Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008254.1 Hibiscus syriacus cultivar Beakdansim tig00110907_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: 246921
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
File 2 of 2
Found at i:231933 original size:14 final size:14
Alignment explanation
Indices: 231914--231966 Score: 81
Period size: 14 Copynumber: 3.8 Consensus size: 14
231904 TTTTGAAATA
231914 TATATTATATAGTT
1 TATATTATATAGTT
*
231928 TATATTATATAGTA
1 TATATTATATAGTT
231942 TATATTATATAGTT
1 TATATTATATAGTT
231956 TA-ATTAATATA
1 TATATT-ATATA
231967 TTTTTATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
13 3 0.08
14 33 0.92
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (14 bp):
TATATTATATAGTT
Found at i:231943 original size:28 final size:28
Alignment explanation
Indices: 231912--231966 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
231902 ATTTTTGAAA
231912 TATATATTATATAGTTTATATT-ATATAG
1 TATATATTATATAGTTTA-ATTAATATAG
231940 TATATATTATATAGTTTAATTAATATA
1 TATATATTATATAGTTTAATTAATATA
231967 TTTTTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 3 0.12
28 23 0.88
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (28 bp):
TATATATTATATAGTTTAATTAATATAG
Found at i:233239 original size:10 final size:10
Alignment explanation
Indices: 233226--233357 Score: 51
Period size: 11 Copynumber: 12.8 Consensus size: 10
233216 TATTTAATAC
233226 TTTTTATTAT
1 TTTTTATTAT
*
233236 TTTTT-GTAT
1 TTTTTATTAT
233245 TTTTTATTTAT
1 TTTTTA-TTAT
233256 TTTTCCT-TTGAT
1 TTTT--TATT-AT
**
233268 TAGTT-TTAT
1 TTTTTATTAT
*
233277 TTGTTATT-T
1 TTTTTATTAT
233286 TATTTTATTTAT
1 T-TTTTA-TTAT
233298 TTTTTA--AT
1 TTTTTATTAT
* *
233306 TTTTAATAAT
1 TTTTTATTAT
233316 TTTTATATATAT
1 TTTT-TAT-TAT
* *
233328 TTTTAATTTT
1 TTTTTATTAT
*
233338 TTTCTTTTTAT
1 TTT-TTATTAT
233349 TTATTTATT
1 TT-TTTATT
233358 TTCTCTAATA
Statistics
Matches: 92, Mismatches: 15, Indels: 29
0.68 0.11 0.21
Matches are distributed among these distances:
8 7 0.08
9 16 0.17
10 25 0.27
11 30 0.33
12 13 0.14
13 1 0.01
ACGTcount: A:0.20, C:0.02, G:0.03, T:0.74
Consensus pattern (10 bp):
TTTTTATTAT
Found at i:233293 original size:17 final size:17
Alignment explanation
Indices: 233271--233308 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
233261 CTTTGATTAG
*
233271 TTTTATTTGTTATTTT-A
1 TTTTATTTATT-TTTTAA
233288 TTTTATTTATTTTTTAA
1 TTTTATTTATTTTTTAA
233305 TTTT
1 TTTT
233309 TAATAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTATTTATTTTTTAA
Found at i:237365 original size:96 final size:98
Alignment explanation
Indices: 237111--237348 Score: 331
Period size: 100 Copynumber: 2.4 Consensus size: 98
237101 TTACATATAT
* * *
237111 ACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGATTAAACGCGCCGGCTTTATGGATATGATT
1 ACAAT-AA-CTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGATATGATT
237176 CAGCTAAGCCTGATAAAGGTGATTATAATATCTAA
64 CAGCTAAGCCTGATAAAGGTGATTATAATATCTAA
237211 ACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGATAAT-AT
1 ACAAT-AA-CTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGAT-ATGAT
*
237275 TCAGCT-AGCCTGATAAATGTGATTATAATATCTACA
63 TCAGCTAAGCCTGATAAAGGTGATTATAATATCTA-A
* * *
237311 ACGAT-A-TTGAGATGTCCCTCTAGAGTAATTGGTTAAAC
