Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006002.1 Hibiscus syriacus cultivar Beakdansim tig00014151_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: 61147
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:11884 original size:29 final size:30
Alignment explanation
Indices: 11851--11938 Score: 94
Period size: 31 Copynumber: 3.0 Consensus size: 30
11841 TGGATTACAT
11851 AACTTTTCAAAATTACACTTTGGTCC-CTA
1 AACTTTTCAAAATTACACTTTGGTCCACTA
* * *
11880 AACTTTTCCAAAGTTTATACTTTAG-CCACTA
1 AACTTTT-CAAA-ATTACACTTTGGTCCACTA
*
11911 AAC-TTTCAAAATTACATTTTGGT-CACTA
1 AACTTTTCAAAATTACACTTTGGTCCACTA
11939 GTTAAAATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
28 13 0.27
29 11 0.23
30 9 0.19
31 15 0.31
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.39
Consensus pattern (30 bp):
AACTTTTCAAAATTACACTTTGGTCCACTA
Found at i:18765 original size:20 final size:20
Alignment explanation
Indices: 18727--18765 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18717 TATTTCCAAA
*
18727 ATTGGTAAGTATTTTGAGCC
1 ATTGGTAAGTATTTCGAGCC
*
18747 ATTGGTAAGTCTTTCGAGC
1 ATTGGTAAGTATTTCGAGC
18766 AAGATGATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.38
Consensus pattern (20 bp):
ATTGGTAAGTATTTCGAGCC
Found at i:19305 original size:21 final size:21
Alignment explanation
Indices: 19228--19305 Score: 52
Period size: 21 Copynumber: 3.7 Consensus size: 21
19218 CATGCCATCA
* *
19228 ATAAGTCTTTCGAGTATGATG
1 ATAAGTCCTTCGAGCATGATG
* * *
19249 ATTAAATCCTTCGGGTCAT-CT-
1 A-TAAGTCCTTCGAG-CATGATG
* * *
19270 ATTAGTCTTTTGAGCATGATG
1 ATAAGTCCTTCGAGCATGATG
19291 ATAAGTCCTTCGAGC
1 ATAAGTCCTTCGAGC
19306 CATCTATAAC
Statistics
Matches: 39, Mismatches: 14, Indels: 8
0.64 0.23 0.13
Matches are distributed among these distances:
19 3 0.08
20 9 0.23
21 14 0.36
22 11 0.28
23 2 0.05
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.37
Consensus pattern (21 bp):
ATAAGTCCTTCGAGCATGATG
Found at i:19312 original size:41 final size:41
Alignment explanation
Indices: 19206--19314 Score: 130
Period size: 42 Copynumber: 2.6 Consensus size: 41
19196 TTTCTATAAT
* *
19206 TGATAAGTCCTTC-ATGCCATCAATAAGTCTTTCGAGTATGA
1 TGATAAGTCCTTCGA-GCCATCTATAAGTCTTTCGAGCATGA
* * * * *
19247 TGATTAAATCCTTCGGGTCATCTATTAGTCTTTTGAGCATGA
1 TGA-TAAGTCCTTCGAGCCATCTATAAGTCTTTCGAGCATGA
19289 TGATAAGTCCTTCGAGCCATCTATAA
1 TGATAAGTCCTTCGAGCCATCTATAA
19315 CACCTTCGGG
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
41 22 0.40
42 33 0.60
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (41 bp):
TGATAAGTCCTTCGAGCCATCTATAAGTCTTTCGAGCATGA
Found at i:19417 original size:16 final size:16
Alignment explanation
Indices: 19396--19440 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
19386 TAAAATTTTC
*
19396 AAAAAATGAAAAATGA
1 AAAAAATGAAAAAAGA
19412 AAAAAAT-AAGAAAAGA
1 AAAAAATGAA-AAAAGA
19428 AAATAAATGAAAA
1 AAA-AAATGAAAA
19441 TTAGAGAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 2 0.08
16 15 0.60
17 6 0.24
18 2 0.08
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (16 bp):
AAAAAATGAAAAAAGA
Found at i:19424 original size:261 final size:261
Alignment explanation
Indices: 18754--19406 Score: 827
Period size: 261 Copynumber: 2.5 Consensus size: 261
18744 GCCATTGGTA
* * * * **
18754 AGTCTTTCGAGCAAGATGATAAGTCGTTCGGGTCATCTATAAGACCCTCGGGCAGGATATTTTCA
1 AGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCATGATGCTTTCA
* **
18819 TAT-G-ATTTATGAA-A-AAAGAGAAAGCAATTTTCAAAGTTTCTCATTTAAGATTTTCAGAATT
66 TATGGTATTTAT-AAGAGAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAAGATTTTCAGAAAA
* * *
18880 TGAATTTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGTAGACTATTTCCAAAAT
130 TGAAATTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCCAGTAGAATATTTCCAAAAT
* *
18945 TGATAAGTCCTTCAGGCCATCAGTAAGTCTTTCGAATATGATGACTAAATCCTTAAGGTCATCTG
195 TGATAAGTCCTTCAGGCCATCAATAAGTCTTTCGAATATGATGACTAAATCCTTAAGGTCATCTA
19010 TC
260 TC
**
19012 AACCTTTCGAGCAAGATGATAAGT-CTCTCGGGCCATCTATAAGACCTTCGGGCATG--GCTTTT
1 AGTCTTTCGAGCAAGATGATAAGTCCT-TCGGGCCATCTATAAGACCTTCGGGCATGATGC--TT
* *** * * *
19074 TCATATGATATTT-GGGGGGAAATGAGAAAGCGATTTTAAAAGTTTCTCATTTAAGATTTTCAGA
63 TCATATGGTATTTATAAGAG-AATGAGAAAGCAATTTTCAAAGTTTCTCATTTAAGATTTTCAGA
