-GGAATTGCTTCACTT-GAAACAAGAT
* * * * * *
16080 TTATCTGACTTGAGATTATTTTTCTTAAAGTCAATTTCATATTGCTTGA-ATCATTTTCCTCTT-
1 TTATCTCACTTGAGATTATTTTTCTTAAAATCAATTTCGTCTCGCTTGAGAT-AGTTTCCT-TTG
* *
16143 AAACATAAAATTTGGAATTGTTTCACTTGAAA-AA-ATT
64 AAACACAAAATTTGGAATTGCTTCACTTGAAACAAGA-T
* * * * *
16180 TTATCCCATTTGAGA-TATCTTTTATTGAAATAAATTTC
1 TTATCTCACTTGAGATTAT-TTTTCTTAAAATCAATTTC
16218 TTTTCTTTCA
Statistics
Matches: 201, Mismatches: 30, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
99 4 0.02
100 38 0.19
101 151 0.75
102 8 0.04
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.41
Consensus pattern (101 bp):
TTATCTCACTTGAGATTATTTTTCTTAAAATCAATTTCGTCTCGCTTGAGATAGTTTCCTTTGAA
ACACAAAATTTGGAATTGCTTCACTTGAAACAAGAT
Found at i:16559 original size:45 final size:43
Alignment explanation
Indices: 16437--16565 Score: 141
Period size: 45 Copynumber: 2.9 Consensus size: 43
16427 TTGTTCGTCC
* ** *
16437 TTTTGCTCGATTCTATCACAGAAGAAGGTATATCATCATCAACA
1 TTTTGCTCGATTCTATCACAGAAGGAGGTGGATCAT-ATTAACA
* * * **
16481 TTTTGTTCAATTCCATCACAGAAGGAGGTGGATCAATATTGTCA
1 TTTTGCTCGATTCTATCACAGAAGGAGGTGGATC-ATATTAACA
16525 TTCTTGCTCGATTCTATCACAGAAGGAGGTGGATCGATATT
1 TT-TTGCTCGATTCTATCACAGAAGGAGGTGGATC-ATATT
16566 TACAATGGAA
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
44 34 0.49
45 36 0.51
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (43 bp):
TTTTGCTCGATTCTATCACAGAAGGAGGTGGATCATATTAACA
Found at i:16695 original size:208 final size:208
Alignment explanation
Indices: 16329--16933 Score: 826
Period size: 208 Copynumber: 2.9 Consensus size: 208
16319 TTCAATTCAA
* * * * *
16329 TCCATCAAAGAAGGAGATGGATC-ATCATTTCCAATGGAAAGGTTCATAATGAGAATAACTCATC
1 TCCATCACAGAAGGAGGTGGATCGATCATTTCCAATGGAAGGGTTCATAATGAGAAGAACTCATA
* *
16393 CGAAGAGGGAGAAGAAATTCATAATAAGAAGAACTTGTTCG-TCCTTTTGCTCGATTCTATCACA
66 CGAAGAGGGAGAA-TAGTTCATAATAAGAAGAACTTGTTCGCT-CTTTTGCTCGATTCTATCACA
* * * * *
16457 GAAGAAGGTATATCATCATCAACATTTTGTTCAATTCCATCACAGAAGGAGGTGGATCAATATTG
129 GAATAAGGTAGATCAACACCAACATTTTGTTCGATTCCATCACAGAAGGAGGTGGATCAATATTG
16522 TCATTCTTG-CTCGAT
194 TCATTCTTGCCT-GAT
* * *
16537 TCTATCACAGAAGGAGGTGGATCGAT-ATTTACAATGGAAGGGTTCATAATGAAAAGAACTCATA
1 TCCATCACAGAAGGAGGTGGATCGATCATTTCCAATGGAAGGGTTCATAATGAGAAGAACTCATA
* *
16601 CGAAGAGGGAGAATTAGTTCATAATGAGAAGAACGTGTTCGCTCTTTTGCTCGATTCTATCACAG
66 CGAAGAGGGAGAA-TAGTTCATAATAAGAAGAACTTGTTCGCTCTTTTGCTCGATTCTATCACAG
* *
16666 AATAAGGTAGATCAACACCAACATTTTGTTCGATTCCATCATAGAAGGAGGTGGATAAATATTGT
130 AATAAGGTAGATCAACACCAACATTTTGTTCGATTCCATCACAGAAGGAGGTGGATCAATATTGT
16731 CATTCTTGCCTGAT
195 CATTCTTGCCTGAT
* * *
16745 TCCATCACAGAAAGAAGTGGATCG-TCATTTCCAATGGAAGGGTTCATAATGAGAAGAACTCGTC