1 ACAATAACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAAC
237349 TCTCTGGATT
Statistics
Matches: 129, Mismatches: 7, Indels: 8
0.90 0.05 0.06
Matches are distributed among these distances:
96 30 0.23
98 1 0.01
99 27 0.21
100 69 0.53
101 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Consensus pattern (98 bp):
ACAATAACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGATATGATTCA
GCTAAGCCTGATAAAGGTGATTATAATATCTAA
Found at i:238621 original size:84 final size:84
Alignment explanation
Indices: 238445--238865 Score: 515
Period size: 84 Copynumber: 5.0 Consensus size: 84
238435 CTTAGAAACT
* **
238445 ATCATTTGCAGTATAACTCAAGGCTAGAAGGGTTATCTGCCCCCAAAA-ACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
*
238509 ACGATCAGCTCCAAGGCAC
66 ACGTTCAGCTCCAAGGCAC
* * * *
238528 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAAGACGTTCGAGATCAACT
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
*
238593 ACGTTCAGCTCCAAGGCAT
66 ACGTTCAGCTCCAAGGCAC
* * * *
238612 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAGGACCTTTGAGTTTGACT
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
*
238677 ACGCTCAGCTCCAAGGCAC
66 ACGTTCAGCTCCAAGGCAC
* * * * * * * *
238696 ATCATTTGCAACATAGCTCAATGCTAGAAGGGCTAT-TGGTCATCAAAATACCTTCGAGTTTGAC
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCT-GCCAACAAAAGACCTTCGAGTTCGAC
* *
238760 TACGTTCAACAT-CAAGGCAT
65 TACGTTCAGC-TCCAAGGCAC
* * * * * *
238780 ATCATTTGCAGTATAACTCAAGGTTAAAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTTGACT
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
* *
238845 ACGCTCAGCCCCAAGGCAC
66 ACGTTCAGCTCCAAGGCAC
238864 AT
1 AT
238866 TATCAACTCC
Statistics
Matches: 287, Mismatches: 46, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
83 47 0.16
84 238 0.83
85 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (84 bp):
ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
ACGTTCAGCTCCAAGGCAC
Found at i:238726 original size:168 final size:168
Alignment explanation
Indices: 238444--238865 Score: 607
Period size: 168 Copynumber: 2.5 Consensus size: 168
238434 TCTTAGAAAC
* * * *
238444 TATCATTTGCAGTATAACTCAAGGCTAGAAGGGTTATCTGCC-CCCAAAAACCTTCGAGTTCGAC
1 TATCATTTGCAGTATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTTGAC
* * *
238508 TACGATCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCT-GCCACC
66 TACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGCTAT-TGGCCACC
* *
238572 AAAAGACGTTCGAGATCAACTACGTTCAGC-TCCAAGGCA
130 AAAAGACCTTCGAGATCAACTACGTTCAACAT-CAAGGCA
* *
238611 TATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAGGACCTTTGAGTTTGAC
1 TATCATTTGCAGTATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTTGAC
* * * *
238676 TACGCTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAATGCTAGAAGGGCTATTGGTCATCA
66 TACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGCTATTGGCCACCA
* * **
238741 AAATACCTTCGAGTTTGACTACGTTCAACATCAAGGCA
131 AAAGACCTTCGAGATCAACTACGTTCAACATCAAGGCA
* *
238779 TATCATTTGCAGTATAACTCAAGGTTAAAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTTGAC
1 TATCATTTGCAGTATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTTGAC
*
238844 TACGCTCAGCCCCAAGGCACAT
66 TACGCTCAGCTCCAAGGCACAT
238866 TATCAACTCC
Statistics