* * * *
19138 AAATGAAATTTTTGAAAAGTAAGAAAGCGATTTCTAAAGTTTCTTACCCAGTAGAATATTTCTAT
127 AAATGAAATTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCCAGTAGAATATTTCCAA
* * * **
19203 AATTGATAAGTCCTTCATGCCATCAATAAGTCTTTCGAGTATGATGATTAAATCCTTCGGGTCAT
192 AATTGATAAGTCCTTCAGGCCATCAATAAGTCTTTCGAATATGATGACTAAATCCTTAAGGTCAT
*
19268 CTATT
257 CTATC
* * * * *
19273 AGTCTTTTGAGCATGATGATAAGTCCTTCGAGCCATCTATAACACCTTCGGGTATGATGCTTTCA
1 AGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCATGATGCTTTCA
* * * *
19338 TATGGTATTTATAAGAGAATGAGAAATCTATTTTCAAAGTTTCTCATTTAAAATTTTCAAAAAAT
66 TATGGTATTTATAAGAGAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAAGATTTTCAGAAAAT
19403 GAAA
131 GAAA
19407 AATGAAAAAA
Statistics
Matches: 333, Mismatches: 50, Indels: 21
0.82 0.12 0.05
Matches are distributed among these distances:
257 1 0.00
258 56 0.17
260 4 0.01
261 266 0.80
262 4 0.01
263 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Consensus pattern (261 bp):
AGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCATGATGCTTTCA
TATGGTATTTATAAGAGAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAAGATTTTCAGAAAAT
GAAATTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCCAGTAGAATATTTCCAAAATT
GATAAGTCCTTCAGGCCATCAATAAGTCTTTCGAATATGATGACTAAATCCTTAAGGTCATCTAT
C
Found at i:22251 original size:23 final size:23
Alignment explanation
Indices: 22144--22245 Score: 114
Period size: 23 Copynumber: 4.4 Consensus size: 23
22134 GAGTTGAGGG
* *
22144 TTCTATGCGGTCCTTCGAGACAA
1 TTCTATGTGGTCCTTCAAGACAA
* *
22167 TTCTATGTGGTCCTTCAGGACAT
1 TTCTATGTGGTCCTTCAAGACAA
* * **
22190 TTCTACGCGGTCCTTCGGGACAA
1 TTCTATGTGGTCCTTCAAGACAA
* *
22213 TACTATGTGGTCCTTCAAGACAT
1 TTCTATGTGGTCCTTCAAGACAA
22236 TTCTATGTGG
1 TTCTATGTGG
22246 CACTTCGGTG
Statistics
Matches: 64, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 64 1.00
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.34
Consensus pattern (23 bp):
TTCTATGTGGTCCTTCAAGACAA
Found at i:22253 original size:46 final size:46
Alignment explanation
Indices: 22144--22240 Score: 158
Period size: 46 Copynumber: 2.1 Consensus size: 46
22134 GAGTTGAGGG
* * * *
22144 TTCTATGCGGTCCTTCGAGACAATTCTATGTGGTCCTTCAGGACAT
1 TTCTACGCGGTCCTTCGGGACAATACTATGTGGTCCTTCAAGACAT
22190 TTCTACGCGGTCCTTCGGGACAATACTATGTGGTCCTTCAAGACAT
1 TTCTACGCGGTCCTTCGGGACAATACTATGTGGTCCTTCAAGACAT
22236 TTCTA
1 TTCTA
22241 TGTGGCACTT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (46 bp):
TTCTACGCGGTCCTTCGGGACAATACTATGTGGTCCTTCAAGACAT
Found at i:25217 original size:16 final size:17
Alignment explanation
Indices: 25192--25239 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
25182 ATCATTTTAT
25192 AAAT-TTTAATAATTAA
1 AAATATTTAATAATTAA
25208 AAA-ATTTAATAA--AA
1 AAATATTTAATAATTAA
25222 AAATATCTT-ATAATTAA
1 AAATAT-TTAATAATTAA
25239 A
1 A
25240 GAATCATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
16 13 0.48
17 3 0.11
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATATTTAATAATTAA
Found at i:30006 original size:23 final size:23
Alignment explanation
Indices: 29980--30027 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
29970 ATAAAGTACA
*
29980 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
30003 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
30026 AT
1 AT
30028 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:30778 original size:18 final size:18
Alignment explanation
Indices: 30755--30791 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
30745 CGAAATATAT
30755 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
30773 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
30791 A
1 A
30792 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:31021 original size:23 final size:23
Alignment explanation
Indices: 30995--31059 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
30985 ATGCGAGATA
30995 GATACCTATTACATTATATAAAC
1 GATACCTATTACATTATATAAAC
* **
31018 GATATCTATTACATTATATAAGG
1 GATACCTATTACATTATATAAAC
* *
31041 GCTACCTATTACATCATAT
1 GATACCTATTACATTATAT
31060 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (23 bp):
GATACCTATTACATTATATAAAC
Found at i:31442 original size:21 final size:22