1 TCCATCACAGAAGGAGGTGGATCGATCATTTCCAATGGAAGGGTTCATAATGAGAAGAACTCAT-
* * * * *
16809 TCGAAGAGGGAGAATAGGTTCATAATAAGAAGAACTTGTCCACCCTTTTGTTCGATTCTATCACA
65 ACGAAGAGGGAGAATA-GTTCATAATAAGAAGAACTTGTTCGCTCTTTTGCTCGATTCTATCACA
* * **
16874 GAATGAGGTAGATCAAC-CTCAACATTTTGTTCGATCCCATCACAGAATAAGGTGGATCAA
129 GAATAAGGTAGATCAACAC-CAACATTTTGTTCGATTCCATCACAGAAGGAGGTGGATCAA
16934 CATTTCCAAT
Statistics
Matches: 351, Mismatches: 39, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
207 1 0.00
208 238 0.68
209 112 0.32
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (208 bp):
TCCATCACAGAAGGAGGTGGATCGATCATTTCCAATGGAAGGGTTCATAATGAGAAGAACTCATA
CGAAGAGGGAGAATAGTTCATAATAAGAAGAACTTGTTCGCTCTTTTGCTCGATTCTATCACAGA
ATAAGGTAGATCAACACCAACATTTTGTTCGATTCCATCACAGAAGGAGGTGGATCAATATTGTC
ATTCTTGCCTGAT
Found at i:17046 original size:157 final size:164
Alignment explanation
Indices: 16746--17047 Score: 381
Period size: 164 Copynumber: 1.9 Consensus size: 164
16736 TTGCCTGATT
** *
16746 CCATCACAGAAAGAAGTGGATCGTCATTTCCAATGGAAGGGTTCATAATGAGAAGAACTCGTCTC
1 CCATCACAGAAAGAAGTGGATCAACATTTCCAATGGAAGGGTTCATAATGAGAAGAACTCATCTC
* * ** * *
16811 GAAGAGGGAGAATAGGTTCATAATAAGAAGAACTTGTCCACCCTTTTGTTCGATTCTATCACAGA
66 GAAGAGGAAGAATAGGTCCATAATAAGAAGAACTTGTCCACCCTTTTACTCAAATCTATCACAGA
*
16876 ATGAGGTAGATCAACCTCAACATTTTGTTCGATC
131 AGGAGGTAGATCAACCTCAACATTTTGTTCGATC
* * *
16910 CCATCACAGAATA-AGGTGGATCAACATTTCCAATGGAGGGGTTTATAATGAGAAGAACTCATC-
1 CCATCACAGAA-AGAAGTGGATCAACATTTCCAATGGAAGGGTTCATAATGAGAAGAACTCATCT
*
16973 C-AA-A-GAAG-A-A-GTCCATAATAAGAAGAACTTGTTCGA-CCTTTTACTCAAATCTATCACA
65 CGAAGAGGAAGAATAGGTCCATAATAAGAAGAACTTG-TCCACCCTTTTACTCAAATCTATCACA
17031 GAAGGAGGT-GAATCAAC
129 GAAGGAGGTAG-ATCAAC
17048 ATTTTAATGG
Statistics
Matches: 121, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
156 1 0.01
157 52 0.43
158 4 0.03
159 1 0.01
160 3 0.02
161 1 0.01
162 2 0.02
163 1 0.01
164 55 0.45
165 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.25
Consensus pattern (164 bp):
CCATCACAGAAAGAAGTGGATCAACATTTCCAATGGAAGGGTTCATAATGAGAAGAACTCATCTC
GAAGAGGAAGAATAGGTCCATAATAAGAAGAACTTGTCCACCCTTTTACTCAAATCTATCACAGA
AGGAGGTAGATCAACCTCAACATTTTGTTCGATC
Found at i:18295 original size:14 final size:14
Alignment explanation
Indices: 18206--18297 Score: 53
Period size: 14 Copynumber: 6.5 Consensus size: 14
18196 TTTTTATTTA
18206 TTTAATTTTAGTCC
1 TTTAATTTTAGTCC
* * *
18220 TTTAATTTCATTAC
1 TTTAATTTTAGTCC
*
18234 TTTAATTTTCTA-T-T
1 TTTAA-TTT-TAGTCC
* * *
18248 TTTTATTTTTGCCC
1 TTTAATTTTAGTCC
* * *
18262 TTCATTTTTCAGTAC
1 TTTAATTTT-AGTCC
18277 TTTAATTTTAGTCC
1 TTTAATTTTAGTCC
18291 TTTAATT
1 TTTAATT
18298 ATTGCGCTTT
Statistics
Matches: 55, Mismatches: 18, Indels: 10