Matches: 228, Mismatches: 24, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
167 42 0.18
168 185 0.81
169 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (168 bp):
TATCATTTGCAGTATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTTGAC
TACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGCTATTGGCCACCA
AAAGACCTTCGAGATCAACTACGTTCAACATCAAGGCA
Found at i:238944 original size:103 final size:103
Alignment explanation
Indices: 238772--238968 Score: 322
Period size: 103 Copynumber: 1.9 Consensus size: 103
238762 CGTTCAACAT
* * * *
238772 CAAGGCATATCATTTGCAGTATAACTCAAGGTTAAAAGGGTTATCTGCCAACCAAAGACCTTTGA
1 CAAGGCATATAATTTGCAGCATAACTCAAGGCTAAAAGGGTTATCTACCAACCAAAGACCTTTGA
* *
238837 GTTTGACTACGCTCAGCCCCAAGGCACATTATCAACTC
66 GTTTGACTACGCTCAACCCCAAGGAACATTATCAACTC
*
238875 CAAGGCATATAATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTACCAACCAAAGACCTTTGA
1 CAAGGCATATAATTTGCAGCATAACTCAAGGCTAAAAGGGTTATCTACCAACCAAAGACCTTTGA
*
238940 GTTTGACTACGCTCAACCTCAAGGAACAT
66 GTTTGACTACGCTCAACCCCAAGGAACAT
238969 CATTTAGTAT
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
103 86 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (103 bp):
CAAGGCATATAATTTGCAGCATAACTCAAGGCTAAAAGGGTTATCTACCAACCAAAGACCTTTGA
GTTTGACTACGCTCAACCCCAAGGAACATTATCAACTC
Found at i:239116 original size:269 final size:270
Alignment explanation
Indices: 238601--239134 Score: 763
Period size: 269 Copynumber: 2.0 Consensus size: 270
238591 CTACGTTCAG
* * *
238601 CTCCAAGGCATATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAGGACCTT
1 CTCCAAGGCATATAATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTACCAACCAAAGACCTT
* * *
238666 TGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAATGCTAGAAGGGCTA
66 TGAGTTTGACTACGCTCACCTCCAAGGAACATCATTT-CAACATAGCTCAAGGCTAGAAGGGCTA
* * * * *
238731 TTGGTCATCAAAATACCTTCGAGTTTGACTACGTTCAACATCAAGGCATATCATTTGCAGTATAA
130 TTGGACATCAAAAGACCTTCGAGTTCGACTACGTTCAACATCAAGGAATATCATTTGCAGCATAA
* * * * *
238796 CTCAAGGTTAAAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTTGACTACGCTCAGCCCCAAGG
195 CTCAAGGCTAAAAGGGTTATCTACCAACCAAAGAACTTCGAGTTCGACTACGCTCAGCCCCAAGG
238861 CACATTATCAA
260 CACATTATCAA
238872 CTCCAAGGCATATAATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTACCAACCAAAGACCTT
1 CTCCAAGGCATATAATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTACCAACCAAAGACCTT
** *
238937 TGAGTTTGACTACGCTCAACCT-CAAGGAACATCATTT-AGTATAGCTCAAGGCTATAAGGGCTA
66 TGAGTTTGACTACGCTC-ACCTCCAAGGAACATCATTTCAACATAGCTCAAGGCTAGAAGGGCTA
* * *
239000 TCT-GACATCAAAAGATCTTCGAGTTCGACTACGTTCAGC-TCCAAGGAATATCATTTG-TGACA
130 T-TGGACATCAAAAGACCTTCGAGTTCGACTACGTTCAACAT-CAAGGAATATCATTTGCAG-CA
* * *
239062 TAACTCAAGGCTAGAATGGTTATCTACCAACCAAAGAACTTCGAGTTCGACTACGCTCAGCTCCA
192 TAACTCAAGGCTAAAAGGGTTATCTACCAACCAAAGAACTTCGAGTTCGACTACGCTCAGCCCCA
239127 AGGCACAT
257 AGGCACAT
239135 CATTTGTAAC
Statistics
Matches: 234, Mismatches: 25, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
268 2 0.01
269 135 0.58
270 1 0.00
271 93 0.40
272 3 0.01
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (270 bp):
CTCCAAGGCATATAATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTACCAACCAAAGACCTT
TGAGTTTGACTACGCTCACCTCCAAGGAACATCATTTCAACATAGCTCAAGGCTAGAAGGGCTAT