Alignment explanation
Indices: 31417--31468 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
31407 ACACTTTACA
*
31417 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
31440 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
31463 ATATAA
1 ATATAA
31469 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:31453 original size:23 final size:23
Alignment explanation
Indices: 31427--31489 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
31417 ATATAACCAC
31427 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
31450 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
31473 TACCTATTACATCATAT
1 TACCTATTACATTATAT
31490 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:31870 original size:21 final size:22
Alignment explanation
Indices: 31845--31896 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
31835 ACACTTTACA
*
31845 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
31868 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
31891 ATATAA
1 ATATAA
31897 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:31881 original size:23 final size:23
Alignment explanation
Indices: 31855--31917 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
31845 ATATAACCAC
31855 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
31878 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
31901 TACCTATTACATCATAT
1 TACCTATTACATTATAT
31918 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:31970 original size:428 final size:431
Alignment explanation
Indices: 30997--32237 Score: 2427
Period size: 428 Copynumber: 2.9 Consensus size: 431
30987 GCGAGATAGA
*
30997 TACCTATTACATTATATAAACGATATCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
31062 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
31127 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
31192 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
31257 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
261 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
31322 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTG-AAAAAGTATGG
326 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
31386 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
391 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
31427 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
*
31492 TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
31557 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
31622 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTAT-AAATATTATTTAGAATTTTT
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
31686 AATTTAATAAT-A-ATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
261 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
31749 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
326 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
31814 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
391 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
31855 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
31920 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
31985 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
32050 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
32115 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
261 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
*
32180 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTCAAAAA
326 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAA
32238 TTAAAAGTTT
Statistics
Matches: 803, Mismatches: 4, Indels: 7
0.99 0.00 0.01
Matches are distributed among these distances:
427 104 0.13
428 291 0.36
429 62 0.08
430 238 0.30
431 108 0.13
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (431 bp):
TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
Found at i:32295 original size:3 final size:3
Alignment explanation
Indices: 32287--32373 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
32277 ACTTGTTTGG
* * * **
32287 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
32335 AGC TTC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
32374 GTCAGCTTCA