0.66 0.22 0.12
Matches are distributed among these distances:
12 1 0.02
13 3 0.05
14 37 0.67
15 13 0.24
16 1 0.02
ACGTcount: A:0.21, C:0.14, G:0.04, T:0.61
Consensus pattern (14 bp):
TTTAATTTTAGTCC
Found at i:24452 original size:6 final size:6
Alignment explanation
Indices: 24443--24480 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
24433 ATGTATATGT
24443 TTGGGA TTGGGA TTGGGA TTGGGA TTGGGA TTGGGA TT
1 TTGGGA TTGGGA TTGGGA TTGGGA TTGGGA TTGGGA TT
24481 ATTAAGAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.16, C:0.00, G:0.47, T:0.37
Consensus pattern (6 bp):
TTGGGA
Found at i:37779 original size:18 final size:18
Alignment explanation
Indices: 37756--37801 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
37746 TATTCTCTTA
*
37756 TTTTTTTACTTTAATTGCT
1 TTTTTTTACTTTAATCG-T
37775 TTTTTTTA-TTTAATCGT
1 TTTTTTTACTTTAATCGT
*
37792 TTTTATTACT
1 TTTTTTTACT
37802 ACTTAAATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 8 0.33
18 8 0.33
19 8 0.33
ACGTcount: A:0.17, C:0.09, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTTTTTACTTTAATCGT
Found at i:40228 original size:11 final size:13
Alignment explanation
Indices: 40203--40231 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
40193 AGATAGAGAG
40203 AAAATATAGGAAA
1 AAAATATAGGAAA
40216 AAAATA-AGGAAA
1 AAAATATAGGAAA
40228 AAAA
1 AAAA
40232 GAGATAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (13 bp):
AAAATATAGGAAA
Found at i:40324 original size:34 final size:34
Alignment explanation
Indices: 40225--40325 Score: 93
Period size: 34 Copynumber: 3.0 Consensus size: 34
40215 AAAAATAAGG
* *
40225 AAAAAAAGAGATAAAAGATAGAAA-A-AGAAGAAAC
1 AAAAAAA-AAATAAAAGA-AAAAACATAGAAGAAAC
* **
40259 AAAAAAAAAATAAAAGAGAAATGATAGAAGAAAC
1 AAAAAAAAAATAAAAGAAAAAACATAGAAGAAAC
40293 GAGAAAAAAAAA-AAAAGAAAAAACATA-AAGAAA
1 -A-AAAAAAAAATAAAAGAAAAAACATAGAAGAAA
40326 ATAAATCAAG
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
32 2 0.04
33 10 0.18
34 22 0.39
35 13 0.23
36 9 0.16
ACGTcount: A:0.76, C:0.03, G:0.15, T:0.06
Consensus pattern (34 bp):
AAAAAAAAAATAAAAGAAAAAACATAGAAGAAAC
Found at i:45303 original size:7 final size:7
Alignment explanation
Indices: 45293--45317 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
45283 AACAAAAACA
45293 AAAAGAT
1 AAAAGAT
45300 AAAAGAT
1 AAAAGAT
45307 AAAAGAT
1 AAAAGAT
45314 AAAA
1 AAAA
45318 ACAAGAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAAGAT
Found at i:45303 original size:14 final size:14
Alignment explanation
Indices: 45266--45327 Score: 51
Period size: 14 Copynumber: 4.5 Consensus size: 14
45256 AAAAATATAT
45266 AAAAAGATAGAAAAC
1 AAAAAGATA-AAAAC
*
45281 --AAA-ACAAAAAC