TGGACATCAAAAGACCTTCGAGTTCGACTACGTTCAACATCAAGGAATATCATTTGCAGCATAAC
TCAAGGCTAAAAGGGTTATCTACCAACCAAAGAACTTCGAGTTCGACTACGCTCAGCCCCAAGGC
ACATTATCAA
Found at i:239675 original size:84 final size:84
Alignment explanation
Indices: 238872--239675 Score: 895
Period size: 84 Copynumber: 9.6 Consensus size: 84
238862 ACATTATCAA
* * * *
238872 CTCCAAGGCATATAATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTACCAACCAAAGACCTT
1 CTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTT
* * *
238937 TGAGTTTGACTACGCTCAA
66 CGAGTTCGACTACGCTCAG
* * * * * * * *
238956 C-CTCAAGGAACATCATTT--AGTATAGCTCAAGGCTATAAGGGCTATCTGACATCAAAAGATCT
1 CTC-CAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCT
*
239018 TCGAGTTCGACTACGTTCAG
65 TCGAGTTCGACTACGCTCAG
* * * * * * *
239038 CTCCAAGGAATATCATTTG-TGACATAACTCAAGGCTAGAATGGTTATCTACCAACCAAAGAACT
1 CTCCAAGGCACATCATTTGCAG-CATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCT
239102 TCGAGTTCGACTACGCTCAG
65 TCGAGTTCGACTACGCTCAG
* * * * * * *
239122 CTCCAAGGCACATCATTTGTAACATAGCTCAAGGCAAGAAGGGCTATTTACCAACAAAAGACCTT
1 CTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTT
* *
239187 CGAGTTTGACTACGCTTAG
66 CGAGTTCGACTACGCTCAG
* * * *
239206 CTCCAAAGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCTAACAAAAGAGCTT
1 CTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTT
* *
239271 TGAGTTCGACTACGCAT-AA
66 CGAGTTCGACTACGC-TCAG
* * ** * * * * *
239290 CTCCAAGGCACATCATTTACAACATAGTTCATGGCAACAAGGGCTATTTGCCAACAAAAGACCTT
1 CTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTT
* *
239355 CGAGTTCGACTACGTTCAA
66 CGAGTTCGACTACGCTCAG
* * * *
239374 CTCCATGACATATGATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTT
1 CTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTT
239439 CGAGTTCGACTACGCTCAG
66 CGAGTTCGACTACGCTCAG
* * *
239458 CTCCAAGGCACATCATTTGCAACATAACTCAAGG-TAAGAAGGGTTATTTTCCAACAAAAGACCT
1 CTCCAAGGCACATCATTTGCAGCATAACTCAAGGCT-AGAAGGGTTATCTGCCAACAAAAGACCT
239522 TCGAGTTCGACTACGCTCAG
65 TCGAGTTCGACTACGCTCAG
* * * *
239542 TTCCAAGGCACATCATTTGCATCATAACTTAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTT
1 CTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTT
* * *
239607 CGAGTTCGATTACACTCAA
66 CGAGTTCGACTACGCTCAG
* ** *
239626 CTCAAAGGCACAAT-ATTTATAGCATAGA-TCAAGGCAAGAAGGGTTATCTG
1 CTCCAAGGCAC-ATCATTTGCAGCATA-ACTCAAGGCTAGAAGGGTTATCTG
239676 TTACCCAAAT
Statistics
Matches: 601, Mismatches: 108, Indels: 22
0.82 0.15 0.03
Matches are distributed among these distances:
82 66 0.11
83 5 0.01
84 525 0.87
85 5 0.01
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (84 bp):
CTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTT
CGAGTTCGACTACGCTCAG
Found at i:240225 original size:2 final size:2
Alignment explanation
Indices: 240218--240257 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
240208 CACCCAGAGT
*
240218 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
240258 GTAATATAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:240305 original size:25 final size:24
Alignment explanation
Indices: 240277--240339 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 24
240267 TTTTTAAAAT
240277 GTTTTTGAAATAAATATATAATATA
1 GTTTTTGAAA-AAATATATAATATA
* *
240302 G-TTTTGAAAACATTTATATTATATA