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.24, C:0.34, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:32310 original size:18 final size:18
Alignment explanation
Indices: 32287--32388 Score: 87
Period size: 18 Copynumber: 5.7 Consensus size: 18
32277 ACTTGTTTGG
32287 ATCATCATCTTCATCATC
1 ATCATCATCTTCATCATC
* *
32305 ATCATCATCATCGTCATC
1 ATCATCATCTTCATCATC
* ** * *
32323 ATCTTCATCGCCAGCTTC
1 ATCATCATCTTCATCATC
* *
32341 ATCGTCATCATCATCATC
1 ATCATCATCTTCATCATC
* *
32359 ATCGTCATCTTCATCGTC
1 ATCATCATCTTCATCATC
* *
32377 AGCTTCATCTTC
1 ATCATCATCTTC
32389 TGCGACCGCT
Statistics
Matches: 67, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 67 1.00
ACGTcount: A:0.23, C:0.34, G:0.07, T:0.36
Consensus pattern (18 bp):
ATCATCATCTTCATCATC
Found at i:32354 original size:42 final size:42
Alignment explanation
Indices: 32295--32385 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
32285 GGATCATCAT
*
32295 CTTCATCATCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
* * *
32337 CTTCATCGTCATCATCATCATCATCGTCATCTTCATCGTCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
32379 CTTCATC
1 CTTCATC
32386 TTCTGCGACC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (42 bp):
CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
Found at i:34374 original size:199 final size:199
Alignment explanation
Indices: 33845--35462 Score: 3046
Period size: 199 Copynumber: 8.1 Consensus size: 199
33835 TTTAAATTAG
33845 TATCGACACAAA-TATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
33909 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
33974 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGG-AA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
34038 AAAA
196 AAAA
*
34042 TATCGAAACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
34107 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
34172 CGACATTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
34237 AAAA
196 AAAA
* *
34241 TATCGAAACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
34306 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
34371 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
34436 AAAA
196 AAAA
34440 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
34505 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
34570 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
34635 AAAA
196 AAAA
* *
34639 TATCGAAACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
34704 ATTGTACCGGTTAGATTGAAAAATTACATATTACATAATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
34769 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
34834 AAAA
196 AAAA
*
34838 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
34903 ATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
34967 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGG-AA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
35031 AAAA
196 AAAA
35035 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
35100 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
35165 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
35230 AAAA
196 AAAA
35234 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* **
35299 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACAGTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
35364 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
35429 AAAAA
195 AAAAA
*
35434 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
35463 TGACCCTTAA
Statistics
Matches: 1398, Mismatches: 18, Indels: 7
0.98 0.01 0.00
Matches are distributed among these distances:
197 99 0.07
198 393 0.28
199 816 0.58
200 90 0.06
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
AAAA
Found at i:35571 original size:19 final size:19
Alignment explanation
Indices: 35544--35588 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
35534 ATTCACATAA
*
35544 AAAAATATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
35563 AAAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
35582 AAAATTA
1 AAAATTA
35589 ACTCGACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:37423 original size:32 final size:32
Alignment explanation
Indices: 37381--37441 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
37371 TTAATATCAC
*