1 AAAAAGATAAAAAC
45292 AAAAAGATAAAAGA-
1 AAAAAGATAAAA-AC
*
45306 TAAAAGATAAAAAC
1 AAAAAGATAAAAAC
45320 AAGAAAGA
1 AA-AAAGA
45328 AGAAGAAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
11 5 0.14
12 2 0.05
13 7 0.19
14 17 0.46
15 6 0.16
ACGTcount: A:0.76, C:0.06, G:0.11, T:0.06
Consensus pattern (14 bp):
AAAAAGATAAAAAC
Found at i:47861 original size:133 final size:134
Alignment explanation
Indices: 47659--48214 Score: 645
Period size: 134 Copynumber: 4.2 Consensus size: 134
47649 AGTCAAACTC
* * * * * *
47659 GATTCAATCTTCCCTGAAGAATAATAGAATGAATCAACATCCCCATATATGATTTTCCTTCAAGA
1 GATTCAATCTTCCCTGAGGAACAATAGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGA
** *
47724 AGAAGTGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAAAAGTGGAACAAGTCTA
66 AGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGGAACAAGTCTA
47789 CCTT
131 CCTT
* * * * *
47793 GATTCAATCTTCCATGAGGAACAATGGAATGAATTAACGT-CTCAGATCTGATTTTCCCTCAAAA
1 GATTCAATCTTCCCTGAGGAACAATAGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGA
* ** * * *
47857 AGAAGCATAACAAATCTTTGTTTTTCAAGATTTGATATTCCCTGAGTAATA-TAGGAACAAGTAT
66 AGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAATAGT-GGAACAAGTCT
* *
47921 GCCTA
130 ACCTT
* * * * * *
47926 GATTCAATCTTCCATGAGTAACAGTAGAATGAATCAATG-CCTCCAGATCTGATATTCCCTTAAG
1 GATTCAATCTTCCCTGAGGAACAATAGAATGAATCAACGTCC-CCAGATCTGATTTTCCCTCAAG
* ** * *
47990 AAGAAGCAAAACGGAT-CC-CTCTTTCAAGATTTGATCTTCCCTGAGTAACAGTGGAACAAGTCT
65 AAGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGGAACAAGTCT
*
48053 ACCTC
130 ACCTT
* ** * *
48058 GATTCAATCTTCCCTGAGTAACGGTGGAATGAATCAAAGTCCCCAGATCTGATTTTCCCTCAAGA
1 GATTCAATCTTCCCTGAGGAACAATAGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGA
* * **
48123 AGAAGTAGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGGTAGTGGAACAAGTCTA
66 AGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGGAACAAGTCTA
48188 CCTT
131 CCTT
* * *
48192 AATTCAATTTTCCCTGAAGAACA
1 GATTCAATCTTCCCTGAGGAACA
48215 GAGAAATAAG
Statistics
Matches: 352, Mismatches: 63, Indels: 14
0.82 0.15 0.03
Matches are distributed among these distances:
132 109 0.31
133 115 0.33
134 128 0.36
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (134 bp):
GATTCAATCTTCCCTGAGGAACAATAGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGA
AGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGGAACAAGTCTA
CCTT
Found at i:48263 original size:134 final size:134
Alignment explanation
Indices: 47685--48232 Score: 567
Period size: 133 Copynumber: 4.1 Consensus size: 134
47675 AAGAATAATA
* * * * * * *
47685 GAATGAATCAACATCCCCATATATGATTTTCCTTCAAGAAGAAGTGGAACAAATCCCTCTCTTTC