1 GTTTTTGAAAA-A-ATATATAATATA
*
240327 GTTTTTAAAAAAA
1 GTTTTTGAAAAAA
240340 ATCATTTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
23 1 0.03
24 9 0.29
25 13 0.42
26 8 0.26
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (24 bp):
GTTTTTGAAAAAATATATAATATA
Found at i:240361 original size:41 final size:38
Alignment explanation
Indices: 240303--240489 Score: 105
Period size: 36 Copynumber: 5.1 Consensus size: 38
240293 TATAATATAG
* *
240303 TTTTGAAAACATTTATAT-TATATAGTTTTTAAAAAAAATCA
1 TTTTGAAAAAATATATATATATATAGTTTTT---AAAAA-CA
* *
240344 TTTTGAAAAAATATATATAATATGTAGTTTTTCAAAACA
1 TTTTGAAAAAATATATAT-ATATATAGTTTTTAAAAACA
* * **
240383 TTTTG----AA-A-ATA-ATATATAGATTTGAAAAGTA
1 TTTTGAAAAAATATATATATATATAGTTTTTAAAAACA
*
240414 TTTT-AAAAAACT-TATATAATATATAG--TTTAAAAAAA
1 TTTTGAAAAAA-TATATAT-ATATATAGTTTTTAAAAACA
* * *
240450 ATTTGAAAAATTATATA-ATATATA-ATTTTAAAAACA
1 TTTTGAAAAAATATATATATATATAGTTTTTAAAAACA
240486 TTTT
1 TTTT
240490 TTAAAACTTA
Statistics
Matches: 114, Mismatches: 17, Indels: 35
0.69 0.10 0.21
Matches are distributed among these distances:
31 18 0.16
33 3 0.03
34 3 0.03
35 9 0.08
36 26 0.23
37 9 0.08
38 8 0.07
39 7 0.06
40 4 0.04
41 16 0.14
43 11 0.10
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (38 bp):
TTTTGAAAAAATATATATATATATAGTTTTTAAAAACA
Found at i:240470 original size:35 final size:35
Alignment explanation
Indices: 240391--240542 Score: 132
Period size: 36 Copynumber: 4.3 Consensus size: 35
240381 CATTTTGAAA
** *
240391 ATAATATATAGATTTGAAAAGTATTTTAAAAAACTTAT
1 ATAATATATAG-TTT-AAAAAAATTTTGAAAAA-TTAT
*
240429 ATAATATATAGTTTAAAAAAAATTTGAAAAATTAT
1 ATAATATATAGTTTAAAAAAATTTTGAAAAATTAT
* * * *
240464 ATAATATATAATTTTAAAAACATTTTTTAAAACTTAT
1 ATAATATAT-AGTTTAAAAA-AATTTTGAAAAATTAT
** *
240501 ATAATAT-T--TTTAAATCATTTTTG-AAAATTAT
1 ATAATATATAGTTTAAAAAAATTTTGAAAAATTAT
240532 ATAATATATAG
1 ATAATATATAG
240543 CGTTGAAAAC
Statistics
Matches: 96, Mismatches: 13, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
31 14 0.15
32 7 0.07
33 6 0.06
35 13 0.14
36 23 0.24
37 22 0.23
38 11 0.11
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.43
Consensus pattern (35 bp):
ATAATATATAGTTTAAAAAAATTTTGAAAAATTAT
Found at i:240473 original size:37 final size:37
Alignment explanation
Indices: 240419--240507 Score: 110
Period size: 37 Copynumber: 2.4 Consensus size: 37
240409 AAGTATTTTA
240419 AAAAACTTATATAATATAT-AGTTTAAAAA-AAATTTG
1 AAAAA-TTATATAATATATAAGTTTAAAAACAAATTTG
* ** *
240455 AAAAATTATATAATATATAATTTTAAAAACATTTTTT
1 AAAAATTATATAATATATAAGTTTAAAAACAAATTTG
*
240492 AAAACTTATATAATAT
1 AAAAATTATATAATAT
240508 TTTTAAATCA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
35 13 0.28
36 14 0.30
37 19 0.41
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.40
Consensus pattern (37 bp):
AAAAATTATATAATATATAAGTTTAAAAACAAATTTG
Found at i:240512 original size:33 final size:34
Alignment explanation
Indices: 240372--240540 Score: 127
Period size: 32 Copynumber: 5.0 Consensus size: 34
240362 AATATGTAGT
* * *
240372 TTTTCAAAACA-TTTTGAAAA-TAATAT-ATAGA
1 TTTTAAAAACATTTTTGAAAACTTATATAATATA
* ** **
240403 TTTGAAAAGTATTTTAAAAAACTTATATAATATA
1 TTTTAAAAACATTTTTGAAAACTTATATAATATA
** *
240437 TAGTTTAAAAA-AAATTTGAAAAATTATATAATATATAA