37381 CCCTTAACACCGAAACTTCTTTCACCACTTCA
1 CCCTCAACACCGAAACTTCTTTCACCACTTCA
***
37413 CCCTCAACACCTCTACTTCTTTCACCACT
1 CCCTCAACACCGAAACTTCTTTCACCACT
37442 CCATCTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.25, C:0.44, G:0.02, T:0.30
Consensus pattern (32 bp):
CCCTCAACACCGAAACTTCTTTCACCACTTCA
Found at i:39789 original size:20 final size:19
Alignment explanation
Indices: 39743--39789 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
39733 TCCGGTATCA
*
39743 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
39762 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
39783 TTTTACC
1 TTTTACC
39790 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:39935 original size:20 final size:20
Alignment explanation
Indices: 39909--39954 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
39899 CACTTTTAAA
39909 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
39928 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
39949 TTTACC
1 TTTACC
39955 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:41724 original size:74 final size:74
Alignment explanation
Indices: 41640--41790 Score: 266
Period size: 74 Copynumber: 2.0 Consensus size: 74
41630 ATAATGATAT
*
41640 ATTTGATCCTCAATATTTATAAATTATATCAATTTGGTCATAATTTTAATTCAATTTAATAAATT
1 ATTTGATCCTCAATATTTATAAATTATATAAATTTGGTCATAATTTTAATTCAATTTAATAAATT
41705 TAATATCCA
66 TAATATCCA
* * *
41714 ATTTGGTCCTCAATATTTGTAAATTCTATAAATTTGGTCATAATTTTAATTCAATTTAATAAATT
1 ATTTGATCCTCAATATTTATAAATTATATAAATTTGGTCATAATTTTAATTCAATTTAATAAATT
41779 TAATATCCA
66 TAATATCCA
41788 ATT
1 ATT
41791 AGGGGGTGAC
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (74 bp):
ATTTGATCCTCAATATTTATAAATTATATAAATTTGGTCATAATTTTAATTCAATTTAATAAATT
TAATATCCA
Found at i:42270 original size:24 final size:24
Alignment explanation
Indices: 42211--42280 Score: 79
Period size: 25 Copynumber: 2.9 Consensus size: 24
42201 TTTGTGATTT
*
42211 ATAAATATATACATTTTAAAATATA
1 ATAAATATA-ATATTTTAAAATATA
* *
42236 GTTAATATAATA-TTTAAAATAATA
1 ATAAATATAATATTTTAAAAT-ATA
*
42260 ATAAATTTAATATTTTAAAAT
1 ATAAATATAATATTTTAAAAT
42281 TAAATTCAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
23 8 0.22
24 14 0.38
25 15 0.41
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (24 bp):
ATAAATATAATATTTTAAAATATA
Found at i:42305 original size:21 final size:20
Alignment explanation
Indices: 42254--42314 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 20
42244 AATATTTAAA
*
42254 ATAATAATAAATTTAATATT
1 ATAAAAATAAATTTAATATT
* * *
42274 TTAAAATTAAATTCAATATGT
1 ATAAAAATAAATTTAATAT-T
42295 ATAAAAATAAATTTAATATT
1 ATAAAAATAAATTTAATATT
42315 TTTTAAAATG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAAAAATAAATTTAATATT
Found at i:42322 original size:21 final size:20
Alignment explanation
Indices: 42259--42323 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 20
42249 TTAAAATAAT
42259 AATAAATTTAATA-TTTTAA
1 AATAAATTTAATATTTTTAA
* * *
42278 AATTAAATTCAATATGTATAAA
1 AA-TAAATTTAATAT-TTTTAA
42300 AATAAATTTAATATTTTTTAA
1 AATAAATTTAATA-TTTTTAA
42321 AAT
1 AAT
42324 GATTTTGAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
19 2 0.06
20 10 0.28
21 17 0.47
22 7 0.19
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (20 bp):
AATAAATTTAATATTTTTAA
Found at i:46179 original size:23 final size:23
Alignment explanation
Indices: 46150--46216 Score: 125
Period size: 23 Copynumber: 2.9 Consensus size: 23
46140 TTCCACATAT
*
46150 TTGTCCCTAAGGACCACATAGGA
1 TTGTCCCGAAGGACCACATAGGA
46173 TTGTCCCGAAGGACCACATAGGA
1 TTGTCCCGAAGGACCACATAGGA
46196 TTGTCCCGAAGGACCACATAG
1 TTGTCCCGAAGGACCACATAG
46217 AACCCTCGAC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.30, C:0.27, G:0.24, T:0.19
Consensus pattern (23 bp):
TTGTCCCGAAGGACCACATAGGA
Found at i:58967 original size:19 final size:19
Alignment explanation
Indices: 58942--58996 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 19
58932 CTATGCTTGT
*
58942 AGTATCGATACACTTTTAC
1 AGTATCGATACACATTTAC
* *
58961 GGTATCGATACCCATTTAC
1 AGTATCGATACACATTTAC
*
58980 AGTATCGATACCCATTT
1 AGTATCGATACACATTT
58997 TCGATTCTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.35
Consensus pattern (19 bp):
AGTATCGATACACATTTAC
Done.