1 GAATGAATCAACGTTCTCAGATCTGATTTTCCCTCAAGAAGAAGTAGAACAAATCCCTCTCTTTC
* * *
47750 AAGATTTGATATTCCCTGAGTAAAAGTGGAACAAGTCTACCTTGATTCAATCTTCCATGAGGAAC
66 AAGATTTGATATTCCCTGAGTAATAGTGGAACAAGTCTACCTTAATTCAATCTTCCATGAGTAAC
47815 A-ATG
131 AGA-G
* * * * ** * *
47819 GAATGAATTAACG-TCTCAGATCTGATTTTCCCTCAAAAAGAAGCATAACAAATCTTTGTTTTTC
1 GAATGAATCAACGTTCTCAGATCTGATTTTCCCTCAAGAAGAAGTAGAACAAATCCCTCTCTTTC
* *
47883 AAGATTTGATATTCCCTGAGTAATA-TAGGAACAAGTATGCC-TAGATTCAATCTTCCATGAGTA
66 AAGATTTGATATTCCCTGAGTAATAGT-GGAACAAGTCTACCTTA-ATTCAATCTTCCATGAGTA
47946 ACAGTA-
129 ACAG-AG
* * * * * * **
47952 GAATGAATCAATG-CCTCCAGATCTGATATTCCCTTAAGAAGAAGCAAAACGGAT-CC-CTCTTT
1 GAATGAATCAACGTTCT-CAGATCTGATTTTCCCTCAAGAAGAAGTAGAACAAATCCCTCTCTTT
* * ** *
48014 CAAGATTTGATCTTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTCCCTGAGTAA
65 CAAGATTTGATATTCCCTGAGTAATAGTGGAACAAGTCTACCTTAATTCAATCTTCCATGAGTAA
* *
48079 CGGTG
130 CAGAG
* * * *
48084 GAATGAATCAAAGTCCCCAGATCTGATTTTCCCTCAAGAAGAAGTAGAACATATCCCTCTCTTTC
1 GAATGAATCAACGTTCTCAGATCTGATTTTCCCTCAAGAAGAAGTAGAACAAATCCCTCTCTTTC
** * *
48149 AAGATTTGATATTCCCTGAGTGGTAGTGGAACAAGTCTACCTTAATTCAATTTTCCCTGAAG-AA
66 AAGATTTGATATTCCCTGAGTAATAGTGGAACAAGTCTACCTTAATTCAATCTTCCATG-AGTAA
48213 CAGAG
130 CAGAG
*
48218 AAAT-AAGTCAACGTT
1 GAATGAA-TCAACGTT
48233 TCTCGATTTG
Statistics
Matches: 339, Mismatches: 62, Indels: 26
0.79 0.15 0.06
Matches are distributed among these distances:
132 106 0.31
133 115 0.34
134 115 0.34
135 3 0.01
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.29
Consensus pattern (134 bp):
GAATGAATCAACGTTCTCAGATCTGATTTTCCCTCAAGAAGAAGTAGAACAAATCCCTCTCTTTC
AAGATTTGATATTCCCTGAGTAATAGTGGAACAAGTCTACCTTAATTCAATCTTCCATGAGTAAC
AGAG
Found at i:48415 original size:3 final size:3
Alignment explanation
Indices: 48407--48447 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
48397 CGTTTTAATT
* *
48407 TTA TTA TTA TTA TTA TTG TTC TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
48448 TAACATTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:53234 original size:169 final size:173
Alignment explanation
Indices: 52917--53275 Score: 606
Period size: 171 Copynumber: 2.1 Consensus size: 173
52907 TGTGTATGTG
*
52917 TATATATATA-TATGT-TTGGTTATAGATTAAGTCTTATGGATTCTTTTATTTTTCCACGATAGA
1 TATATATATATTATATATTGGTTATAGATTAAGTCTTATGGATTCTTTTATTTTTCCACGATAGA
52980 GGTAAATGTCCTATAGTATTTTTTATGGGATTCTATTGTACAAAGAAATGTGAGTGCATAGCTTT
66 GGTAAATGTCCTATAGTATTTTTTATGGGATTCTATTGTACAAAGAAA-GTGAGTGCATAGCTTT
53045 TGCTTCGATAATTATTAAGTTTGG-TTTTTGTT-CCCATTTTTAT
130 TGCTTCGATAATTATTAAGTTTGGTTTTTTGTTCCCCA-TTTTAT
* *
53088 TATATATATATTATATATTGGTT-TAGATTAAGTCTTATGGATTC-TTTATTTTTCCTCGATTGA