1 T--TTTAAAAACATTTTTGAAAACTTATAT-A-ATAT-A
*
240475 TTTTAAAAACATTTTTTAAAACTTATATAATAT-
1 TTTTAAAAACATTTTTGAAAACTTATATAATATA
*
240508 TTTT-AAATCATTTTTGAAAA-TTATATAATATA
1 TTTTAAAAACATTTTTGAAAACTTATATAATATA
240540 T
1 T
240541 AGCGTTGAAA
Statistics
Matches: 107, Mismatches: 21, Indels: 19
0.73 0.14 0.13
Matches are distributed among these distances:
31 18 0.17
32 22 0.21
33 9 0.08
34 5 0.05
35 17 0.16
36 16 0.15
37 18 0.17
38 2 0.02
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (34 bp):
TTTTAAAAACATTTTTGAAAACTTATATAATATA
Found at i:240532 original size:31 final size:33
Alignment explanation
Indices: 240372--240540 Score: 123
Period size: 36 Copynumber: 5.0 Consensus size: 33
240362 AATATGTAGT
* * *
240372 TTTTCAAAACA-TTTTGAAAATAATAT-ATAGA
1 TTTTAAAAACATTTTTGAAAATTATATAATATA
* ** **
240403 TTTGAAAAGTATTTTAAAAAACTTATATAATATA
1 TTTTAAAAACATTTTTGAAAA-TTATATAATATA
**
240437 TAGTTTAAAAA-AAATTTGAAAAATTATATAATATATAA
1 T--TTTAAAAACATTTTTG-AAAATTATAT-A-ATAT-A
*
240475 TTTTAAAAACATTTTTTAAAACTTATATAATAT-
1 TTTTAAAAACATTTTTGAAAA-TTATATAATATA
*
240508 TTTT-AAATCATTTTTGAAAATTATATAATATA
1 TTTTAAAAACATTTTTGAAAATTATATAATATA
240540 T
1 T
240541 AGCGTTGAAA
Statistics
Matches: 107, Mismatches: 19, Indels: 23
0.72 0.13 0.15
Matches are distributed among these distances:
31 18 0.17
32 22 0.21
33 9 0.08
34 5 0.05
35 13 0.12
36 24 0.22
37 14 0.13
38 2 0.02
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (33 bp):
TTTTAAAAACATTTTTGAAAATTATATAATATA
Found at i:240552 original size:68 final size:71
Alignment explanation
Indices: 240391--240582 Score: 186
Period size: 68 Copynumber: 2.8 Consensus size: 71
240381 CATTTTGAAA
* *
240391 ATAATATATAGATTTGAAAAGTATTTTAAAAAACTTATATAATATATAGTTTAAAAAAAATTTGA
1 ATAATATATAGATTTGAAAA-CATTTTTAAAAACTTATATAATATATA-TTTAAAAAAAATTTGA
240456 AAAATTAT
64 AAAATTAT
* * ** **
240464 ATAATATATA-ATTTTAAAAACATTTTTTAAAACTTATATAATAT-T-TTTAAATCATTTTTG-A
1 ATAATATATAGA-TTTGAAAACATTTTTAAAAACTTATATAATATATATTTAAAAAAAATTTGAA
240525 AAATTAT
65 AAATTAT
** *
240532 ATAATATATAGCGTTGAAAAC-TTTTT-AAGA---ATATAATATATAGTTTAAAAA
1 ATAATATATAGATTTGAAAACATTTTTAAAAACTTATATAATATATA-TTTAAAAA
240583 TATTATATAT
Statistics
Matches: 100, Mismatches: 14, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
63 9 0.09
64 1 0.01
66 9 0.09
67 5 0.05
68 25 0.25
69 11 0.11
71 1 0.01
72 22 0.22
73 17 0.17
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (71 bp):
ATAATATATAGATTTGAAAACATTTTTAAAAACTTATATAATATATATTTAAAAAAAATTTGAAA
AATTAT
Found at i:240584 original size:20 final size:20
Alignment explanation
Indices: 240555--240615 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 20
240545 TTGAAAACTT
*
240555 TTTAAGAATATAATATATAG
1 TTTAAAAATATAATATATAG
*
240575 TTTAAAAATATTATATATA-
1 TTTAAAAATATAATATATAG
* *
240594 TTT--ATATATATTATATAG
1 TTTAAAAATATAATATATAG
240612 TTTA
1 TTTA
240616 TATTATATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
17 11 0.32
18 3 0.09
19 3 0.09
20 17 0.50
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
TTTAAAAATATAATATATAG
Found at i:240608 original size:17 final size:17
Alignment explanation
Indices: 240588--240639 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
240578 AAAAATATTA
240588 TATATATTTATATATAT
1 TATATATTTATATATAT
240605 TATATAGTTTATATTATAT
1 TATATA-TTTATA-TATAT
*
240624 TAT-TAATTA-ATATAT
1 TATATATTTATATATAT
240639 T
1 T
240640 TTTATTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 6 0.19
16 1 0.03
17 9 0.28
18 8 0.25
19 8 0.25
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
TATATATTTATATATAT
Found at i:241925 original size:3 final size:3
Alignment explanation
Indices: 241862--241911 Score: 84
Period size: 3 Copynumber: 16.7 Consensus size: 3
241852 TTTTAATCAT
241862 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
241907 TTA TT
1 TTA TT
241912 TACCTCTTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 1 0.02
3 43 0.96
4 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:241939 original size:20 final size:20
Alignment explanation
Indices: 241877--241941 Score: 69
Period size: 21 Copynumber: 3.2 Consensus size: 20
241867 ATTATTATTA
* *
241877 TTATTATTATTATTTATATTA
1 TTATTATTATTATTTACA-TC
*
241898 TTATTATTATTATTTACCTC
1 TTATTATTATTATTTACATC
*
241918 TTATTATTCTTTATTT-CATC
1 TTATTATT-ATTATTTACATC
241938 TTAT
1 TTAT
241942 ATTTTTTTGG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
20 16 0.42
21 22 0.58
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTATTATTATTTACATC
Found at i:241986 original size:19 final size:22
Alignment explanation
Indices: 241964--242009 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 22
241954 TATTTAATAC
241964 TTTTTATTATT-TTTTT-TGT-
1 TTTTTATTATTATTTTTATGTA
241983 TTTTTATTATTATTTTTATGTA
1 TTTTTATTATTATTTTTATGTA
242005 TTTTT
1 TTTTT
242010 CCTTTGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.46
20 5 0.21
21 3 0.12
22 5 0.21
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.80
Consensus pattern (22 bp):
TTTTTATTATTATTTTTATGTA
Found at i:242059 original size:10 final size:10
Alignment explanation
Indices: 241964--242059 Score: 50
Period size: 10 Copynumber: 8.8 Consensus size: 10
241954 TATTTAATAC
*
241964 TTTTTATTAT
1 TTTTTTTTAT
241974 TTTTTTTGT-T
1 TTTTTTT-TAT
241984 TTTTATTATTAT
1 TTTT-TT-TTAT
* *
241996 TTTTATGTAT
1 TTTTTTTTAT
*
242006 TTTTCCTTTGAT
1 TTTT--TTTTAT
*
242018 TTGTTTTTATT
1 TTTTTTTTA-T
242029 TGTTATTTATTAT
1 T-TT-TTT-TTAT
*
242042 TTATTTTTAT
1 TTTTTTTTAT
242052 TTTTTTTT
1 TTTTTTTT
242060 TAAAAAATAT
Statistics
Matches: 65, Mismatches: 11, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
10 33 0.51
11 10 0.15
12 14 0.22
13 5 0.08
14 3 0.05
ACGTcount: A:0.15, C:0.02, G:0.05, T:0.78
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:242059 original size:11 final size:11
Alignment explanation
Indices: 241964--242061 Score: 56
Period size: 11 Copynumber: 8.5 Consensus size: 11
241954 TATTTAATAC
241964 TTTTTATTATTT
1 TTTTTATT-TTT
*
241976 TTTTTGTTTTT
1 TTTTTATTTTT
241987 TATTATTA-TTTT
1 T-TT-TTATTTTT
* *
241999 TATGTATTTTT
1 TTTTTATTTTT
* * *
242010 CCTTTGA-TTTG
1 -TTTTTATTTTT
*
242021 TTTTTATTTGT
1 TTTTTATTTTT
*
242032 TATTTATTATTT
1 TTTTTATT-TTT
242044 ATTTTTATTTTT
1 -TTTTTATTTTT
242056 TTTTTA
1 TTTTTA
242062 AAAAATATTT
Statistics
Matches: 63, Mismatches: 16, Indels: 15
0.67 0.17 0.16
Matches are distributed among these distances:
10 6 0.10
11 27 0.43
12 21 0.33
13 9 0.14
ACGTcount: A:0.15, C:0.02, G:0.05, T:0.78
Consensus pattern (11 bp):
TTTTTATTTTT
Done.