1 TATATATATATTATATATTGGTTATAGATTAAGTCTTATGGATTCTTTTATTTTTCCACGATAGA
53151 GGTAAATGTCCTATAGTATTTTTTATGGGATTCTATTGTACAAAGAAA-TGAGTGCATAGCTTTT
66 GGTAAATGTCCTATAGTATTTTTTATGGGATTCTATTGTACAAAGAAAGTGAGTGCATAGCTTTT
*
53215 GCTTGGATAATTATTAAGTTTGGTTTTTTGTTCCCCATTTTAT
131 GCTTCGATAATTATTAAGTTTGGTTTTTTGTTCCCCATTTTAT
53258 TATATATATATATATATA
1 TATATATATAT-TATATA
53276 ATATATATAT
Statistics
Matches: 179, Mismatches: 4, Indels: 10
0.93 0.02 0.05
Matches are distributed among these distances:
169 38 0.21
170 25 0.14
171 85 0.47
172 25 0.14
173 6 0.03
ACGTcount: A:0.27, C:0.09, G:0.16, T:0.48
Consensus pattern (173 bp):
TATATATATATTATATATTGGTTATAGATTAAGTCTTATGGATTCTTTTATTTTTCCACGATAGA
GGTAAATGTCCTATAGTATTTTTTATGGGATTCTATTGTACAAAGAAAGTGAGTGCATAGCTTTT
GCTTCGATAATTATTAAGTTTGGTTTTTTGTTCCCCATTTTAT
Found at i:53265 original size:2 final size:2
Alignment explanation
Indices: 53258--53297 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
53248 CCCATTTTAT
53258 TA TA TA TA TA TA TA TA TA -A 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 TA TA TA TA TA TA TA T
53298 GTTTGGTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53315 original size:197 final size:197
Alignment explanation
Indices: 53088--53470 Score: 666
Period size: 198 Copynumber: 1.9 Consensus size: 197
53078 CCATTTTTAT
53088 TATATATATATTATATATTGGTTTAGATTAAGTCTTATGGATTC-TTTATTTTTCCTCGATTGAG
1 TATATATATATTATATATTGGTTTAGATTAAGTCTTATGGATTCTTTTATTTTTCCTCGATTGAG
53152 GTAAATGTCCTATAGTATTTTTTATGGGATTCTATTGTACAAAG-AA-ATGAGTGCATAGCTTTT
66 GTAAATGTCCTATAGTATTTTTTATGGGATTCTATTGTACAAAGAAATATGAGTGCATAGCTTTT
* *
53215 GCTTGGATAATTATTAAGTTTGGTTTTTTGTTCCCCA-TTTTATTATATATATATATATATAATA
131 GCTTCGATAATTATTAAGTTTGGTTTTATGTTCCCCATTTTTATTATATATATATATATATAATA
53279 TA
196 TA
*
53281 TATATATATATATATATGTTTGGTTTATAGATTAAGTCTTATGGATTCTTTTATTTTTCCTCGAT
1 TATATATATAT-TATAT-ATTGG-TT-TAGATTAAGTCTTATGGATTCTTTTATTTTTCCTCGAT
*
53346 TGAGGTAAATGTCCTATAGTATTTTTTATGGGATTTTATTGTACAAAGAAATATGAGTGCATAGC
62 TGAGGTAAATGTCCTATAGTATTTTTTATGGGATTCTATTGTACAAAGAAATATGAGTGCATAGC
53411 TTTTGCTTCGATAATTATTAAGTTTGGTTTTATGTTCCCCATTTTTATTATATATATATA
127 TTTTGCTTCGATAATTATTAAGTTTGGTTTTATGTTCCCCATTTTTATTATATATATATA
53471 CATAAAAACT
Statistics
Matches: 178, Mismatches: 4, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
193 11 0.06
194 5 0.03
195 4 0.02
196 2 0.01
197 21 0.12
198 63 0.35
199 2 0.01
200 52 0.29
201 18 0.10
ACGTcount: A:0.28, C:0.08, G:0.15, T:0.49
Consensus pattern (197 bp):
TATATATATATTATATATTGGTTTAGATTAAGTCTTATGGATTCTTTTATTTTTCCTCGATTGAG
GTAAATGTCCTATAGTATTTTTTATGGGATTCTATTGTACAAAGAAATATGAGTGCATAGCTTTT
GCTTCGATAATTATTAAGTTTGGTTTTATGTTCCCCATTTTTATTATATATATATATATATAATA
TA
Done.